# Date 2008-01-16 Time 04:56:06 PST -0800 (1200488166.20 s)
#phil __OFF__

Command line arguments: "../523.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17541
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 523

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.4607, 86.822, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.98202
Completeness in resolution range: 0.969177
Completeness with d_max=infinity: 0.966165

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9592
                             d_min =   1.9820

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.98202
Completeness in resolution range: 0.969177
Completeness with d_max=infinity: 0.966165

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9596 -  4.2407 [2127/2151]  1913   214  10.1%
  bin  2:  4.2407 -  3.3788 [2032/2052]  1830   202   9.9%
  bin  3:  3.3788 -  2.9554 [2016/2035]  1813   203  10.1%
  bin  4:  2.9554 -  2.6869 [1982/2012]  1784   198  10.0%
  bin  5:  2.6869 -  2.4952 [1993/2012]  1791   202  10.1%
  bin  6:  2.4952 -  2.3487 [1972/1997]  1777   195   9.9%
  bin  7:  2.3487 -  2.2315 [1949/1977]  1754   195  10.0%
  bin  8:  2.2315 -  2.1346 [1973/2009]  1780   193   9.8%
  bin  9:  2.1346 -  2.0527 [1926/1968]  1729   197  10.2%
  bin 10:  2.0527 -  1.9820 [1619/1999]  1459   160   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_523/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2204
        3.04 -     3.66: 4720
        3.66 -     4.28: 9098
        4.28 -     4.90: 12376
  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
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.004 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.170 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  42 " - " O   HOH Z 183 "  2.276 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28412 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_523/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_523/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.4607 86.82195 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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2912   r_free= 0.2887   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.964578                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7297 0.99   1382  152 0.2714 0.2615      6.3134      6.2415|
|  2:  4.7297 -  3.7740 0.99   1318  151 0.2237 0.2097      6.3129      6.2579|
|  3:  3.7740 -  3.3028 0.99   1300  142 0.2393 0.2424        6.23      6.3181|
|  4:  3.3028 -  3.0035 0.99   1300  142 0.2592 0.2952      6.1348      6.2212|
|  5:  3.0035 -  2.7897 0.99   1272  145 0.2971 0.2370      6.0179      5.8399|
|  6:  2.7897 -  2.6261 0.99   1292  141 0.2909 0.3354      5.9359      5.9149|
|  7:  2.6261 -  2.4952 0.99   1267  146 0.2981 0.2743      5.8985      5.8036|
|  8:  2.4952 -  2.3871 0.98   1276  134 0.3172 0.3377      5.8907      5.9697|
|  9:  2.3871 -  2.2955 0.98   1256  142 0.3203 0.3221      5.8543      5.8268|
| 10:  2.2955 -  2.2166 1.00   1279  144 0.3304 0.2939      5.8473      5.7414|
| 11:  2.2166 -  2.1475 0.97   1242  138 0.3378 0.3574      5.8058      5.8439|
| 12:  2.1475 -  2.0863 0.98   1252  136 0.3461 0.3165      5.7805      5.7538|
| 13:  2.0863 -  2.0315 0.99   1256  138 0.3423 0.3357      5.6543      5.6569|
| 14:  2.0315 -  1.9820 0.73    938  108 0.3688 0.3553      5.6934      5.5608|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7297  1382   152  0.81  23.90   0.87     0.83      36328.04|
|  2:  4.7297 -  3.7740  1318   151  0.86  19.66   0.99     0.94      36824.46|
|  3:  3.7740 -  3.3028  1300   142  0.85  21.94   1.01     0.99      34342.82|
|  4:  3.3028 -  3.0035  1300   142  0.83  23.47   1.01     0.98      29400.26|
|  5:  3.0035 -  2.7897  1272   145  0.79  27.14   1.02     0.96      23001.39|
|  6:  2.7897 -  2.6261  1292   141  0.80  27.18   1.00     0.96      19832.35|
|  7:  2.6261 -  2.4952  1267   146  0.77  29.16   1.03     0.96      18942.60|
|  8:  2.4952 -  2.3871  1276   134  0.76  30.26   1.03     0.95      19206.96|
|  9:  2.3871 -  2.2955  1256   142  0.76  30.31   1.05     0.96      18387.84|
| 10:  2.2955 -  2.2166  1279   144  0.74  31.94   1.06     0.97      17476.41|
| 11:  2.2166 -  2.1475  1242   138  0.74  32.50   1.05     1.00      16836.07|
| 12:  2.1475 -  2.0863  1252   136  0.73  33.40   1.07     0.99      16060.17|
| 13:  2.0863 -  2.0315  1256   138  0.71  35.03   1.06     0.96      14270.44|
| 14:  2.0315 -  1.9820   938   108  0.73  33.86   1.08     0.92      11634.61|
|alpha:            min =        0.83 max =            1.00 mean =         0.96|
|beta:             min =    11634.61 max =        36824.46 mean =     22705.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.78|
|phase err.(work): min =        0.00 max =           89.99 mean =        28.36|
|phase err.(test): min =        0.00 max =           89.91 mean =        28.23|
|-----------------------------------------------------------------------------|

============================== 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 = 3.512066              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.545   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.510304              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.062   (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:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      208 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1996 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1863 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2857 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4662 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4436 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5665 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6711 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.175 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2912   r_free= 0.2887   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| 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:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.964578                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2750   r_free= 0.2724   ksol= 0.33   Bsol= 42.57   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,0.37,-0.91,0.00,-0.00,-0.00); trace/3= -1.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.939423                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.072039              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.459   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.274976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.009   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2750      final r-factor (work) = 0.1616          |
| start r-factor (free) = 0.2724      final r-factor (free) = 0.1840          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3015 = 3.07 * 0.50 * 5.9503 + 1.00 * 0.1617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6811 = 3.07 * 0.50 * 5.6115 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1616      final r-factor (work) = 0.1473          |
| start r-factor (free) = 0.1840      final r-factor (free) = 0.1921          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5490 = 0.27 * 1.00 * 5.6115 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4793 = 0.27 * 1.00 * 5.3507 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    68.48   16.91    None  None   None       |
|    all(noH): 2823   0      1.04    68.48   16.91    None  None   None       |
|    Sol.    : 438    0      6.54    68.48   38.45    None  None   None       |
|    Mac.    : 2385   0      1.04    65.08   12.95    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:     1.041 -   7.785:  439   |   5:    34.762 -  41.507:  103        |
|      1:     7.785 -  14.529: 1333   |   6:    41.507 -  48.251:   96        |
|      2:    14.529 -  21.274:  451   |   7:    48.251 -  54.995:   80        |
|      3:    21.274 -  28.018:  159   |   8:    54.995 -  61.739:   40        |
|      4:    28.018 -  34.762:  106   |   9:    61.739 -  68.484:   16        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1473 r_free = 0.1921             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1471 r_free = 0.1917             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1471   r_free= 0.1917   ksol= 0.33   Bsol= 42.57   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,0.37,-0.91,0.00,-0.00,-0.00); trace/3= -1.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.366065                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1459   r_free= 0.1895   ksol= 0.33   Bsol= 50.12   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.98,-1.35,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.359660                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.513865              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.490  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.106588              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.161  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1459      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1895      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4808 = 3.51 * 0.50 * 5.3611 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3061 = 3.51 * 0.50 * 5.2603 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1610      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5687 = 0.11 * 1.00 * 5.2603 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5562 = 0.11 * 1.00 * 5.1602 + 1.00 * 0.0061                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.40    68.75   16.48    None  None   None       |
|    all(noH): 2823   0      2.40    68.75   16.48    None  None   None       |
|    Sol.    : 438    0      6.52    68.75   36.45    None  None   None       |
|    Mac.    : 2385   0      2.40    66.27   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:     2.397 -   9.033:  693   |   5:    35.575 -  42.210:  115        |
|      1:     9.033 -  15.668: 1231   |   6:    42.210 -  48.846:   77        |
|      2:    15.668 -  22.304:  365   |   7:    48.846 -  55.481:   69        |
|      3:    22.304 -  28.939:  121   |   8:    55.481 -  62.117:   23        |
|      4:    28.939 -  35.575:  120   |   9:    62.117 -  68.752:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1548             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1549             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1549   ksol= 0.33   Bsol= 50.12   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-1.98,-1.35,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1547   ksol= 0.33   Bsol= 50.12   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.44,-1.22,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138848                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.188251              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.373  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.197227              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.782  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.1294 = 1.19 * 0.50 * 5.1593 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.1043 = 1.19 * 0.50 * 5.1433 + 1.00 * 0.0485                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1638 = 1.20 * 1.00 * 5.1433 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1480 = 1.20 * 1.00 * 5.1277 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    81.42   17.14    None  None   None       |
|    all(noH): 2823   0      0.87    81.42   17.14    None  None   None       |
|    Sol.    : 438    0      6.39    75.58   39.91    None  None   None       |
|    Mac.    : 2385   0      0.87    81.42   12.95    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:     0.873 -   8.927:  747   |   5:    41.146 -  49.200:  103        |
|      1:     8.927 -  16.982: 1277   |   6:    49.200 -  57.255:   77        |
|      2:    16.982 -  25.036:  298   |   7:    57.255 -  65.309:   55        |
|      3:    25.036 -  33.091:  128   |   8:    65.309 -  73.364:   22        |
|      4:    33.091 -  41.146:  109   |   9:    73.364 -  81.419:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1540             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1540             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1540   ksol= 0.33   Bsol= 50.12   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.44,-1.22,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132626                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1540   ksol= 0.32   Bsol= 50.12   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.41,-1.06,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132204                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.395833              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.618  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.524609              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.198  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6269 = 1.40 * 0.50 * 5.1278 + 1.00 * 0.0481                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6253 = 1.40 * 0.50 * 5.1215 + 1.00 * 0.0509                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1536      final r-factor (free) = 0.1533          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6957 = 0.52 * 1.00 * 5.1215 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6944 = 0.52 * 1.00 * 5.1190 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 39     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    83.50   16.93    None  None   None       |
|    all(noH): 2823   0      0.76    83.50   16.93    None  None   None       |
|    Sol.    : 438    0      6.09    77.00   39.53    None  None   None       |
|    Mac.    : 2385   0      0.76    83.50   12.78    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:     0.760 -   9.033:  835   |   5:    42.128 -  50.402:  102        |
|      1:     9.033 -  17.307: 1226   |   6:    50.402 -  58.675:   82        |
|      2:    17.307 -  25.581:  277   |   7:    58.675 -  66.949:   39        |
|      3:    25.581 -  33.854:  125   |   8:    66.949 -  75.223:   21        |
|      4:    33.854 -  42.128:  112   |   9:    75.223 -  83.496:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1533             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1533             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1533   ksol= 0.32   Bsol= 50.12   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-2.41,-1.06,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.118901                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1532   ksol= 0.32   Bsol= 50.12   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.23,-0.83,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118969                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.111310              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.603  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.205423              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.652  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4560 = 2.11 * 0.50 * 5.1201 + 1.00 * 0.0509                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4511 = 2.11 * 0.50 * 5.1088 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1063      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.6026 = 5.21 * 1.00 * 5.1088 + 1.00 * 0.0090                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.5952 = 5.21 * 1.00 * 5.1072 + 1.00 * 0.0099                              |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.05    88.40   16.87    None  None   None       |
|    all(noH): 2823   0      0.05    88.40   16.87    None  None   None       |
|    Sol.    : 438    0      5.84    79.08   39.89    None  None   None       |
|    Mac.    : 2385   0      0.05    88.40   12.65    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:     0.048 -   8.883:  847   |   5:    44.222 -  53.056:   92        |
|      1:     8.883 -  17.717: 1248   |   6:    53.056 -  61.891:   73        |
|      2:    17.717 -  26.552:  255   |   7:    61.891 -  70.726:   34        |
|      3:    26.552 -  35.387:  133   |   8:    70.726 -  79.560:   16        |
|      4:    35.387 -  44.222:  121   |   9:    79.560 -  88.395:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1063 r_free = 0.1544             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1062 r_free = 0.1544             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1544   ksol= 0.32   Bsol= 50.12   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.23,-0.83,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110343                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7297 0.99   1382  152 0.0974 0.1262      5.3697      5.5091|
|  2:  4.7297 -  3.7740 0.99   1318  151 0.0817 0.1090       5.409      5.6093|
|  3:  3.7740 -  3.3028 0.99   1300  142 0.1010 0.1510      5.4455      5.8499|
|  4:  3.3028 -  3.0035 0.99   1300  142 0.1149 0.1565      5.4175      5.5588|
|  5:  3.0035 -  2.7897 0.99   1272  145 0.1235 0.1642      5.2913      5.5266|
|  6:  2.7897 -  2.6261 0.99   1292  141 0.1136 0.1962       5.175      5.4879|
|  7:  2.6261 -  2.4952 0.99   1267  146 0.1204 0.1533      5.1317      5.3114|
|  8:  2.4952 -  2.3871 0.98   1276  134 0.1100 0.1656      5.0298      5.3148|
|  9:  2.3871 -  2.2955 0.98   1256  142 0.1093 0.1720      4.9924      5.2555|
| 10:  2.2955 -  2.2166 1.00   1279  144 0.1058 0.1672      4.9246      5.2065|
| 11:  2.2166 -  2.1475 0.97   1242  138 0.1068 0.1687      4.9151      5.2047|
| 12:  2.1475 -  2.0863 0.98   1252  136 0.1075 0.1684      4.8549      5.2399|
| 13:  2.0863 -  2.0315 0.99   1256  138 0.1036 0.1714      4.7569      5.0217|
| 14:  2.0315 -  1.9820 0.73    938  108 0.0980 0.1677      4.6487      4.9163|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7297  1382   152  0.94   9.11   0.98     0.95       7013.06|
|  2:  4.7297 -  3.7740  1318   151  0.95   7.69   1.02     1.01       8765.92|
|  3:  3.7740 -  3.3028  1300   142  0.94  10.74   1.03     1.02       9817.30|
|  4:  3.3028 -  3.0035  1300   142  0.92  13.05   1.01     0.99       9781.06|
|  5:  3.0035 -  2.7897  1272   145  0.91  15.16   1.00     0.97       7964.12|
|  6:  2.7897 -  2.6261  1292   141  0.90  15.62   0.99     0.96       6773.07|
|  7:  2.6261 -  2.4952  1267   146  0.91  15.44   0.98     0.95       5942.18|
|  8:  2.4952 -  2.3871  1276   134  0.92  14.31   0.99     0.97       4915.98|
|  9:  2.3871 -  2.2955  1256   142  0.91  14.66   1.00     0.97       4725.90|
| 10:  2.2955 -  2.2166  1279   144  0.91  15.00   0.99     0.96       4162.78|
| 11:  2.2166 -  2.1475  1242   138  0.90  15.96   0.99     0.96       4310.59|
| 12:  2.1475 -  2.0863  1252   136  0.91  14.97   1.00     0.99       3797.52|
| 13:  2.0863 -  2.0315  1256   138  0.91  15.46   0.99     0.97       3221.55|
| 14:  2.0315 -  1.9820   938   108  0.92  13.90   0.97     0.94       2545.99|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2545.99 max =         9817.30 mean =      6081.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.59|
|phase err.(test): min =        0.00 max =           89.19 mean =        13.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1544   ksol= 0.32   Bsol= 50.12   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.05,-0.62,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110383                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1544   ksol= 0.32   Bsol= 50.12   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.05,-0.62,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110383                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7297 0.99   1382  152 0.0974 0.1263      5.3703        5.51|
|  2:  4.7297 -  3.7740 0.99   1318  151 0.0817 0.1090      5.4095      5.6093|
|  3:  3.7740 -  3.3028 0.99   1300  142 0.1010 0.1510      5.4456      5.8504|
|  4:  3.3028 -  3.0035 0.99   1300  142 0.1149 0.1565      5.4175      5.5589|
|  5:  3.0035 -  2.7897 0.99   1272  145 0.1235 0.1642      5.2911      5.5263|
|  6:  2.7897 -  2.6261 0.99   1292  141 0.1136 0.1961      5.1749      5.4877|
|  7:  2.6261 -  2.4952 0.99   1267  146 0.1204 0.1533      5.1317      5.3116|
|  8:  2.4952 -  2.3871 0.98   1276  134 0.1100 0.1656      5.0298      5.3147|
|  9:  2.3871 -  2.2955 0.98   1256  142 0.1093 0.1719      4.9925      5.2553|
| 10:  2.2955 -  2.2166 1.00   1279  144 0.1057 0.1672      4.9246      5.2071|
| 11:  2.2166 -  2.1475 0.97   1242  138 0.1068 0.1686      4.9151      5.2045|
| 12:  2.1475 -  2.0863 0.98   1252  136 0.1075 0.1683      4.8547      5.2397|
| 13:  2.0863 -  2.0315 0.99   1256  138 0.1036 0.1713      4.7567      5.0214|
| 14:  2.0315 -  1.9820 0.73    938  108 0.0980 0.1676      4.6484      4.9159|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9596 -  4.7297  1382   152  0.94   9.12   0.98     0.95       7022.53|
|  2:  4.7297 -  3.7740  1318   151  0.95   7.70   1.02     1.01       8774.73|
|  3:  3.7740 -  3.3028  1300   142  0.94  10.74   1.03     1.03       9820.12|
|  4:  3.3028 -  3.0035  1300   142  0.92  13.05   1.01     1.00       9779.40|
|  5:  3.0035 -  2.7897  1272   145  0.91  15.15   1.01     0.98       7959.99|
|  6:  2.7897 -  2.6261  1292   141  0.90  15.61   0.99     0.97       6770.39|
|  7:  2.6261 -  2.4952  1267   146  0.91  15.44   0.99     0.96       5941.52|
|  8:  2.4952 -  2.3871  1276   134  0.92  14.31   1.00     0.98       4915.26|
|  9:  2.3871 -  2.2955  1256   142  0.91  14.67   1.01     0.98       4727.02|
| 10:  2.2955 -  2.2166  1279   144  0.91  15.01   1.00     0.97       4162.60|
| 11:  2.2166 -  2.1475  1242   138  0.90  15.96   1.00     0.97       4310.71|
| 12:  2.1475 -  2.0863  1252   136  0.91  14.97   1.01     1.00       3796.68|
| 13:  2.0863 -  2.0315  1256   138  0.91  15.46   1.00     0.98       3219.61|
| 14:  2.0315 -  1.9820   938   108  0.92  13.89   0.98     0.95       2543.11|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2543.11 max =         9820.12 mean =      6081.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.87 mean =        13.59|
|phase err.(test): min =        0.00 max =           89.20 mean =        13.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.05    88.40   16.87    None  None   None       |
|    all(noH): 2823   0      0.05    88.40   16.87    None  None   None       |
|    Sol.    : 438    0      5.84    79.09   39.89    None  None   None       |
|    Mac.    : 2385   0      0.05    88.40   12.65    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:     0.049 -   8.884:  847   |   5:    44.223 -  53.057:   92        |
|      1:     8.884 -  17.719: 1248   |   6:    53.057 -  61.892:   73        |
|      2:    17.719 -  26.553:  255   |   7:    61.892 -  70.727:   34        |
|      3:    26.553 -  35.388:  133   |   8:    70.727 -  79.562:   16        |
|      4:    35.388 -  44.223:  121   |   9:    79.562 -  88.396:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.433 - 4.682
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 295
   mapped sites are within: 0.725 - 4.682

peak=    5.812 closest distance to " NE2 GLN A  11 " =    1.174
peak=    5.488 closest distance to " O   HOH Z 144 " =    1.793
peak=    5.331 closest distance to " CG  PRO A  54 " =    1.272
peak=    5.326 closest distance to " O   HOH Z 126 " =    1.819
peak=    5.198 closest distance to " O   HOH Z 232 " =    2.380
peak=    5.133 closest distance to " NH2 ARG A  56 " =    2.128
peak=    5.073 closest distance to " CB  ARG A 275 " =    0.929
peak=    5.070 closest distance to " CB  GLN A 223 " =    1.476
peak=    4.858 closest distance to " CG  PRO A 213 " =    1.235
peak=    4.804 closest distance to " CB  GLN A 183 " =    1.232
peak=    4.738 closest distance to " O   HOH Z 427 " =    2.883
peak=    4.613 closest distance to " CB  PRO A  54 " =    0.973
peak=    4.581 closest distance to " O   HOH Z  78 " =    1.782
peak=    4.551 closest distance to " CB  ARG A  79 " =    1.407
peak=    4.537 closest distance to " O   HOH Z 298 " =    1.908
peak=    4.522 closest distance to " O   HOH Z 287 " =    2.089
peak=    4.473 closest distance to " CB  SER A  63 " =    1.169
peak=    4.457 closest distance to " O   HOH Z 369 " =    2.135
peak=    4.455 closest distance to " ND2 ASN A 187 " =    1.463
peak=    4.418 closest distance to " O   HOH Z 303 " =    2.144
peak=    4.418 closest distance to " CB  VAL A 265 " =    1.253
peak=    4.400 closest distance to " CG2 VAL A 257 " =    0.862
peak=    4.370 closest distance to " O   HOH Z  15 " =    2.298
peak=    4.357 closest distance to " CA  TYR A  30 " =    0.919
peak=    4.354 closest distance to " O   HOH Z 158 " =    3.005
peak=    4.350 closest distance to " CB  ARG A 190 " =    1.650
peak=    4.342 closest distance to " C   PRO A 198 " =    1.453
peak=    4.278 closest distance to " O   HOH Z 193 " =    1.792
peak=    4.242 closest distance to " CB  GLU A 152 " =    1.289
peak=    4.203 closest distance to " O   HOH Z 250 " =    1.479
peak=    4.192 closest distance to " O   HOH Z 189 " =    2.322
peak=    4.157 closest distance to " O   HOH Z  61 " =    1.648
peak=    4.136 closest distance to " O   HOH Z 272 " =    1.810
peak=    4.113 closest distance to " O   HOH Z 209 " =    2.271
peak=    4.112 closest distance to " NZ  LYS A 117 " =    3.150
peak=    4.101 closest distance to " CB  ASN A 148 " =    1.404
peak=    4.101 closest distance to " CZ  PHE A 218 " =    1.041
peak=    4.095 closest distance to " OG ASER A 258 " =    3.091
peak=    4.065 closest distance to " O   HOH Z 203 " =    1.771
peak=    4.061 closest distance to " CA  ASN A 215 " =    1.078
peak=    4.051 closest distance to " OD1 ASN A  69 " =    2.644
peak=    4.038 closest distance to " O   HOH Z 346 " =    1.655
peak=    4.037 closest distance to " CB  TRP A 266 " =    1.061
peak=    4.031 closest distance to " O   HOH Z 234 " =    3.621
peak=    4.031 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.015 closest distance to " CG  PRO A 243 " =    1.050
peak=    3.991 closest distance to " CB  LEU A 228 " =    1.102
peak=    3.989 closest distance to " CE  LYS A  76 " =    0.857
peak=    3.956 closest distance to " CD  ARG A  66 " =    2.341
peak=    3.944 closest distance to " O   HOH Z 371 " =    1.772
peak=    3.909 closest distance to " O   SER A  87 " =    2.145
peak=    3.909 closest distance to " O   HOH Z 419 " =    2.177
peak=    3.905 closest distance to " CB  TYR A 169 " =    0.796
peak=    3.875 closest distance to " O   HOH Z 133 " =    2.612
peak=    3.869 closest distance to " O   HOH Z 132 " =    2.372
peak=    3.864 closest distance to " CD2 TRP A 179 " =    1.352
peak=    3.855 closest distance to " O   HOH Z 261 " =    2.148
peak=    3.844 closest distance to " O   HOH Z 403 " =    1.624
peak=    3.840 closest distance to " O   HOH Z  40 " =    1.623
peak=    3.817 closest distance to " O   HOH Z 392 " =    3.153
peak=    3.814 closest distance to " O   HOH Z 368 " =    2.080
peak=    3.794 closest distance to " CB  SER A   3 " =    1.269
peak=    3.793 closest distance to " CB  ASP A 140 " =    0.989
peak=    3.790 closest distance to " CB  GLU A 128 " =    1.000
peak=    3.781 closest distance to " O   HOH Z 265 " =    2.452
peak=    3.773 closest distance to " OG BSER A 164 " =    2.260
peak=    3.767 closest distance to " O   HOH Z 214 " =    2.149
peak=    3.765 closest distance to " O   HOH Z   1 " =    1.835
peak=    3.764 closest distance to " O   HOH Z 353 " =    2.607
peak=    3.764 closest distance to " O   HOH Z 327 " =    1.558
peak=    3.760 closest distance to " O   HOH Z 180 " =    2.199
peak=    3.760 closest distance to " O   HOH Z 402 " =    1.383
peak=    3.758 closest distance to " CD  ARG A 159 " =    0.725
peak=    3.756 closest distance to " CB  VAL A 202 " =    1.598
peak=    3.745 closest distance to " O   HOH Z  93 " =    2.539
peak=    3.734 closest distance to " CB  SER A 212 " =    1.084
peak=    3.733 closest distance to " O   HOH Z 407 " =    2.342
peak=    3.720 closest distance to " CG1 ILE A  33 " =    1.190
peak=    3.718 closest distance to " O   HOH Z 389 " =    1.804
peak=    3.712 closest distance to " NH1AARG A 145 " =    1.176
peak=    3.683 closest distance to " CB  GLU A 277 " =    3.559
peak=    3.678 closest distance to " O   HOH Z   1 " =    1.666
peak=    3.674 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.672 closest distance to " ND1 HIS A  86 " =    1.805
peak=    3.671 closest distance to " O   HOH Z 425 " =    2.067
peak=    3.669 closest distance to " O   HOH Z  44 " =    1.722
peak=    3.647 closest distance to " O   HOH Z  61 " =    1.460
peak=    3.645 closest distance to " O   HOH Z 371 " =    3.014
peak=    3.645 closest distance to " O   HOH Z   9 " =    1.959
peak=    3.645 closest distance to " O   HOH Z 344 " =    3.248
peak=    3.644 closest distance to " CG2 ILE A 120 " =    1.107
peak=    3.644 closest distance to " O   HOH Z  10 " =    1.843
peak=    3.636 closest distance to " O   HOH Z  43 " =    1.817
peak=    3.632 closest distance to " CG  LEU A 167 " =    1.263
peak=    3.628 closest distance to " CB  TYR A 116 " =    0.771
peak=    3.619 closest distance to " O   HOH Z 305 " =    3.571
peak=    3.615 closest distance to " CB  LYS A 117 " =    1.226
peak=    3.600 closest distance to " O   HOH Z 128 " =    2.198
peak=    3.594 closest distance to " CB  ARG A 139 " =    0.975
peak=    3.580 closest distance to " O   HOH Z 313 " =    1.937
peak=    3.579 closest distance to " O   HOH Z  66 " =    2.128
peak=    3.578 closest distance to " CD BLYS A 290 " =    1.167
peak=    3.563 closest distance to " O   HOH Z 245 " =    1.296
peak=    3.561 closest distance to " O   HOH Z 193 " =    1.982
peak=    3.546 closest distance to " O   HOH Z 193 " =    1.680
peak=    3.544 closest distance to " CB  GLN A  89 " =    1.458
peak=    3.543 closest distance to " O   HOH Z   3 " =    1.863
peak=    3.536 closest distance to " O   HOH Z 172 " =    3.123
peak=    3.535 closest distance to " CA  ARG A 195 " =    1.191
peak=    3.529 closest distance to " CB  THR A 157 " =    1.118
peak=    3.526 closest distance to " O   HOH Z  59 " =    1.677
peak=    3.523 closest distance to " O   HOH Z 298 " =    2.435
peak=    3.523 closest distance to " O   HOH Z 280 " =    3.016
peak=    3.521 closest distance to " O   HOH Z 290 " =    0.913
peak=    3.519 closest distance to " CG1BVAL A  72 " =    1.527
peak=    3.518 closest distance to " O   HOH Z 128 " =    2.116
peak=    3.518 closest distance to " O   HOH Z 337 " =    3.649
peak=    3.506 closest distance to " CD  ARG A  66 " =    2.307
peak=    3.506 closest distance to " O   HOH Z 423 " =    1.815
peak=    3.504 closest distance to " CB  GLN A  88 " =    1.200
peak=    3.502 closest distance to " CB  SER A  62 " =    1.312
peak=    3.501 closest distance to " CA  ALA A 233 " =    1.055
peak=    3.497 closest distance to " O  BHOH Z 338 " =    2.359
peak=    3.495 closest distance to " CB  SER A  26 " =    1.655
peak=    3.495 closest distance to " O   HOH Z  40 " =    2.003
peak=    3.492 closest distance to " O   HOH Z 391 " =    2.868
peak=    3.491 closest distance to " O   HOH Z 291 " =    1.501
peak=    3.490 closest distance to " CB  ASN A 142 " =    1.019
peak=    3.487 closest distance to " O   HOH Z 248 " =    1.544
peak=    3.486 closest distance to " CB  ALA A  34 " =    1.101
peak=    3.485 closest distance to " OD2 ASP A 286 " =    2.776
peak=    3.485 closest distance to " O   HOH Z 285 " =    2.626
peak=    3.481 closest distance to " O   HOH Z 405 " =    1.083
peak=    3.478 closest distance to " O   HOH Z 406 " =    1.573
peak=    3.471 closest distance to " CA  THR A 264 " =    0.861
peak=    3.469 closest distance to " O   HOH Z 213 " =    1.982
peak=    3.468 closest distance to " O   HOH Z 365 " =    2.775
peak=    3.465 closest distance to " CA  ALA A  84 " =    1.307
peak=    3.461 closest distance to " CA  ALA A 291 " =    0.801
peak=    3.448 closest distance to " O   HOH Z 329 " =    3.906
peak=    3.447 closest distance to " N   ASN A  39 " =    1.283
peak=    3.444 closest distance to " N   PHE A 130 " =    1.218
peak=    3.442 closest distance to " CA  ARG A  36 " =    1.014
peak=    3.440 closest distance to " CB  ASN A 110 " =    1.098
peak=    3.435 closest distance to " O   HOH Z 325 " =    3.841
peak=    3.432 closest distance to " N   TYR A 116 " =    1.547
peak=    3.430 closest distance to " CB  TRP A 179 " =    1.352
peak=    3.428 closest distance to " O   HOH Z  21 " =    1.744
peak=    3.426 closest distance to " O   HOH Z  53 " =    2.517
peak=    3.423 closest distance to " CD  ARG A 269 " =    0.955
peak=    3.422 closest distance to " NH2BARG A 145 " =    2.059
peak=    3.420 closest distance to " O   HOH Z 261 " =    2.346
peak=    3.417 closest distance to " O   HOH Z 175 " =    2.229
peak=    3.410 closest distance to " CB  HIS A 108 " =    0.795
peak=    3.402 closest distance to " O   HOH Z 411 " =    3.819
peak=    3.401 closest distance to " N   ARG A 156 " =    1.295
peak=    3.397 closest distance to " CD2 LEU A 297 " =    0.900
peak=    3.396 closest distance to " C   ILE A 106 " =    1.880
peak=    3.394 closest distance to " O   HOH Z 422 " =    2.627
peak=    3.390 closest distance to " O   HOH Z 437 " =    1.367
peak=    3.388 closest distance to " ND2 ASN A 249 " =    0.851
peak=    3.388 closest distance to " O   ASN A  74 " =    1.526
peak=    3.381 closest distance to " CB  GLU A  46 " =    0.964
peak=    3.373 closest distance to " OG  SER A  22 " =    2.737
peak=    3.372 closest distance to " CD1 ILE A 263 " =    1.342
peak=    3.371 closest distance to " CA  THR A 221 " =    1.020
peak=    3.370 closest distance to " O   HOH Z 417 " =    3.271
peak=    3.370 closest distance to " CD  PRO A 243 " =    1.514
peak=    3.366 closest distance to " NE2 GLN A  73 " =    3.761
peak=    3.365 closest distance to " O   HOH Z 426 " =    1.924
peak=    3.364 closest distance to " OD1BASN A 224 " =    2.339
peak=    3.362 closest distance to " O   HOH Z  88 " =    2.528
peak=    3.361 closest distance to " CB  THR A  31 " =    1.657
peak=    3.360 closest distance to " CB  ASN A  39 " =    0.871
peak=    3.357 closest distance to " CD1 ILE A 106 " =    0.810
peak=    3.356 closest distance to " O   HOH Z 357 " =    1.917
peak=    3.356 closest distance to " OG  SER A  62 " =    2.862
peak=    3.351 closest distance to " CA  ALA A  21 " =    1.109
peak=    3.349 closest distance to " O   HOH Z 173 " =    1.838
peak=    3.349 closest distance to " CB  ILE A 120 " =    1.362
peak=    3.346 closest distance to " CG2 VAL A 197 " =    1.104
peak=    3.345 closest distance to " CB  MET A  47 " =    1.114
peak=    3.345 closest distance to " O   HOH Z 433 " =    1.815
peak=    3.342 closest distance to " CA  MET A  40 " =    1.111
peak=    3.341 closest distance to " O   HOH Z 359 " =    1.403
peak=    3.337 closest distance to " CD1 LEU A  96 " =    0.813
peak=    3.330 closest distance to " O   HOH Z 343 " =    3.404
peak=    3.325 closest distance to " O   HOH Z  97 " =    2.023
peak=    3.320 closest distance to " O   HOH Z 147 " =    1.769
peak=    3.319 closest distance to " O   HOH Z 261 " =    1.540
peak=    3.318 closest distance to " O   HOH Z 286 " =    2.335
peak=    3.313 closest distance to " O   HOH Z 135 " =    1.623
peak=    3.310 closest distance to " O   HOH Z 409 " =    2.638
peak=    3.307 closest distance to " NH1BARG A 145 " =    1.123
peak=    3.306 closest distance to " CG2 THR A 221 " =    1.112
peak=    3.303 closest distance to " O   HOH Z 148 " =    3.436
peak=    3.300 closest distance to " CA  ALA A 158 " =    1.244
peak=    3.297 closest distance to " OH  TYR A 116 " =    1.060
peak=    3.293 closest distance to " O   HOH Z   6 " =    2.053
peak=    3.293 closest distance to " CA  ALA A  51 " =    0.897
peak=    3.291 closest distance to " ND2 ASN A 110 " =    1.719
peak=    3.290 closest distance to " CG AARG A 275 " =    1.071
peak=    3.289 closest distance to " CG  MET A 185 " =    1.216
peak=    3.286 closest distance to " CB  ALA A 291 " =    1.331
peak=    3.286 closest distance to " O   HOH Z 403 " =    1.397
peak=    3.282 closest distance to " O   HOH Z 126 " =    1.533
peak=    3.279 closest distance to " O   HOH Z 287 " =    2.300
peak=    3.278 closest distance to " NE2 GLN A  77 " =    3.189
peak=    3.272 closest distance to " O   HOH Z 336 " =    1.842
peak=    3.265 closest distance to " N   ASN A 127 " =    1.297
peak=    3.264 closest distance to " CB  PRO A  90 " =    1.180
peak=    3.260 closest distance to " O   HOH Z 325 " =    2.523
peak=    3.257 closest distance to " CD  LYS A 166 " =    1.271
peak=    3.255 closest distance to " NE2 HIS A 207 " =    1.363
peak=    3.254 closest distance to " CG  LYS A  76 " =    0.972
peak=    3.253 closest distance to " O   HOH Z 163 " =    1.878
peak=    3.252 closest distance to " CB  SER A 216 " =    0.866
peak=    3.248 closest distance to " O   THR A 220 " =    1.313
peak=    3.246 closest distance to " O   HOH Z  64 " =    2.208
peak=    3.245 closest distance to " O   ALA A   1 " =    1.688
peak=    3.243 closest distance to " CG2 ILE A  20 " =    1.457
peak=    3.241 closest distance to " OG BSER A 134 " =    2.914
peak=    3.236 closest distance to " O   HOH Z 234 " =    1.875
peak=    3.235 closest distance to " CA  SER A 146 " =    1.730
peak=    3.229 closest distance to " O   HOH Z 219 " =    1.983
peak=    3.229 closest distance to " CD1 LEU A 300 " =    1.261
peak=    3.227 closest distance to " O   HOH Z 213 " =    1.796
peak=    3.226 closest distance to " CG  MET A 113 " =    1.205
peak=    3.221 closest distance to " CG  GLN A  89 " =    1.485
peak=    3.221 closest distance to " CB  SER A 273 " =    0.850
peak=    3.216 closest distance to " OG1 THR A 294 " =    2.409
peak=    3.212 closest distance to " CA  ARG A 102 " =    1.048
peak=    3.212 closest distance to " N   GLN A 278 " =    1.275
peak=    3.210 closest distance to " CB  MET A  40 " =    0.808
peak=    3.209 closest distance to " O   HOH Z  44 " =    2.937
peak=    3.208 closest distance to " OG BSER A  99 " =    2.240
peak=    3.206 closest distance to " O   HOH Z 146 " =    1.583
peak=    3.206 closest distance to " NZ  LYS A  48 " =    1.204
peak=    3.194 closest distance to " CA  ASP A 162 " =    1.071
peak=    3.193 closest distance to " CB  ALA A   1 " =    4.682
peak=    3.193 closest distance to " CD2 LEU A 255 " =    1.427
peak=    3.191 closest distance to " CB  ALA A   9 " =    1.589
peak=    3.190 closest distance to " CZ2 TRP A 179 " =    1.654
peak=    3.188 closest distance to " CG  GLN A  77 " =    2.246
peak=    3.187 closest distance to " O   HOH Z  88 " =    2.443
peak=    3.182 closest distance to " CB  THR A 235 " =    1.189
peak=    3.180 closest distance to " O   HOH Z 423 " =    2.745
peak=    3.173 closest distance to " CB  SER A 141 " =    1.003
peak=    3.172 closest distance to " O   HOH Z 279 " =    2.201
peak=    3.170 closest distance to " CG1 VAL A 153 " =    0.953
peak=    3.169 closest distance to " O   HOH Z 227 " =    2.091
peak=    3.168 closest distance to " CA  SER A  87 " =    1.036
peak=    3.167 closest distance to " O   HOH Z 273 " =    2.818
peak=    3.166 closest distance to " O   HOH Z  66 " =    2.048
peak=    3.162 closest distance to " CA  TYR A 116 " =    1.292
peak=    3.162 closest distance to " O   HOH Z 380 " =    1.634
peak=    3.158 closest distance to " CA  LYS A 117 " =    1.199
peak=    3.155 closest distance to " CB  ASN A 215 " =    1.096
peak=    3.154 closest distance to " CA  MET A 105 " =    0.977
peak=    3.150 closest distance to " O   HOH Z 421 " =    1.910
peak=    3.149 closest distance to " CB  ALA A 114 " =    1.390
peak=    3.140 closest distance to " CA  LYS A 290 " =    1.321
peak=    3.139 closest distance to " CZ3 TRP A 266 " =    1.101
peak=    3.134 closest distance to " CB  ALA A 248 " =    0.887
peak=    3.129 closest distance to " N   ASP A 162 " =    1.203
peak=    3.125 closest distance to " CB  ASP A 200 " =    0.834
peak=    3.121 closest distance to " O   HOH Z 152 " =    1.770
peak=    3.120 closest distance to " CE  LYS A  48 " =    1.095
peak=    3.119 closest distance to " O   HOH Z 116 " =    1.756
peak=    3.119 closest distance to " O   HOH Z 266 " =    3.363
peak=    3.113 closest distance to " CB  ARG A 138 " =    0.887
peak=    3.112 closest distance to " CA  SER A  32 " =    1.630
peak=    3.100 closest distance to " CB  LYS A 290 " =    1.155
peak=    3.099 closest distance to " CB  LEU A 255 " =    0.765
peak=    3.099 closest distance to " CA  ARG A 159 " =    1.223
peak=    3.091 closest distance to " O   HOH Z 153 " =    1.569
peak=    3.091 closest distance to " O   HOH Z 302 " =    1.830
peak=    3.089 closest distance to " OE2 GLU A  53 " =    2.075
peak=    3.086 closest distance to " CG1 ILE A  49 " =    1.467
peak=    3.075 closest distance to " O   HOH Z 156 " =    2.958
peak=    3.072 closest distance to " CG BARG A 102 " =    1.751
peak=    3.069 closest distance to " CG1 VAL A 189 " =    1.894
peak=    3.052 closest distance to " O   HOH Z 163 " =    1.657
peak=    3.052 closest distance to " CE AMET A  47 " =    1.448
peak=    3.050 closest distance to " CA  ALA A 299 " =    0.902
peak=    3.043 closest distance to " O   HOH Z 238 " =    3.737
peak=    3.023 closest distance to " O   HOH Z 361 " =    3.129
peak=    3.019 closest distance to " CB  PHE A 204 " =    0.765
peak=    3.010 closest distance to " O   HOH Z 132 " =    3.301
peak=    3.002 closest distance to " O   HOH Z 391 " =    2.610

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.684 - 5.906
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.792 - 5.906

peak=   -4.695 closest distance to " O   HOH Z 377 " =    2.100
peak=   -4.642 closest distance to " OG BSER A 134 " =    1.245
peak=   -4.622 closest distance to " O   HOH Z 266 " =    5.107
peak=   -4.589 closest distance to " CG  GLN A 223 " =    1.982
peak=   -4.552 closest distance to " CD  ARG A 156 " =    2.047
peak=   -4.515 closest distance to " CB  PRO A 243 " =    2.654
peak=   -4.383 closest distance to " SG  CYS A 254 " =    3.436
peak=   -4.338 closest distance to " C   HIS A 108 " =    1.110
peak=   -4.330 closest distance to " O   HOH Z 231 " =    2.303
peak=   -4.219 closest distance to " CG1 VAL A 112 " =    2.829
peak=   -4.159 closest distance to " O   VAL A  67 " =    2.658
peak=   -4.158 closest distance to " CD  GLN A  58 " =    1.092
peak=   -4.036 closest distance to " CE  MET A 105 " =    2.343
peak=   -4.035 closest distance to " CB  PHE A 192 " =    1.962
peak=   -4.030 closest distance to " O   HOH Z 435 " =    2.862
peak=   -4.024 closest distance to " CG1 VAL A  67 " =    2.960
peak=   -4.016 closest distance to " O   HOH Z 198 " =    1.902
peak=   -4.004 closest distance to " ND2 ASN A  45 " =    1.778
peak=   -3.987 closest distance to " O   HOH Z 313 " =    1.797
peak=   -3.985 closest distance to " O   HOH Z 372 " =    2.366
peak=   -3.953 closest distance to " O   HOH Z 389 " =    1.972
peak=   -3.936 closest distance to " N   ALA A  43 " =    2.580
peak=   -3.882 closest distance to " O   PRO A 198 " =    1.271
peak=   -3.876 closest distance to " CE2 PHE A 218 " =    2.411
peak=   -3.862 closest distance to " CB  ASN A  39 " =    2.298
peak=   -3.844 closest distance to " CZ3 TRP A 179 " =    1.199
peak=   -3.835 closest distance to " O   HOH Z 185 " =    2.211
peak=   -3.834 closest distance to " O   HOH Z 290 " =    1.208
peak=   -3.825 closest distance to " CB  ALA A 291 " =    2.206
peak=   -3.795 closest distance to " CD  ARG A 139 " =    1.562
peak=   -3.785 closest distance to " CB  ALA A 291 " =    2.197
peak=   -3.775 closest distance to " CE2 TYR A  30 " =    2.750
peak=   -3.760 closest distance to " O   HOH Z 351 " =    1.544
peak=   -3.729 closest distance to " OD1 ASN A 148 " =    1.547
peak=   -3.729 closest distance to " OG  SER A  97 " =    2.156
peak=   -3.719 closest distance to " O   HOH Z 407 " =    2.996
peak=   -3.705 closest distance to " OD1 ASP A 171 " =    1.622
peak=   -3.694 closest distance to " ND2 ASN A  45 " =    1.131
peak=   -3.685 closest distance to " OD1 ASN A 187 " =    1.579
peak=   -3.670 closest distance to " CB  TYR A  15 " =    2.195
peak=   -3.667 closest distance to " CB  ALA A  43 " =    2.523
peak=   -3.663 closest distance to " CZ  PHE A  59 " =    1.505
peak=   -3.661 closest distance to " CD2 TYR A 247 " =    2.483
peak=   -3.649 closest distance to " O   HOH Z  13 " =    1.699
peak=   -3.644 closest distance to " O   HOH Z 114 " =    2.980
peak=   -3.642 closest distance to " CD2 LEU A 237 " =    2.828
peak=   -3.629 closest distance to " CB  ALA A 161 " =    2.512
peak=   -3.621 closest distance to " O   PHE A 218 " =    1.566
peak=   -3.621 closest distance to " CG2 THR A 178 " =    2.243
peak=   -3.619 closest distance to " CG2 ILE A 263 " =    2.258
peak=   -3.618 closest distance to " O   HOH Z 348 " =    2.213
peak=   -3.615 closest distance to " CG  PHE A 283 " =    2.634
peak=   -3.611 closest distance to " O   ARG A 145 " =    1.569
peak=   -3.610 closest distance to " O   HOH Z 298 " =    1.287
peak=   -3.606 closest distance to " CD1 PHE A  59 " =    1.956
peak=   -3.602 closest distance to " CZ  TYR A 169 " =    1.713
peak=   -3.599 closest distance to " OXT GLY A 302 " =    2.864
peak=   -3.598 closest distance to " CB  ALA A 248 " =    2.323
peak=   -3.593 closest distance to " OD2 ASP A 191 " =    1.372
peak=   -3.581 closest distance to " O   HOH Z 211 " =    1.632
peak=   -3.579 closest distance to " NH2BARG A 275 " =    1.842
peak=   -3.570 closest distance to " O   SER A 135 " =    1.441
peak=   -3.546 closest distance to " CA  GLY A 203 " =    2.330
peak=   -3.528 closest distance to " O   HOH Z 395 " =    5.175
peak=   -3.522 closest distance to " O   HOH Z  60 " =    2.227
peak=   -3.518 closest distance to " O   HOH Z 353 " =    2.175
peak=   -3.513 closest distance to " ND2 ASN A 249 " =    2.366
peak=   -3.513 closest distance to " O   ALA A 161 " =    1.684
peak=   -3.510 closest distance to " O   HOH Z 253 " =    3.877
peak=   -3.506 closest distance to " O   HOH Z 102 " =    1.570
peak=   -3.494 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.491 closest distance to " N   ALA A 248 " =    1.574
peak=   -3.483 closest distance to " O   HOH Z 317 " =    1.543
peak=   -3.483 closest distance to " O   PRO A 163 " =    1.998
peak=   -3.474 closest distance to " O   HOH Z 362 " =    5.906
peak=   -3.471 closest distance to " O   HOH Z 198 " =    1.625
peak=   -3.470 closest distance to " CA  GLY A 133 " =    1.988
peak=   -3.458 closest distance to " N   THR A 157 " =    1.481
peak=   -3.447 closest distance to " O   HOH Z  38 " =    1.641
peak=   -3.446 closest distance to " N   GLN A  58 " =    1.656
peak=   -3.441 closest distance to " O   HOH Z 394 " =    1.434
peak=   -3.432 closest distance to " O   MET A  40 " =    2.785
peak=   -3.427 closest distance to " CB  TRP A  85 " =    2.476
peak=   -3.426 closest distance to " CE BMET A  47 " =    1.357
peak=   -3.420 closest distance to " CB  ALA A 248 " =    2.075
peak=   -3.418 closest distance to " O   SER A 210 " =    1.983
peak=   -3.414 closest distance to " O   HOH Z  73 " =    2.329
peak=   -3.408 closest distance to " O   HOH Z 243 " =    2.045
peak=   -3.406 closest distance to " ND2 ASN A 187 " =    1.502
peak=   -3.404 closest distance to " O   HOH Z  43 " =    1.765
peak=   -3.400 closest distance to " CB  ASP A 132 " =    2.260
peak=   -3.398 closest distance to " O   VAL A 189 " =    2.589
peak=   -3.397 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.396 closest distance to " CA  GLY A 241 " =    2.256
peak=   -3.394 closest distance to " O   SER A  95 " =    1.499
peak=   -3.394 closest distance to " O   HOH Z  63 " =    1.727
peak=   -3.391 closest distance to " NE  ARG A  36 " =    1.946
peak=   -3.389 closest distance to " O   HOH Z 126 " =    1.901
peak=   -3.371 closest distance to " O   HOH Z 196 " =    2.188
peak=   -3.371 closest distance to " CD2 PHE A 225 " =    1.112
peak=   -3.359 closest distance to " O   HOH Z 351 " =    1.682
peak=   -3.359 closest distance to " CG  ARG A 269 " =    2.407
peak=   -3.358 closest distance to " O   HOH Z 140 " =    1.651
peak=   -3.351 closest distance to " O   HOH Z  10 " =    1.446
peak=   -3.349 closest distance to " CB  ASP A 286 " =    1.707
peak=   -3.345 closest distance to " NH2AARG A 275 " =    5.218
peak=   -3.345 closest distance to " OD1 ASP A 191 " =    1.841
peak=   -3.342 closest distance to " N   ASP A 286 " =    2.340
peak=   -3.330 closest distance to " CA  GLY A  98 " =    1.841
peak=   -3.329 closest distance to " O   HOH Z 263 " =    3.051
peak=   -3.327 closest distance to " O   ALA A  10 " =    1.628
peak=   -3.325 closest distance to " NE2 GLN A 278 " =    1.637
peak=   -3.322 closest distance to " O   VAL A 174 " =    2.175
peak=   -3.321 closest distance to " CD1 LEU A 101 " =    2.252
peak=   -3.320 closest distance to " O   HOH Z 165 " =    2.171
peak=   -3.313 closest distance to " O   HOH Z 131 " =    4.100
peak=   -3.311 closest distance to " O   HOH Z 385 " =    2.002
peak=   -3.307 closest distance to " O   TRP A  70 " =    1.442
peak=   -3.304 closest distance to " CG1 VAL A 230 " =    2.073
peak=   -3.294 closest distance to " CD  GLU A 236 " =    1.093
peak=   -3.294 closest distance to " O   HOH Z 357 " =    2.066
peak=   -3.285 closest distance to " C   LEU A 143 " =    1.084
peak=   -3.285 closest distance to " O   HOH Z  11 " =    1.795
peak=   -3.283 closest distance to " CB  ASP A 286 " =    2.108
peak=   -3.276 closest distance to " O   VAL A 189 " =    1.653
peak=   -3.273 closest distance to " O   HOH Z  15 " =    1.531
peak=   -3.272 closest distance to " O   HOH Z 266 " =    4.852
peak=   -3.270 closest distance to " N   ASN A  60 " =    1.383
peak=   -3.259 closest distance to " O   HOH Z 359 " =    3.282
peak=   -3.255 closest distance to " O   HOH Z 348 " =    1.839
peak=   -3.254 closest distance to " OE2 GLU A 152 " =    1.198
peak=   -3.250 closest distance to " CB  GLN A  11 " =    1.824
peak=   -3.244 closest distance to " C   ALA A 158 " =    1.400
peak=   -3.241 closest distance to " CA  GLY A  57 " =    2.181
peak=   -3.241 closest distance to " O   HOH Z  52 " =    1.309
peak=   -3.239 closest distance to " CB  ASP A 132 " =    2.370
peak=   -3.238 closest distance to " O   ALA A 292 " =    2.033
peak=   -3.236 closest distance to " CB  PRO A 163 " =    2.436
peak=   -3.236 closest distance to " O   HOH Z 244 " =    2.053
peak=   -3.233 closest distance to " O   SER A  22 " =    2.452
peak=   -3.226 closest distance to " O   ALA A 180 " =    1.296
peak=   -3.224 closest distance to " CG1 VAL A 268 " =    2.417
peak=   -3.221 closest distance to " CD1 LEU A 228 " =    2.119
peak=   -3.221 closest distance to " O   HOH Z 134 " =    3.189
peak=   -3.217 closest distance to " O   ALA A  34 " =    2.482
peak=   -3.213 closest distance to " CG  ASP A 231 " =    0.792
peak=   -3.212 closest distance to " O   HOH Z 111 " =    2.024
peak=   -3.204 closest distance to " OG  SER A  87 " =    1.373
peak=   -3.202 closest distance to " OD2 ASP A  50 " =    1.632
peak=   -3.202 closest distance to " O   HOH Z 191 " =    5.688
peak=   -3.201 closest distance to " CD2 PHE A  61 " =    2.164
peak=   -3.199 closest distance to " O   HOH Z 281 " =    2.666
peak=   -3.196 closest distance to " C   PRO A  90 " =    1.545
peak=   -3.187 closest distance to " O   HOH Z 421 " =    3.068
peak=   -3.187 closest distance to " CG1 VAL A 250 " =    2.576
peak=   -3.185 closest distance to " CE2 PHE A  61 " =    2.618
peak=   -3.183 closest distance to " CB  ALA A 244 " =    2.093
peak=   -3.183 closest distance to " CG1 VAL A 197 " =    2.156
peak=   -3.181 closest distance to " CG2 VAL A 189 " =    1.987
peak=   -3.181 closest distance to " OG BSER A 134 " =    1.691
peak=   -3.180 closest distance to " O   ILE A 106 " =    2.034
peak=   -3.176 closest distance to " O   HOH Z  93 " =    2.429
peak=   -3.175 closest distance to " CG  GLU A 277 " =    1.291
peak=   -3.174 closest distance to " CD2 TYR A 293 " =    1.929
peak=   -3.158 closest distance to " OE1 GLN A  88 " =    1.191
peak=   -3.156 closest distance to " O   HOH Z  71 " =    2.117
peak=   -3.154 closest distance to " NH1 ARG A 195 " =    2.645
peak=   -3.147 closest distance to " N   SER A 276 " =    1.210
peak=   -3.139 closest distance to " OH  TYR A 214 " =    1.256
peak=   -3.139 closest distance to " O   GLN A 240 " =    1.996
peak=   -3.134 closest distance to " O   HOH Z 369 " =    2.219
peak=   -3.133 closest distance to " OE1 GLN A  58 " =    3.075
peak=   -3.133 closest distance to " O   HOH Z 123 " =    2.359
peak=   -3.126 closest distance to " O   GLY A  80 " =    2.458
peak=   -3.126 closest distance to " O   HOH Z 393 " =    3.469
peak=   -3.126 closest distance to " OE1 GLN A 183 " =    1.485
peak=   -3.125 closest distance to " O   GLN A 240 " =    2.397
peak=   -3.124 closest distance to " OG1 THR A 246 " =    1.348
peak=   -3.124 closest distance to " OD1AASN A 224 " =    1.856
peak=   -3.123 closest distance to " O   HOH Z 310 " =    1.673
peak=   -3.121 closest distance to " O   HOH Z 311 " =    3.698
peak=   -3.121 closest distance to " CE3 TRP A 150 " =    2.134
peak=   -3.118 closest distance to " CA  GLY A 241 " =    3.188
peak=   -3.115 closest distance to " CZ2 TRP A 274 " =    0.958
peak=   -3.114 closest distance to " CD1 LEU A 297 " =    2.458
peak=   -3.114 closest distance to " SG ACYS A 201 " =    1.700
peak=   -3.113 closest distance to " NH2 ARG A  79 " =    2.035
peak=   -3.113 closest distance to " CG  TRP A 266 " =    1.958
peak=   -3.107 closest distance to " OD2 ASP A 171 " =    1.744
peak=   -3.107 closest distance to " CA  ASP A  27 " =    2.438
peak=   -3.106 closest distance to " CG1 VAL A 125 " =    1.899
peak=   -3.104 closest distance to " O   ALA A  51 " =    1.313
peak=   -3.104 closest distance to " O   HOH Z   6 " =    1.500
peak=   -3.103 closest distance to " O   HOH Z 423 " =    1.240
peak=   -3.099 closest distance to " O   HOH Z  51 " =    1.728
peak=   -3.099 closest distance to " CA  TYR A  68 " =    3.158
peak=   -3.097 closest distance to " CG  GLU A 152 " =    1.307
peak=   -3.091 closest distance to " CD  GLN A  77 " =    1.537
peak=   -3.088 closest distance to " C   MET A 188 " =    1.410
peak=   -3.087 closest distance to " CG  GLU A   2 " =    2.043
peak=   -3.081 closest distance to " OG  SER A 206 " =    1.731
peak=   -3.081 closest distance to " O   HOH Z 174 " =    2.606
peak=   -3.066 closest distance to " O   HOH Z 166 " =    1.489
peak=   -3.066 closest distance to " CB  CYS A 201 " =    2.473
peak=   -3.061 closest distance to " O   HOH Z  51 " =    1.303
peak=   -3.057 closest distance to " O   HOH Z 283 " =    5.586
peak=   -3.052 closest distance to " CB  ALA A 100 " =    2.154
peak=   -3.035 closest distance to " O   HOH Z 323 " =    1.461
peak=   -3.032 closest distance to " O   HOH Z 350 " =    1.729
peak=   -3.029 closest distance to " OD1 ASP A 200 " =    1.496
peak=   -3.004 closest distance to " CD2 LEU A 143 " =    2.704

================= 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    :  0.2912 0.2887   5.964578e+00   5.934995e+00
   1_bss:  0.2750 0.2724   5.939423e+00   5.900630e+00
   1_xyz:  0.1616 0.1840   5.418568e+00   5.523509e+00
   1_adp:  0.1473 0.1921   5.367358e+00   5.562953e+00
   1_occ:  0.1471 0.1917   5.366065e+00   5.561803e+00
   2_bss:  0.1459 0.1895   5.359660e+00   5.551564e+00
   2_xyz:  0.1162 0.1610   5.168399e+00   5.398750e+00
   2_adp:  0.1138 0.1548   5.140421e+00   5.363839e+00
   2_occ:  0.1137 0.1549   5.139794e+00   5.363853e+00
   3_bss:  0.1139 0.1547   5.138848e+00   5.361815e+00
   3_xyz:  0.1144 0.1532   5.141282e+00   5.359103e+00
   3_adp:  0.1118 0.1540   5.132640e+00   5.364942e+00
   3_occ:  0.1118 0.1540   5.132626e+00   5.365045e+00
   4_bss:  0.1117 0.1540   5.132204e+00   5.364684e+00
   4_xyz:  0.1091 0.1536   5.121033e+00   5.365009e+00
   4_adp:  0.1089 0.1533   5.118950e+00   5.363619e+00
   4_occ:  0.1089 0.1533   5.118901e+00   5.363629e+00
   5_bss:  0.1088 0.1532   5.118969e+00   5.363702e+00
   5_xyz:  0.1063 0.1538   5.109260e+00   5.366083e+00
   5_adp:  0.1063 0.1544   5.110425e+00   5.369169e+00
   5_occ:  0.1062 0.1544   5.110343e+00   5.369110e+00
   5_bss:  0.1061 0.1544   5.110383e+00   5.369139e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.332  42.572  -2.795   0.367  -0.913   0.000  -0.000  -0.000
   1_xyz:  0.332  42.572  -2.795   0.367  -0.913   0.000  -0.000  -0.000
   1_adp:  0.332  42.572  -2.795   0.367  -0.913   0.000  -0.000  -0.000
   1_occ:  0.332  42.572  -2.795   0.367  -0.913   0.000  -0.000  -0.000
   2_bss:  0.325  50.119  -3.060  -1.976  -1.353  -0.000  -0.000  -0.000
   2_xyz:  0.325  50.119  -3.060  -1.976  -1.353  -0.000  -0.000  -0.000
   2_adp:  0.325  50.119  -3.060  -1.976  -1.353  -0.000  -0.000  -0.000
   2_occ:  0.325  50.119  -3.060  -1.976  -1.353  -0.000  -0.000  -0.000
   3_bss:  0.328  50.119  -2.944  -2.444  -1.216  -0.000  -0.000  -0.000
   3_xyz:  0.328  50.119  -2.944  -2.444  -1.216  -0.000  -0.000  -0.000
   3_adp:  0.328  50.119  -2.944  -2.444  -1.216  -0.000  -0.000  -0.000
   3_occ:  0.328  50.119  -2.944  -2.444  -1.216  -0.000  -0.000  -0.000
   4_bss:  0.322  50.119  -2.740  -2.412  -1.064  -0.000  -0.000  -0.000
   4_xyz:  0.322  50.119  -2.740  -2.412  -1.064  -0.000  -0.000  -0.000
   4_adp:  0.322  50.119  -2.740  -2.412  -1.064  -0.000  -0.000  -0.000
   4_occ:  0.322  50.119  -2.740  -2.412  -1.064  -0.000  -0.000  -0.000
   5_bss:  0.322  50.119  -2.488  -2.227  -0.826  -0.000  -0.000  -0.000
   5_xyz:  0.322  50.119  -2.488  -2.227  -0.826  -0.000  -0.000  -0.000
   5_adp:  0.322  50.119  -2.488  -2.227  -0.826  -0.000  -0.000  -0.000
   5_occ:  0.322  50.119  -2.488  -2.227  -0.826  -0.000  -0.000  -0.000
   5_bss:  0.321  50.120  -2.266  -2.049  -0.625  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  28.349 0.7800  0.9561    22704.759
   1_bss:  27.017 0.7918  0.9324    19597.106
   1_xyz:  16.803 0.8922  1.0080     8494.093
   1_adp:  17.750 0.8832  1.0032     9120.968
   1_occ:  17.733 0.8833  1.0030     9088.195
   2_bss:  17.442 0.8859  0.9703     8866.710
   2_xyz:  14.360 0.9115  0.9821     6448.307
   2_adp:  13.608 0.9178  0.9812     6076.811
   2_occ:  13.610 0.9178  0.9810     6070.843
   3_bss:  13.578 0.9180  0.9790     6052.959
   3_xyz:  13.382 0.9200  0.9793     5994.062
   3_adp:  13.500 0.9192  0.9735     6025.154
   3_occ:  13.503 0.9191  0.9734     6027.336
   4_bss:  13.494 0.9192  0.9781     6020.411
   4_xyz:  13.471 0.9194  0.9776     6030.450
   4_adp:  13.441 0.9197  0.9713     6003.912
   4_occ:  13.443 0.9197  0.9712     6003.724
   5_bss:  13.444 0.9197  0.9792     6005.546
   5_xyz:  13.471 0.9194  0.9797     6056.894
   5_adp:  13.542 0.9189  0.9725     6081.245
   5_occ:  13.542 0.9189  0.9725     6080.900
   5_bss:  13.544 0.9189  0.9797     6081.520
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6168e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6168e-01
   1_xyz:   1.005  0.007  0.070 15.256  0.004  4.110   6.1757e-02
   1_adp:   1.005  0.007  0.070 15.256  0.004  4.110   6.1757e-02
   1_occ:   1.005  0.007  0.070 15.256  0.004  4.110   6.1757e-02
   2_bss:   1.005  0.007  0.070 15.256  0.004  4.110   6.1757e-02
   2_xyz:   1.034  0.008  0.078 15.134  0.004  4.109   6.4147e-02
   2_adp:   1.034  0.008  0.078 15.134  0.004  4.109   6.4147e-02
   2_occ:   1.034  0.008  0.078 15.134  0.004  4.109   6.4147e-02
   3_bss:   1.034  0.008  0.078 15.134  0.004  4.109   6.4147e-02
   3_xyz:   0.860  0.005  0.068 14.762  0.003  4.109   4.8529e-02
   3_adp:   0.860  0.005  0.068 14.762  0.003  4.109   4.8529e-02
   3_occ:   0.860  0.005  0.068 14.762  0.003  4.109   4.8529e-02
   4_bss:   0.860  0.005  0.068 14.762  0.003  4.109   4.8529e-02
   4_xyz:   0.902  0.005  0.071 14.736  0.003  4.114   5.0912e-02
   4_adp:   0.902  0.005  0.071 14.736  0.003  4.114   5.0912e-02
   4_occ:   0.902  0.005  0.071 14.736  0.003  4.114   5.0912e-02
   5_bss:   0.902  0.005  0.071 14.736  0.003  4.114   5.0912e-02
   5_xyz:   0.969  0.007  0.075 14.859  0.004  4.114   5.7969e-02
   5_adp:   0.969  0.007  0.075 14.859  0.004  4.114   5.7969e-02
   5_occ:   0.969  0.007  0.075 14.859  0.004  4.114   5.7969e-02
   5_bss:   0.969  0.007  0.075 14.859  0.004  4.114   5.7969e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4006e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4006e-01
   1_xyz:   6.938  0.039  0.224 84.967  0.043  2.245   5.3933e-02
   1_adp:   6.938  0.039  0.224 84.967  0.043  2.245   5.3933e-02
   1_occ:   6.938  0.039  0.224 84.967  0.043  2.245   5.3933e-02
   2_bss:   6.938  0.039  0.224 84.967  0.043  2.245   5.3933e-02
   2_xyz:   6.463  0.047  0.254 83.979  0.028  2.315   5.5650e-02
   2_adp:   6.463  0.047  0.254 83.979  0.028  2.315   5.5650e-02
   2_occ:   6.463  0.047  0.254 83.979  0.028  2.315   5.5650e-02
   3_bss:   6.463  0.047  0.254 83.979  0.028  2.315   5.5650e-02
   3_xyz:   6.464  0.040  0.207 83.578  0.030  2.370   3.3074e-02
   3_adp:   6.464  0.040  0.207 83.578  0.030  2.370   3.3074e-02
   3_occ:   6.464  0.040  0.207 83.578  0.030  2.370   3.3074e-02
   4_bss:   6.464  0.040  0.207 83.578  0.030  2.370   3.3074e-02
   4_xyz:   6.355  0.041  0.213 83.729  0.032  2.362   3.4921e-02
   4_adp:   6.355  0.041  0.213 83.729  0.032  2.362   3.4921e-02
   4_occ:   6.355  0.041  0.213 83.729  0.032  2.362   3.4921e-02
   5_bss:   6.355  0.041  0.213 83.729  0.032  2.362   3.4921e-02
   5_xyz:   6.242  0.045  0.246 83.581  0.033  2.302   4.1914e-02
   5_adp:   6.242  0.045  0.246 83.581  0.033  2.302   4.1914e-02
   5_occ:   6.242  0.045  0.246 83.581  0.033  2.302   4.1914e-02
   5_bss:   6.242  0.045  0.246 83.581  0.033  2.302   4.1914e-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:  68.48   1.04  16.91  65.08   1.04  12.95  68.48   6.54  38.45
   1_occ:  68.48   1.04  16.91  65.08   1.04  12.95  68.48   6.54  38.45
   2_bss:  68.48   1.04  16.91  65.08   1.04  12.95  68.48   6.54  38.45
   2_xyz:  68.48   1.04  16.91  65.08   1.04  12.95  68.48   6.54  38.45
   2_adp:  68.75   2.40  16.48  66.27   2.40  12.81  68.75   6.52  36.45
   2_occ:  68.75   2.40  16.48  66.27   2.40  12.81  68.75   6.52  36.45
   3_bss:  68.75   2.40  16.48  66.27   2.40  12.81  68.75   6.52  36.45
   3_xyz:  68.75   2.40  16.48  66.27   2.40  12.81  68.75   6.52  36.45
   3_adp:  81.42   0.87  17.14  81.42   0.87  12.95  75.58   6.39  39.91
   3_occ:  81.42   0.87  17.14  81.42   0.87  12.95  75.58   6.39  39.91
   4_bss:  81.42   0.87  17.14  81.42   0.87  12.95  75.58   6.39  39.91
   4_xyz:  81.42   0.87  17.14  81.42   0.87  12.95  75.58   6.39  39.91
   4_adp:  83.50   0.76  16.93  83.50   0.76  12.78  77.00   6.09  39.53
   4_occ:  83.50   0.76  16.93  83.50   0.76  12.78  77.00   6.09  39.53
   5_bss:  83.50   0.76  16.93  83.50   0.76  12.78  77.00   6.09  39.53
   5_xyz:  83.50   0.76  16.93  83.50   0.76  12.78  77.00   6.09  39.53
   5_adp:  88.40   0.05  16.87  88.40   0.05  12.65  79.08   5.84  39.89
   5_occ:  88.40   0.05  16.87  88.40   0.05  12.65  79.08   5.84  39.89
   5_bss:  88.40   0.05  16.87  88.40   0.05  12.65  79.09   5.84  39.89
------------------------------------------------------------------------
 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:    0.851    0.007    0.272
   1_adp:    0.851    0.007    0.272
   1_occ:    0.851    0.007    0.272
   2_bss:    0.851    0.007    0.272
   2_xyz:    0.788    0.014    0.326
   2_adp:    0.788    0.014    0.326
   2_occ:    0.788    0.014    0.326
   3_bss:    0.788    0.014    0.326
   3_xyz:    0.930    0.027    0.334
   3_adp:    0.930    0.027    0.334
   3_occ:    0.930    0.027    0.334
   4_bss:    0.930    0.027    0.334
   4_xyz:    1.093    0.038    0.346
   4_adp:    1.093    0.038    0.346
   4_occ:    1.093    0.038    0.346
   5_bss:    1.093    0.038    0.346
   5_xyz:    1.143    0.028    0.352
   5_adp:    1.143    0.028    0.352
   5_occ:    1.143    0.028    0.352
   5_bss:    1.143    0.028    0.352
------------------------------------------------------------------------

CPU time actual refinement: 331.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_523/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_523/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_523/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_523/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_523/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.08 
  Macro-tasks:
    bulk solvent and scale       = 37.10  
    individual site refinement   = 134.91 
    weights calculation          = 30.66  
    collect and process          = 6.79   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 209.59 
  Micro-tasks:
    mask                            = 1.19   
    f_calc                          = 105.72 
    alpha_beta                      = 8.19   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.36 
    fmodel                         = 6.98   
    r_factors                      = 0.25   
    phase_errors                   = 11.26  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 249.41 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.678 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    657 calls, 105.29 s
gradients_fft:          602 calls, 100.71 s

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

# Date 2008-01-16 Time 05:01:51 PST -0800 (1200488511.35 s)
Start R-work = 0.2912, R-free = 0.2887 (no bulk solvent and anisotropic scale)
Final R-work = 0.1295, R-free = 0.1732 (no bulk solvent and anisotropic scale)

Start R-work = 0.2750, R-free = 0.2724
Final R-work = 0.1061, R-free = 0.1544