# Date 2008-01-16 Time 05:19:18 PST -0800 (1200489558.19 s)
#phil __OFF__

Command line arguments: "../686.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 948
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 686

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.3993, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9735 1.99115
Completeness in resolution range: 0.967884
Completeness with d_max=infinity: 0.964833

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9735
                             d_min =   1.9912

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9735 1.99115
Completeness in resolution range: 0.967884
Completeness with d_max=infinity: 0.964833

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9740 -  4.2600 [2122/2149]  1910   212  10.0%
  bin  2:  4.2600 -  3.3942 [2035/2051]  1831   204  10.0%
  bin  3:  3.3942 -  2.9690 [2018/2037]  1815   203  10.1%
  bin  4:  2.9690 -  2.6992 [1997/2027]  1799   198   9.9%
  bin  5:  2.6992 -  2.5067 [1978/1997]  1780   198  10.0%
  bin  6:  2.5067 -  2.3595 [1967/2003]  1775   192   9.8%
  bin  7:  2.3595 -  2.2418 [1974/2007]  1770   204  10.3%
  bin  8:  2.2418 -  2.1445 [1948/1981]  1752   196  10.1%
  bin  9:  2.1445 -  2.0621 [1948/1977]  1757   191   9.8%
  bin 10:  2.0621 -  1.9911 [1602/2010]  1441   161  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_686/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 14
        2.42 -     3.04: 2183
        3.04 -     3.66: 4674
        3.66 -     4.28: 8975
        4.28 -     4.90: 12386
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.112 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 206 " - " O   HOH Z 342 "  2.260 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.302 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28227 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_686/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_686/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.3993 85.95805 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: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2747   r_free= 0.2679   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:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.917538                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7510 0.99   1376  154 0.2652 0.2695      6.2941      6.2653|
|  2:  4.7510 -  3.7912 0.99   1334  145 0.2108 0.2095      6.2702      6.2516|
|  3:  3.7912 -  3.3179 0.99   1300  148 0.2230 0.2208      6.1691      6.2257|
|  4:  3.3179 -  3.0173 0.99   1293  143 0.2512 0.2285      6.1023      5.9633|
|  5:  3.0173 -  2.8025 0.99   1286  139 0.2657 0.2218      5.9475      5.8669|
|  6:  2.8025 -  2.6382 0.99   1278  145 0.2758 0.2628       5.898      5.8296|
|  7:  2.6382 -  2.5067 0.99   1268  141 0.2866 0.2454      5.8761      5.7169|
|  8:  2.5067 -  2.3981 0.98   1276  140 0.2988 0.3311      5.8558      5.9866|
|  9:  2.3981 -  2.3061 0.98   1276  144 0.3062 0.3088      5.8048      5.8314|
| 10:  2.3061 -  2.2268 0.98   1232  133 0.3192 0.3097      5.8314      5.7412|
| 11:  2.2268 -  2.1574 1.00   1274  148 0.3073 0.3020      5.7215       5.781|
| 12:  2.1574 -  2.0959 0.97   1252  129 0.3147 0.3175      5.7195      5.7422|
| 13:  2.0959 -  2.0408 0.98   1241  143 0.3284 0.3255      5.6404      5.5982|
| 14:  2.0408 -  1.9911 0.73    944  107 0.3118 0.3123      5.5515      5.5493|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.7510  1376   154  0.80  25.34   0.87     0.81      40091.38|
|  2:  4.7510 -  3.7912  1334   145  0.87  19.19   0.99     0.92      34824.98|
|  3:  3.7912 -  3.3179  1300   148  0.86  20.17   1.01     0.98      29030.59|
|  4:  3.3179 -  3.0173  1293   143  0.86  21.22   1.00     0.98      23353.71|
|  5:  3.0173 -  2.8025  1286   139  0.82  24.47   1.01     0.97      19319.03|
|  6:  2.8025 -  2.6382  1278   145  0.81  25.83   1.03     0.97      17534.40|
|  7:  2.6382 -  2.5067  1268   141  0.81  26.24   1.02     0.97      16765.61|
|  8:  2.5067 -  2.3981  1276   140  0.78  28.47   1.04     0.97      17319.48|
|  9:  2.3981 -  2.3061  1276   144  0.76  30.48   1.05     0.96      16659.07|
| 10:  2.3061 -  2.2268  1232   133  0.76  30.63   1.05     0.96      16265.81|
| 11:  2.2268 -  2.1574  1274   148  0.75  31.16   1.07     0.99      15271.62|
| 12:  2.1574 -  2.0959  1252   129  0.76  30.88   1.07     1.00      14477.85|
| 13:  2.0959 -  2.0408  1241   143  0.74  32.40   1.05     1.00      13079.89|
| 14:  2.0408 -  1.9911   944   107  0.73  32.82   1.07     0.98      11479.72|
|alpha:            min =        0.81 max =            1.00 mean =         0.96|
|beta:             min =    11479.72 max =        40091.38 mean =     20766.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.80|
|phase err.(work): min =        0.00 max =           89.96 mean =        26.91|
|phase err.(test): min =        0.00 max =           89.83 mean =        26.91|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.041222              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.905   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.467544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.577   (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:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      188 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1995 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1856 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2818 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4603 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4372 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5647 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6739 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.147 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    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: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2747   r_free= 0.2679   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:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.917538                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2581   r_free= 0.2509   ksol= 0.31   Bsol= 45.59   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,0.84,-1.49,0.00,-0.00,-0.00); trace/3= -1.31                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.885612                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.848316              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.015   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261024              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.491   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2581      final r-factor (work) = 0.1600          |
| start r-factor (free) = 0.2509      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5777 = 2.85 * 0.50 * 5.9102 + 1.00 * 0.1606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0078 = 2.85 * 0.50 * 5.5802 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1600      final r-factor (work) = 0.1453          |
| start r-factor (free) = 0.1762      final r-factor (free) = 0.1796          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4626 = 0.26 * 1.00 * 5.5802 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4008 = 0.26 * 1.00 * 5.3360 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.47    73.28   16.80    None  None   None       |
|    all(noH): 2823   0      1.47    73.28   16.80    None  None   None       |
|    Sol.    : 438    0      5.83    70.49   37.82    None  None   None       |
|    Mac.    : 2385   0      1.47    73.28   12.94    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:     1.470 -   8.651:  653   |   5:    37.374 -  44.555:  125        |
|      1:     8.651 -  15.832: 1283   |   6:    44.555 -  51.735:   86        |
|      2:    15.832 -  23.012:  347   |   7:    51.735 -  58.916:   66        |
|      3:    23.012 -  30.193:  137   |   8:    58.916 -  66.097:   22        |
|      4:    30.193 -  37.374:  101   |   9:    66.097 -  73.277:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1453 r_free = 0.1796             target_work(ml) = 5.344         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1448 r_free = 0.1794             target_work(ml) = 5.343         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1448   r_free= 0.1794   ksol= 0.31   Bsol= 45.59   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.27,0.84,-1.49,0.00,-0.00,-0.00); trace/3= -1.31                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.342883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1440   r_free= 0.1784   ksol= 0.33   Bsol= 51.94   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,-1.27,-1.61,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.337227                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.849630              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.573  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.134416              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.875  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1440      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1784      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9968 = 1.85 * 0.50 * 5.3374 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9121 = 1.85 * 0.50 * 5.2528 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7140 = 0.13 * 1.00 * 5.2528 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7025 = 0.13 * 1.00 * 5.1758 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.45    74.26   16.44    None  None   None       |
|    all(noH): 2823   0      2.45    74.26   16.44    None  None   None       |
|    Sol.    : 438    0      5.39    67.86   36.65    None  None   None       |
|    Mac.    : 2385   0      2.45    74.26   12.73    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:     2.450 -   9.631:  898   |   5:    38.356 -  45.537:  118        |
|      1:     9.631 -  16.812: 1121   |   6:    45.537 -  52.719:   86        |
|      2:    16.812 -  23.994:  303   |   7:    52.719 -  59.900:   44        |
|      3:    23.994 -  31.175:  128   |   8:    59.900 -  67.081:   10        |
|      4:    31.175 -  38.356:  112   |   9:    67.081 -  74.262:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1183 r_free = 0.1541             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1540             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1540   ksol= 0.33   Bsol= 51.94   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.13,-1.27,-1.61,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164860                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1538   ksol= 0.33   Bsol= 51.94   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.69,-1.40,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163292                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.618481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.427  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.371033              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.065  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1538      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2419 = 1.62 * 0.50 * 5.1748 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2169 = 1.62 * 0.50 * 5.1415 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9144 = 0.37 * 1.00 * 5.1415 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9102 = 0.37 * 1.00 * 5.1270 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.15    76.66   16.49    None  None   None       |
|    all(noH): 2823   0      1.15    76.66   16.49    None  None   None       |
|    Sol.    : 438    0      5.78    67.68   37.49    None  None   None       |
|    Mac.    : 2385   0      1.15    76.66   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.145 -   8.696:  733   |   5:    38.902 -  46.454:  119        |
|      1:     8.696 -  16.248: 1245   |   6:    46.454 -  54.005:   96        |
|      2:    16.248 -  23.799:  335   |   7:    54.005 -  61.557:   43        |
|      3:    23.799 -  31.351:  126   |   8:    61.557 -  69.108:    9        |
|      4:    31.351 -  38.902:  114   |   9:    69.108 -  76.659:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1532             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1533             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1533   ksol= 0.33   Bsol= 51.94   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.69,-1.40,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131230                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1529   ksol= 0.33   Bsol= 51.94   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.78,-1.27,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133010                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.422683              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.840  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.324382              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.795  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2683 = 2.42 * 0.50 * 5.1283 + 1.00 * 0.0562                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2649 = 2.42 * 0.50 * 5.1181 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.2585 = 5.32 * 1.00 * 5.1181 + 1.00 * 0.0078                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.2439 = 5.32 * 1.00 * 5.1149 + 1.00 * 0.0100                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.80   16.87    None  None   None       |
|    all(noH): 2823   0      0.00    94.80   16.87    None  None   None       |
|    Sol.    : 438    0      5.67    79.56   39.67    None  None   None       |
|    Mac.    : 2385   0      0.00    94.80   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.480:  994   |   5:    47.402 -  56.882:   98        |
|      1:     9.480 -  18.961: 1168   |   6:    56.882 -  66.363:   62        |
|      2:    18.961 -  28.441:  214   |   7:    66.363 -  75.843:   17        |
|      3:    28.441 -  37.922:  139   |   8:    75.843 -  85.323:    4        |
|      4:    37.922 -  47.402:  123   |   9:    85.323 -  94.804:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1068 r_free = 0.1567             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1568             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1568   ksol= 0.33   Bsol= 51.94   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.78,-1.27,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121516                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1567   ksol= 0.32   Bsol= 51.94   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.54,-1.00,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121363                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.740870              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.590  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.965361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.456  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1060          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0766 = 2.74 * 0.50 * 5.1163 + 1.00 * 0.0651                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0805 = 2.74 * 0.50 * 5.1190 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1060      final r-factor (work) = 0.1060          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0705 = 1.97 * 1.00 * 5.1190 + 1.00 * 0.0099                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0725 = 1.97 * 1.00 * 5.1198 + 1.00 * 0.0102                              |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.91   16.68    None  None   None       |
|    all(noH): 2823   0      0.00    96.91   16.68    None  None   None       |
|    Sol.    : 438    0      5.51    80.88   39.57    None  None   None       |
|    Mac.    : 2385   0      0.00    96.91   12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.691: 1099   |   5:    48.457 -  58.149:   98        |
|      1:     9.691 -  19.383: 1082   |   6:    58.149 -  67.840:   57        |
|      2:    19.383 -  29.074:  210   |   7:    67.840 -  77.531:   14        |
|      3:    29.074 -  38.766:  132   |   8:    77.531 -  87.223:    4        |
|      4:    38.766 -  48.457:  123   |   9:    87.223 -  96.914:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1060 r_free = 0.1576             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1060 r_free = 0.1576             target_work(ml) = 5.121         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1576   ksol= 0.32   Bsol= 51.94   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.54,-1.00,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120713                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7510 0.99   1376  154 0.0952 0.1280      5.3558      5.5123|
|  2:  4.7510 -  3.7912 0.99   1334  145 0.0813 0.1068      5.4033      5.5985|
|  3:  3.7912 -  3.3179 0.99   1300  148 0.0980 0.1496      5.4325      5.8608|
|  4:  3.3179 -  3.0173 0.99   1293  143 0.1166 0.1535      5.4388       5.589|
|  5:  3.0173 -  2.8025 0.99   1286  139 0.1241 0.1763      5.2994      5.5417|
|  6:  2.8025 -  2.6382 0.99   1278  145 0.1160 0.1855      5.1997      5.4583|
|  7:  2.6382 -  2.5067 0.99   1268  141 0.1163 0.1634      5.1228      5.3328|
|  8:  2.5067 -  2.3981 0.98   1276  140 0.1090 0.1716       5.052      5.3463|
|  9:  2.3981 -  2.3061 0.98   1276  144 0.1110 0.1813       4.996      5.3329|
| 10:  2.3061 -  2.2268 0.98   1232  133 0.1050 0.1745      4.9559      5.1802|
| 11:  2.2268 -  2.1574 1.00   1274  148 0.1100 0.1777      4.9242      5.2738|
| 12:  2.1574 -  2.0959 0.97   1252  129 0.1047 0.1685      4.8712      5.1843|
| 13:  2.0959 -  2.0408 0.98   1241  143 0.1095 0.1716      4.7879      5.0418|
| 14:  2.0408 -  1.9911 0.73    944  107 0.1016 0.1807      4.6706      4.9801|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.7510  1376   154  0.94   9.13   0.97     0.95       7056.07|
|  2:  4.7510 -  3.7912  1334   145  0.95   7.73   1.01     1.00       8676.26|
|  3:  3.7912 -  3.3179  1300   148  0.94  10.78   1.02     1.02       9914.20|
|  4:  3.3179 -  3.0173  1293   143  0.92  13.47   1.01     0.99      10354.93|
|  5:  3.0173 -  2.8025  1286   139  0.90  15.74   0.99     0.97       8210.15|
|  6:  2.8025 -  2.6382  1278   145  0.90  15.84   0.98     0.95       7088.12|
|  7:  2.6382 -  2.5067  1268   141  0.91  15.08   0.98     0.96       5910.11|
|  8:  2.5067 -  2.3981  1276   140  0.91  14.88   0.99     0.96       5345.28|
|  9:  2.3981 -  2.3061  1276   144  0.91  15.18   0.99     0.95       4784.67|
| 10:  2.3061 -  2.2268  1232   133  0.90  15.38   0.99     0.95       4479.89|
| 11:  2.2268 -  2.1574  1274   148  0.90  16.36   0.99     0.95       4375.67|
| 12:  2.1574 -  2.0959  1252   129  0.92  14.97   0.99     0.97       4008.47|
| 13:  2.0959 -  2.0408  1241   143  0.90  15.98   0.98     0.97       3441.74|
| 14:  2.0408 -  1.9911   944   107  0.91  15.11   0.96     0.93       2681.16|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2681.16 max =        10354.93 mean =      6268.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.89|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1576   ksol= 0.32   Bsol= 51.94   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-1.31,-0.75,-0.00,-0.00,-0.00); trace/3= -1.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1576   ksol= 0.32   Bsol= 51.94   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-1.31,-0.75,-0.00,-0.00,-0.00); trace/3= -1.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120823                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7510 0.99   1376  154 0.0952 0.1282       5.357       5.514|
|  2:  4.7510 -  3.7912 0.99   1334  145 0.0813 0.1067      5.4038      5.5982|
|  3:  3.7912 -  3.3179 0.99   1300  148 0.0980 0.1497      5.4326      5.8612|
|  4:  3.3179 -  3.0173 0.99   1293  143 0.1166 0.1536      5.4387      5.5891|
|  5:  3.0173 -  2.8025 0.99   1286  139 0.1241 0.1763      5.2992      5.5413|
|  6:  2.8025 -  2.6382 0.99   1278  145 0.1160 0.1854      5.1996      5.4579|
|  7:  2.6382 -  2.5067 0.99   1268  141 0.1163 0.1635      5.1228      5.3331|
|  8:  2.5067 -  2.3981 0.98   1276  140 0.1090 0.1715      5.0521      5.3462|
|  9:  2.3981 -  2.3061 0.98   1276  144 0.1110 0.1813      4.9962       5.333|
| 10:  2.3061 -  2.2268 0.98   1232  133 0.1050 0.1746       4.956      5.1806|
| 11:  2.2268 -  2.1574 1.00   1274  148 0.1100 0.1776      4.9242      5.2737|
| 12:  2.1574 -  2.0959 0.97   1252  129 0.1046 0.1685      4.8711      5.1842|
| 13:  2.0959 -  2.0408 0.98   1241  143 0.1095 0.1716      4.7878      5.0418|
| 14:  2.0408 -  1.9911 0.73    944  107 0.1016 0.1807      4.6705      4.9799|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.7510  1376   154  0.94   9.14   0.97     0.95       7076.67|
|  2:  4.7510 -  3.7912  1334   145  0.95   7.74   1.01     1.00       8688.49|
|  3:  3.7912 -  3.3179  1300   148  0.94  10.78   1.03     1.02       9916.35|
|  4:  3.3179 -  3.0173  1293   143  0.92  13.47   1.01     1.00      10353.36|
|  5:  3.0173 -  2.8025  1286   139  0.90  15.74   1.00     0.97       8206.10|
|  6:  2.8025 -  2.6382  1278   145  0.90  15.84   0.99     0.96       7084.40|
|  7:  2.6382 -  2.5067  1268   141  0.91  15.08   0.99     0.97       5908.92|
|  8:  2.5067 -  2.3981  1276   140  0.91  14.88   1.00     0.97       5345.16|
|  9:  2.3981 -  2.3061  1276   144  0.91  15.19   1.00     0.96       4785.80|
| 10:  2.3061 -  2.2268  1232   133  0.90  15.38   1.00     0.96       4479.94|
| 11:  2.2268 -  2.1574  1274   148  0.90  16.36   1.00     0.96       4375.27|
| 12:  2.1574 -  2.0959  1252   129  0.92  14.97   1.00     0.99       4007.39|
| 13:  2.0959 -  2.0408  1241   143  0.90  15.97   1.00     0.98       3440.19|
| 14:  2.0408 -  1.9911   944   107  0.91  15.11   0.98     0.94       2679.74|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2679.74 max =        10353.36 mean =      6270.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.89|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.970)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.92   16.68    None  None   None       |
|    all(noH): 2823   0      0.00    96.92   16.68    None  None   None       |
|    Sol.    : 438    0      5.51    80.88   39.58    None  None   None       |
|    Mac.    : 2385   0      0.00    96.92   12.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.694: 1099   |   5:    48.460 -  58.151:   98        |
|      1:     9.694 -  19.386: 1082   |   6:    58.151 -  67.843:   57        |
|      2:    19.386 -  29.077:  210   |   7:    67.843 -  77.534:   14        |
|      3:    29.077 -  38.769:  132   |   8:    77.534 -  87.226:    4        |
|      4:    38.769 -  48.460:  123   |   9:    87.226 -  96.917:    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)= 293         
Filter by distance & map next to the model:
   mapped sites are within: 0.554 - 4.715
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 293
   mapped sites are within: 0.721 - 4.715

peak=    5.841 closest distance to " NH2 ARG A  56 " =    2.316
peak=    5.377 closest distance to " CB  GLN A 223 " =    1.442
peak=    5.128 closest distance to " CB  ARG A 275 " =    0.925
peak=    5.001 closest distance to " CB  SER A  63 " =    1.168
peak=    4.838 closest distance to " O   HOH Z 126 " =    1.867
peak=    4.821 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.752 closest distance to " O   HOH Z 142 " =    1.604
peak=    4.737 closest distance to " CG  PRO A 213 " =    1.198
peak=    4.729 closest distance to " CA  TYR A  30 " =    0.918
peak=    4.694 closest distance to " C   PRO A 198 " =    1.489
peak=    4.669 closest distance to " NE2 GLN A  11 " =    1.046
peak=    4.503 closest distance to " O   HOH Z 232 " =    2.323
peak=    4.459 closest distance to " O   HOH Z 369 " =    2.139
peak=    4.449 closest distance to " O   HOH Z 298 " =    1.884
peak=    4.443 closest distance to " CB  GLU A 152 " =    1.171
peak=    4.431 closest distance to " O   HOH Z  15 " =    2.147
peak=    4.418 closest distance to " O   HOH Z  78 " =    1.634
peak=    4.411 closest distance to " CB  TYR A 169 " =    0.789
peak=    4.391 closest distance to " CB  ARG A 190 " =    1.703
peak=    4.385 closest distance to " O   HOH Z 427 " =    3.010
peak=    4.343 closest distance to " CB  ARG A  79 " =    1.354
peak=    4.261 closest distance to " O   HOH Z 203 " =    1.795
peak=    4.252 closest distance to " O   HOH Z 261 " =    2.099
peak=    4.237 closest distance to " O   HOH Z 234 " =    3.704
peak=    4.232 closest distance to " O   HOH Z 236 " =    2.080
peak=    4.222 closest distance to " CG  PRO A  90 " =    1.129
peak=    4.203 closest distance to " CB  LEU A 228 " =    1.099
peak=    4.173 closest distance to " CB  ASN A 148 " =    1.440
peak=    4.169 closest distance to " OD1 ASN A  69 " =    2.487
peak=    4.169 closest distance to " O   HOH Z  40 " =    1.846
peak=    4.165 closest distance to " O   HOH Z 250 " =    1.444
peak=    4.131 closest distance to " O   HOH Z 303 " =    2.102
peak=    4.118 closest distance to " O   HOH Z  43 " =    1.944
peak=    4.115 closest distance to " CG  ARG A  66 " =    2.433
peak=    4.113 closest distance to " O   HOH Z 209 " =    2.272
peak=    4.106 closest distance to " CG  PRO A 198 " =    1.247
peak=    4.092 closest distance to " NZ  LYS A 117 " =    3.290
peak=    4.091 closest distance to " O   HOH Z 193 " =    1.759
peak=    4.066 closest distance to " O   HOH Z 403 " =    1.687
peak=    4.065 closest distance to " CB  GLU A 277 " =    3.618
peak=    4.063 closest distance to " ND2 ASN A 187 " =    1.435
peak=    4.049 closest distance to " O   HOH Z 158 " =    3.055
peak=    4.046 closest distance to " O   HOH Z 346 " =    1.711
peak=    4.015 closest distance to " CA  ALA A  21 " =    1.226
peak=    3.981 closest distance to " O   HOH Z 197 " =    2.829
peak=    3.970 closest distance to " CB  GLU A 128 " =    1.129
peak=    3.957 closest distance to " O   SER A  87 " =    2.268
peak=    3.954 closest distance to " CA  ASN A 176 " =    1.211
peak=    3.951 closest distance to " CB  SER A   3 " =    1.292
peak=    3.949 closest distance to " CZ  PHE A 218 " =    1.084
peak=    3.948 closest distance to " OG ASER A 258 " =    3.123
peak=    3.947 closest distance to " CB  VAL A 265 " =    1.269
peak=    3.943 closest distance to " CG1 ILE A  33 " =    1.201
peak=    3.929 closest distance to " CD2 LEU A 297 " =    0.854
peak=    3.916 closest distance to " CG2 ILE A 120 " =    1.062
peak=    3.902 closest distance to " O   HOH Z 272 " =    1.829
peak=    3.892 closest distance to " O   HOH Z 423 " =    1.980
peak=    3.880 closest distance to " O   MET A 105 " =    1.886
peak=    3.879 closest distance to " O   HOH Z 147 " =    1.794
peak=    3.861 closest distance to " O   HOH Z 189 " =    2.283
peak=    3.861 closest distance to " O   HOH Z  61 " =    1.566
peak=    3.859 closest distance to " CG1BVAL A  72 " =    1.681
peak=    3.835 closest distance to " O   HOH Z  19 " =    2.214
peak=    3.832 closest distance to " O   HOH Z 265 " =    2.349
peak=    3.829 closest distance to " O   HOH Z 426 " =    1.577
peak=    3.817 closest distance to " CG  PRO A 243 " =    1.094
peak=    3.814 closest distance to " CA  ARG A 195 " =    1.272
peak=    3.803 closest distance to " O   HOH Z 368 " =    2.044
peak=    3.800 closest distance to " CB  ASP A 140 " =    0.922
peak=    3.791 closest distance to " O   HOH Z 344 " =    3.206
peak=    3.786 closest distance to " O   HOH Z 402 " =    1.433
peak=    3.784 closest distance to " OD2 ASP A 286 " =    2.861
peak=    3.775 closest distance to " O   HOH Z  97 " =    1.925
peak=    3.772 closest distance to " O   HOH Z 128 " =    2.077
peak=    3.768 closest distance to " CB  TRP A 179 " =    1.353
peak=    3.759 closest distance to " CA  ARG A  36 " =    1.093
peak=    3.750 closest distance to " O   HOH Z 180 " =    2.170
peak=    3.734 closest distance to " O   HOH Z 389 " =    1.910
peak=    3.732 closest distance to " CB  TRP A 266 " =    0.977
peak=    3.730 closest distance to " O   HOH Z 132 " =    2.588
peak=    3.729 closest distance to " O   HOH Z 214 " =    2.076
peak=    3.728 closest distance to " CD  ARG A 269 " =    0.941
peak=    3.721 closest distance to " NH2BARG A 145 " =    2.145
peak=    3.718 closest distance to " O   HOH Z 371 " =    3.410
peak=    3.713 closest distance to " O   HOH Z 172 " =    3.888
peak=    3.711 closest distance to " O   HOH Z  59 " =    2.218
peak=    3.706 closest distance to " CB  VAL A 202 " =    1.541
peak=    3.704 closest distance to " O   HOH Z 133 " =    2.539
peak=    3.701 closest distance to " O   HOH Z  21 " =    1.759
peak=    3.687 closest distance to " O   HOH Z  66 " =    2.066
peak=    3.687 closest distance to " CD1 LEU A 300 " =    1.220
peak=    3.659 closest distance to " CA  THR A 221 " =    0.977
peak=    3.653 closest distance to " CE  LYS A  76 " =    0.858
peak=    3.651 closest distance to " O   HOH Z 108 " =    2.693
peak=    3.649 closest distance to " O   HOH Z 291 " =    1.544
peak=    3.647 closest distance to " CA  ASN A 215 " =    1.190
peak=    3.642 closest distance to " O   HOH Z 280 " =    2.942
peak=    3.635 closest distance to " CG2 THR A 221 " =    1.136
peak=    3.616 closest distance to " OG BSER A 164 " =    2.313
peak=    3.615 closest distance to " O   HOH Z 425 " =    1.961
peak=    3.609 closest distance to " CB  TYR A 169 " =    0.903
peak=    3.606 closest distance to " O   HOH Z  63 " =    1.990
peak=    3.606 closest distance to " O   HOH Z 279 " =    2.220
peak=    3.605 closest distance to " CA  ALA A  51 " =    0.881
peak=    3.600 closest distance to " O   HOH Z 359 " =    1.469
peak=    3.590 closest distance to " CD  ARG A 159 " =    0.771
peak=    3.589 closest distance to " CB  ALA A 291 " =    1.392
peak=    3.588 closest distance to " CD  LYS A 166 " =    1.316
peak=    3.579 closest distance to " O   HOH Z 406 " =    1.554
peak=    3.578 closest distance to " O   HOH Z 411 " =    3.853
peak=    3.578 closest distance to " O   HOH Z 193 " =    1.643
peak=    3.576 closest distance to " CD BLYS A 290 " =    1.040
peak=    3.574 closest distance to " CA  ASP A 140 " =    1.152
peak=    3.565 closest distance to " CD1 ILE A 106 " =    0.861
peak=    3.562 closest distance to " OE1 GLU A   2 " =    2.241
peak=    3.554 closest distance to " CD2 TRP A 179 " =    1.383
peak=    3.552 closest distance to " CG2 VAL A 257 " =    0.858
peak=    3.541 closest distance to " O   HOH Z 368 " =    3.686
peak=    3.541 closest distance to " NH2 ARG A 156 " =    1.150
peak=    3.535 closest distance to " O   HOH Z 173 " =    2.038
peak=    3.535 closest distance to " O   HOH Z  54 " =    1.711
peak=    3.532 closest distance to " ND1 HIS A  81 " =    1.622
peak=    3.530 closest distance to " O   HOH Z 126 " =    1.591
peak=    3.518 closest distance to " ND2 ASN A 110 " =    1.647
peak=    3.513 closest distance to " NH2AARG A 275 " =    3.622
peak=    3.513 closest distance to " CB  ASN A  39 " =    0.849
peak=    3.512 closest distance to " CA  ALA A 291 " =    0.844
peak=    3.510 closest distance to " CD  LYS A 119 " =    1.275
peak=    3.510 closest distance to " CB  SER A 212 " =    1.050
peak=    3.507 closest distance to " OG1 THR A 294 " =    2.374
peak=    3.505 closest distance to " O   HOH Z  44 " =    1.790
peak=    3.502 closest distance to " O   HOH Z 245 " =    1.319
peak=    3.499 closest distance to " NE2 GLN A  77 " =    3.323
peak=    3.497 closest distance to " CA  LYS A 117 " =    1.233
peak=    3.488 closest distance to " O   HOH Z 183 " =    1.441
peak=    3.484 closest distance to " CB  ARG A 139 " =    0.887
peak=    3.482 closest distance to " CB  GLN A  88 " =    1.210
peak=    3.481 closest distance to " O   HOH Z 327 " =    1.604
peak=    3.479 closest distance to " CA  MET A  40 " =    1.087
peak=    3.478 closest distance to " O   HOH Z 135 " =    1.699
peak=    3.473 closest distance to " O   HOH Z  97 " =    2.546
peak=    3.467 closest distance to " O   HOH Z 258 " =    2.184
peak=    3.467 closest distance to " CB  ASN A 215 " =    1.161
peak=    3.465 closest distance to " CE1 TYR A 186 " =    1.266
peak=    3.464 closest distance to " O   HOH Z 391 " =    2.971
peak=    3.461 closest distance to " O   TRP A 274 " =    1.930
peak=    3.460 closest distance to " O   HOH Z  66 " =    2.100
peak=    3.458 closest distance to " O   HOH Z  68 " =    1.667
peak=    3.454 closest distance to " CG  GLN A  58 " =    2.758
peak=    3.448 closest distance to " O   ALA A 165 " =    1.485
peak=    3.448 closest distance to " N   ARG A 156 " =    1.364
peak=    3.445 closest distance to " NZ  LYS A 166 " =    3.049
peak=    3.445 closest distance to " O   HOH Z 299 " =    4.471
peak=    3.441 closest distance to " O   HOH Z 305 " =    3.651
peak=    3.440 closest distance to " CB  SER A  26 " =    1.674
peak=    3.438 closest distance to " O  BHOH Z 338 " =    2.278
peak=    3.421 closest distance to " CD1 LEU A  96 " =    0.721
peak=    3.420 closest distance to " CG2 VAL A 197 " =    1.086
peak=    3.417 closest distance to " O   HOH Z 417 " =    2.914
peak=    3.413 closest distance to " CA  MET A 105 " =    1.027
peak=    3.413 closest distance to " O   HOH Z 185 " =    1.748
peak=    3.408 closest distance to " O   HOH Z   1 " =    2.081
peak=    3.402 closest distance to " CA  ALA A 160 " =    0.868
peak=    3.394 closest distance to " NH1AARG A 145 " =    1.208
peak=    3.387 closest distance to " CA  ALA A 248 " =    1.230
peak=    3.387 closest distance to " O   HOH Z 393 " =    3.281
peak=    3.382 closest distance to " O   HOH Z 407 " =    2.693
peak=    3.381 closest distance to " O   HOH Z 345 " =    3.177
peak=    3.381 closest distance to " O   HOH Z 193 " =    2.141
peak=    3.372 closest distance to " CB  SER A 141 " =    1.005
peak=    3.368 closest distance to " CB  ILE A 120 " =    1.261
peak=    3.367 closest distance to " CG2BVAL A  41 " =    0.810
peak=    3.361 closest distance to " CA  ALA A  84 " =    1.301
peak=    3.357 closest distance to " O   HOH Z 403 " =    1.339
peak=    3.351 closest distance to " O   HOH Z  61 " =    1.511
peak=    3.350 closest distance to " O   HOH Z 421 " =    1.725
peak=    3.343 closest distance to " O   HOH Z  88 " =    3.254
peak=    3.338 closest distance to " O   HOH Z 357 " =    1.979
peak=    3.336 closest distance to " CB  MET A  47 " =    1.020
peak=    3.336 closest distance to " OG  SER A  22 " =    2.662
peak=    3.334 closest distance to " N   ASN A 127 " =    1.243
peak=    3.334 closest distance to " CG2 ILE A  20 " =    1.394
peak=    3.330 closest distance to " O   HOH Z 227 " =    1.650
peak=    3.329 closest distance to " O   HOH Z  35 " =    2.567
peak=    3.329 closest distance to " O   HOH Z 383 " =    1.925
peak=    3.311 closest distance to " O   HOH Z 148 " =    3.258
peak=    3.305 closest distance to " O   HOH Z  10 " =    1.812
peak=    3.303 closest distance to " CB  ALA A  34 " =    1.012
peak=    3.296 closest distance to " O   HOH Z 234 " =    1.815
peak=    3.296 closest distance to " O   HOH Z 437 " =    1.346
peak=    3.294 closest distance to " CD  LYS A  76 " =    2.021
peak=    3.291 closest distance to " CB  GLN A  89 " =    1.271
peak=    3.289 closest distance to " O   HOH Z 281 " =    4.715
peak=    3.289 closest distance to " CB  THR A  31 " =    1.786
peak=    3.287 closest distance to " O   HOH Z 199 " =    1.513
peak=    3.287 closest distance to " CA  THR A 264 " =    0.918
peak=    3.284 closest distance to " N   ASN A  39 " =    1.332
peak=    3.283 closest distance to " O   THR A 251 " =    1.149
peak=    3.280 closest distance to " CB  SER A  62 " =    0.781
peak=    3.279 closest distance to " O   HOH Z 365 " =    2.876
peak=    3.272 closest distance to " CB  GLU A  46 " =    1.012
peak=    3.268 closest distance to " CZ2 TRP A 179 " =    1.633
peak=    3.268 closest distance to " CB  PHE A  16 " =    1.018
peak=    3.268 closest distance to " O   HOH Z 128 " =    2.358
peak=    3.268 closest distance to " CB  ARG A  79 " =    0.828
peak=    3.267 closest distance to " O   HOH Z 435 " =    1.865
peak=    3.266 closest distance to " O   HOH Z 387 " =    3.040
peak=    3.265 closest distance to " CD2 LEU A 255 " =    1.495
peak=    3.265 closest distance to " CD2 HIS A  81 " =    1.076
peak=    3.262 closest distance to " O   HOH Z 171 " =    2.004
peak=    3.259 closest distance to " CD1AILE A 234 " =    0.952
peak=    3.257 closest distance to " O   HOH Z 175 " =    2.112
peak=    3.257 closest distance to " C   TYR A 214 " =    1.435
peak=    3.252 closest distance to " CG  MET A 185 " =    1.160
peak=    3.248 closest distance to " O   HOH Z 427 " =    3.155
peak=    3.244 closest distance to " O   HOH Z  80 " =    1.573
peak=    3.242 closest distance to " CA  ALA A 295 " =    1.057
peak=    3.239 closest distance to " CB  GLN A 103 " =    0.849
peak=    3.237 closest distance to " CA  ASN A  74 " =    1.284
peak=    3.234 closest distance to " CG1 VAL A 153 " =    0.930
peak=    3.232 closest distance to " O   HOH Z 273 " =    2.833
peak=    3.230 closest distance to " O   HOH Z 417 " =    2.020
peak=    3.229 closest distance to " CA  ASP A 162 " =    1.138
peak=    3.223 closest distance to " CA  ALA A 154 " =    0.926
peak=    3.222 closest distance to " O   HOH Z 345 " =    1.583
peak=    3.222 closest distance to " CG  MET A 185 " =    1.071
peak=    3.220 closest distance to " CB  ASN A 142 " =    1.144
peak=    3.218 closest distance to " O   HOH Z 163 " =    1.902
peak=    3.217 closest distance to " CA  ASN A 217 " =    1.205
peak=    3.216 closest distance to " O   HOH Z 422 " =    2.662
peak=    3.215 closest distance to " CG  LEU A 167 " =    1.191
peak=    3.214 closest distance to " CB  TYR A 116 " =    0.816
peak=    3.212 closest distance to " CB  MET A 113 " =    1.811
peak=    3.211 closest distance to " O   THR A 220 " =    1.272
peak=    3.209 closest distance to " O   HOH Z 325 " =    2.480
peak=    3.206 closest distance to " O   HOH Z 392 " =    2.008
peak=    3.206 closest distance to " CG  LYS A  76 " =    0.984
peak=    3.204 closest distance to " O   HOH Z 374 " =    2.682
peak=    3.204 closest distance to " O   HOH Z 261 " =    1.520
peak=    3.198 closest distance to " O   HOH Z 250 " =    1.538
peak=    3.197 closest distance to " O   HOH Z 353 " =    2.756
peak=    3.194 closest distance to " O   HOH Z 295 " =    1.473
peak=    3.194 closest distance to " O   ALA A 158 " =    1.245
peak=    3.194 closest distance to " O   HOH Z  49 " =    2.896
peak=    3.191 closest distance to " CA  ALA A 158 " =    1.201
peak=    3.187 closest distance to " O   HOH Z 248 " =    1.659
peak=    3.186 closest distance to " CG2 VAL A 202 " =    1.174
peak=    3.186 closest distance to " CG  GLN A  77 " =    2.153
peak=    3.185 closest distance to " O   HOH Z 411 " =    1.764
peak=    3.185 closest distance to " CA  MET A 188 " =    0.967
peak=    3.184 closest distance to " CG1 ILE A 151 " =    1.004
peak=    3.180 closest distance to " CD  GLU A 152 " =    0.794
peak=    3.176 closest distance to " CB  MET A  40 " =    0.843
peak=    3.175 closest distance to " CA  TYR A 116 " =    1.375
peak=    3.173 closest distance to " N   VAL A 126 " =    1.399
peak=    3.171 closest distance to " O   HOH Z 271 " =    2.380
peak=    3.168 closest distance to " CB  ALA A   9 " =    1.573
peak=    3.167 closest distance to " O   HOH Z  85 " =    2.186
peak=    3.163 closest distance to " O   ASP A 124 " =    1.151
peak=    3.162 closest distance to " O   HOH Z 213 " =    1.696
peak=    3.158 closest distance to " O   HOH Z 329 " =    3.805
peak=    3.155 closest distance to " O   HOH Z 261 " =    2.176
peak=    3.150 closest distance to " CE  LYS A  48 " =    1.031
peak=    3.150 closest distance to " CB  SER A 273 " =    0.843
peak=    3.142 closest distance to " CG  GLN A  11 " =    1.549
peak=    3.142 closest distance to " O   HOH Z 163 " =    1.733
peak=    3.141 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.140 closest distance to " CB  SER A 216 " =    0.842
peak=    3.137 closest distance to " NE2 GLN A  58 " =    2.927
peak=    3.135 closest distance to " O   HOH Z  88 " =    2.727
peak=    3.131 closest distance to " O   HOH Z 163 " =    1.466
peak=    3.128 closest distance to " NZ  LYS A  76 " =    1.507
peak=    3.127 closest distance to " CB  ALA A 248 " =    0.925
peak=    3.122 closest distance to " O   HOH Z  20 " =    1.503
peak=    3.122 closest distance to " CG BARG A 275 " =    1.327
peak=    3.121 closest distance to " CB  ASN A 285 " =    0.940
peak=    3.121 closest distance to " CB  ASN A 110 " =    1.144
peak=    3.104 closest distance to " CB  GLN A 278 " =    0.884
peak=    3.101 closest distance to " CA  ALA A 233 " =    1.453
peak=    3.097 closest distance to " O   HOH Z 371 " =    3.488
peak=    3.097 closest distance to " O   HOH Z 327 " =    2.259
peak=    3.092 closest distance to " O   HOH Z 430 " =    1.551
peak=    3.082 closest distance to " OG  SER A  62 " =    2.858
peak=    3.077 closest distance to " O   HOH Z 336 " =    1.711
peak=    3.050 closest distance to " CA  GLY A  80 " =    0.960
peak=    3.048 closest distance to " O   HOH Z 124 " =    2.172
peak=    3.046 closest distance to " N   SER A 135 " =    1.357
peak=    3.020 closest distance to " O   HOH Z  49 " =    2.225

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.850 - 5.760
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 201
   mapped sites are within: 0.850 - 5.760

peak=   -4.874 closest distance to " O   HOH Z 266 " =    4.804
peak=   -4.477 closest distance to " CD  ARG A 156 " =    2.031
peak=   -4.416 closest distance to " C   HIS A 108 " =    1.104
peak=   -4.410 closest distance to " CB  ALA A 161 " =    2.584
peak=   -4.360 closest distance to " CB  PRO A 243 " =    2.649
peak=   -4.328 closest distance to " O   VAL A  67 " =    2.752
peak=   -4.283 closest distance to " SG  CYS A 254 " =    3.399
peak=   -4.238 closest distance to " CG  GLN A 223 " =    2.014
peak=   -4.225 closest distance to " O   HOH Z 377 " =    2.113
peak=   -4.225 closest distance to " O   HOH Z 198 " =    2.141
peak=   -4.223 closest distance to " O   HOH Z 196 " =    2.019
peak=   -4.166 closest distance to " CD  GLN A  58 " =    1.080
peak=   -4.059 closest distance to " O   HOH Z 372 " =    2.363
peak=   -4.005 closest distance to " O   HOH Z  10 " =    1.574
peak=   -4.000 closest distance to " N   ALA A  43 " =    2.640
peak=   -3.997 closest distance to " O   HOH Z 126 " =    1.950
peak=   -3.991 closest distance to " O   HOH Z 231 " =    2.333
peak=   -3.945 closest distance to " OXT GLY A 302 " =    2.837
peak=   -3.904 closest distance to " O   HOH Z  13 " =    1.669
peak=   -3.883 closest distance to " O   HOH Z  52 " =    1.361
peak=   -3.864 closest distance to " O   HOH Z 114 " =    3.242
peak=   -3.857 closest distance to " OG BSER A 134 " =    1.297
peak=   -3.851 closest distance to " CA  ASP A 298 " =    1.041
peak=   -3.849 closest distance to " OG  SER A  97 " =    2.166
peak=   -3.842 closest distance to " O   PRO A 163 " =    2.156
peak=   -3.828 closest distance to " ND2 ASN A  45 " =    1.694
peak=   -3.811 closest distance to " O   HOH Z  73 " =    2.315
peak=   -3.798 closest distance to " CG2 ILE A 263 " =    2.291
peak=   -3.796 closest distance to " ND2 ASN A  45 " =    1.051
peak=   -3.788 closest distance to " CE2 TYR A  30 " =    2.687
peak=   -3.780 closest distance to " CD1 LEU A 101 " =    2.401
peak=   -3.778 closest distance to " O   PRO A 198 " =    1.312
peak=   -3.777 closest distance to " O   HOH Z 290 " =    1.176
peak=   -3.758 closest distance to " O   HOH Z 292 " =    4.572
peak=   -3.746 closest distance to " O   HOH Z 353 " =    2.195
peak=   -3.745 closest distance to " CB  ASP A 132 " =    2.353
peak=   -3.723 closest distance to " CZ3 TRP A 179 " =    1.186
peak=   -3.721 closest distance to " CG1 VAL A 112 " =    2.800
peak=   -3.708 closest distance to " CD  ARG A 139 " =    1.565
peak=   -3.702 closest distance to " O   HOH Z 166 " =    1.800
peak=   -3.689 closest distance to " CD1 PHE A  59 " =    1.869
peak=   -3.678 closest distance to " CB  ALA A 291 " =    2.257
peak=   -3.677 closest distance to " NE2 GLN A  88 " =    1.847
peak=   -3.643 closest distance to " O   HOH Z 165 " =    1.961
peak=   -3.633 closest distance to " O   HOH Z 311 " =    3.654
peak=   -3.633 closest distance to " NH2AARG A 275 " =    5.297
peak=   -3.625 closest distance to " CD1 LEU A 228 " =    2.231
peak=   -3.623 closest distance to " O   HOH Z 389 " =    1.767
peak=   -3.623 closest distance to " CB  ASN A  39 " =    2.350
peak=   -3.622 closest distance to " CA  VAL A  67 " =    2.766
peak=   -3.621 closest distance to " OG  SER A  62 " =    1.736
peak=   -3.607 closest distance to " O   HOH Z 185 " =    2.343
peak=   -3.604 closest distance to " CD1 LEU A  25 " =    2.474
peak=   -3.599 closest distance to " CG  ASP A 231 " =    0.850
peak=   -3.584 closest distance to " CB  ALA A 248 " =    2.304
peak=   -3.582 closest distance to " CB  ALA A 291 " =    2.349
peak=   -3.574 closest distance to " C   LEU A 143 " =    1.068
peak=   -3.566 closest distance to " N   GLN A  58 " =    1.583
peak=   -3.553 closest distance to " O   HOH Z 407 " =    3.017
peak=   -3.550 closest distance to " CG1 VAL A 250 " =    2.636
peak=   -3.547 closest distance to " CG  GLU A 277 " =    1.137
peak=   -3.541 closest distance to " O   HOH Z 211 " =    1.657
peak=   -3.535 closest distance to " O   HOH Z 166 " =    1.557
peak=   -3.534 closest distance to " OG BSER A 134 " =    1.819
peak=   -3.534 closest distance to " CG1 VAL A 112 " =    2.855
peak=   -3.533 closest distance to " SG ACYS A 201 " =    1.968
peak=   -3.532 closest distance to " CE  MET A 105 " =    2.277
peak=   -3.526 closest distance to " O   HOH Z 394 " =    1.541
peak=   -3.523 closest distance to " CB  PHE A 208 " =    2.267
peak=   -3.518 closest distance to " O   HOH Z  43 " =    1.585
peak=   -3.515 closest distance to " CD  ARG A 195 " =    5.163
peak=   -3.513 closest distance to " CB  TYR A  15 " =    2.197
peak=   -3.511 closest distance to " CG  PHE A 283 " =    2.744
peak=   -3.511 closest distance to " CA  GLY A 203 " =    2.403
peak=   -3.510 closest distance to " CE3 TRP A 150 " =    2.108
peak=   -3.500 closest distance to " CZ  TYR A 169 " =    1.810
peak=   -3.500 closest distance to " CG2 VAL A 189 " =    2.171
peak=   -3.499 closest distance to " CE2 PHE A 218 " =    2.415
peak=   -3.495 closest distance to " CD2 LEU A 300 " =    2.839
peak=   -3.488 closest distance to " CB  ALA A  43 " =    2.587
peak=   -3.480 closest distance to " O   HOH Z   6 " =    2.163
peak=   -3.470 closest distance to " CG  GLU A   2 " =    1.833
peak=   -3.466 closest distance to " O   HOH Z 252 " =    3.838
peak=   -3.464 closest distance to " O   HOH Z 198 " =    1.437
peak=   -3.463 closest distance to " O   HOH Z 234 " =    4.119
peak=   -3.454 closest distance to " CZ  PHE A  59 " =    1.681
peak=   -3.451 closest distance to " C   ALA A 158 " =    1.251
peak=   -3.449 closest distance to " N   ALA A 226 " =    2.061
peak=   -3.440 closest distance to " CG  ARG A 269 " =    2.410
peak=   -3.432 closest distance to " CB  PHE A 192 " =    2.021
peak=   -3.431 closest distance to " O   SER A 210 " =    1.934
peak=   -3.430 closest distance to " O   PHE A 218 " =    1.612
peak=   -3.408 closest distance to " O   HOH Z 351 " =    1.518
peak=   -3.402 closest distance to " CD1 ILE A 239 " =    2.395
peak=   -3.398 closest distance to " CB  ASP A 286 " =    1.968
peak=   -3.392 closest distance to " CB  ALA A 248 " =    2.058
peak=   -3.389 closest distance to " NH2 ARG A 159 " =    2.355
peak=   -3.389 closest distance to " NH1 ARG A 195 " =    2.609
peak=   -3.380 closest distance to " O   HOH Z 435 " =    2.699
peak=   -3.379 closest distance to " OD1 ASN A 148 " =    1.575
peak=   -3.375 closest distance to " O   HOH Z   6 " =    1.563
peak=   -3.374 closest distance to " CD  LYS A 289 " =    2.461
peak=   -3.372 closest distance to " CG1 VAL A 112 " =    2.548
peak=   -3.367 closest distance to " ND2 ASN A 249 " =    2.366
peak=   -3.366 closest distance to " O   HOH Z 377 " =    1.759
peak=   -3.366 closest distance to " O   HOH Z 393 " =    1.419
peak=   -3.360 closest distance to " O   VAL A 189 " =    2.613
peak=   -3.359 closest distance to " O   MET A  40 " =    2.727
peak=   -3.353 closest distance to " O   HOH Z  11 " =    1.766
peak=   -3.352 closest distance to " CD2 PHE A  61 " =    2.544
peak=   -3.346 closest distance to " O   SER A  95 " =    1.639
peak=   -3.339 closest distance to " OD2 ASP A 171 " =    1.774
peak=   -3.330 closest distance to " OD1 ASN A 187 " =    1.685
peak=   -3.318 closest distance to " O   HOH Z 193 " =    1.834
peak=   -3.317 closest distance to " O   HOH Z  93 " =    2.011
peak=   -3.310 closest distance to " OD2 ASP A 191 " =    1.521
peak=   -3.309 closest distance to " O   HOH Z  38 " =    1.533
peak=   -3.309 closest distance to " O   HOH Z 313 " =    2.024
peak=   -3.302 closest distance to " NH2 ARG A  79 " =    1.588
peak=   -3.298 closest distance to " OG BSER A 210 " =    2.244
peak=   -3.297 closest distance to " CG  PRO A 163 " =    2.555
peak=   -3.296 closest distance to " O   HOH Z 123 " =    2.271
peak=   -3.290 closest distance to " NH2BARG A 275 " =    2.259
peak=   -3.288 closest distance to " CD2 LEU A 237 " =    2.697
peak=   -3.286 closest distance to " O   HOH Z 322 " =    1.682
peak=   -3.280 closest distance to " N   SER A 276 " =    1.395
peak=   -3.280 closest distance to " N   ALA A 248 " =    1.652
peak=   -3.278 closest distance to " NH2 ARG A  79 " =    2.029
peak=   -3.277 closest distance to " O   ALA A  10 " =    1.710
peak=   -3.274 closest distance to " OG ASER A 134 " =    1.221
peak=   -3.272 closest distance to " OE1 GLN A  88 " =    1.162
peak=   -3.270 closest distance to " C   ASN A 285 " =    2.448
peak=   -3.270 closest distance to " CA  PRO A 243 " =    2.400
peak=   -3.263 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.257 closest distance to " OD1 ASP A 191 " =    1.725
peak=   -3.252 closest distance to " O   HOH Z 357 " =    2.030
peak=   -3.249 closest distance to " O   SER A 135 " =    1.551
peak=   -3.247 closest distance to " O   HOH Z 177 " =    1.691
peak=   -3.245 closest distance to " CD2 PHE A 225 " =    1.204
peak=   -3.241 closest distance to " O   HOH Z 396 " =    1.771
peak=   -3.236 closest distance to " C   SER A 206 " =    1.543
peak=   -3.232 closest distance to " O   HOH Z 102 " =    1.534
peak=   -3.230 closest distance to " O   HOH Z  41 " =    2.411
peak=   -3.229 closest distance to " CG1AVAL A  41 " =    2.872
peak=   -3.227 closest distance to " O   HOH Z 243 " =    2.099
peak=   -3.226 closest distance to " O   GLY A  80 " =    2.512
peak=   -3.220 closest distance to " NH2 ARG A  66 " =    5.538
peak=   -3.219 closest distance to " OD2 ASP A 171 " =    2.348
peak=   -3.218 closest distance to " O   HOH Z  90 " =    2.874
peak=   -3.216 closest distance to " CB  PHE A  16 " =    2.602
peak=   -3.213 closest distance to " O   PRO A 198 " =    1.966
peak=   -3.213 closest distance to " N   THR A  52 " =    1.688
peak=   -3.212 closest distance to " NH2 ARG A  66 " =    2.009
peak=   -3.211 closest distance to " O   HOH Z  37 " =    1.879
peak=   -3.210 closest distance to " CZ2 TRP A 274 " =    1.052
peak=   -3.209 closest distance to " O   HOH Z 414 " =    1.628
peak=   -3.202 closest distance to " CG  ASN A 301 " =    2.013
peak=   -3.202 closest distance to " O   HOH Z  60 " =    2.258
peak=   -3.195 closest distance to " O   HOH Z 357 " =    2.141
peak=   -3.194 closest distance to " O   HOH Z 385 " =    1.988
peak=   -3.193 closest distance to " CB  GLN A  11 " =    1.753
peak=   -3.192 closest distance to " O   HOH Z 128 " =    2.551
peak=   -3.188 closest distance to " CD1 LEU A 297 " =    2.467
peak=   -3.188 closest distance to " CB  ALA A  10 " =    2.242
peak=   -3.186 closest distance to " NE2 GLN A  58 " =    1.198
peak=   -3.180 closest distance to " CA  GLY A 241 " =    3.085
peak=   -3.179 closest distance to " CG  TRP A 266 " =    1.864
peak=   -3.165 closest distance to " O   GLY A 196 " =    1.101
peak=   -3.162 closest distance to " N   MET A 105 " =    2.581
peak=   -3.162 closest distance to " CZ3 TRP A 274 " =    2.472
peak=   -3.156 closest distance to " O   GLY A  80 " =    2.593
peak=   -3.155 closest distance to " O   HOH Z 171 " =    1.954
peak=   -3.149 closest distance to " CG1 VAL A 125 " =    2.041
peak=   -3.149 closest distance to " O   HOH Z  44 " =    2.108
peak=   -3.147 closest distance to " CA  GLY A 133 " =    2.300
peak=   -3.146 closest distance to " OG  SER A  26 " =    1.369
peak=   -3.145 closest distance to " CG2BVAL A  41 " =    1.816
peak=   -3.138 closest distance to " O   ALA A 160 " =    1.495
peak=   -3.137 closest distance to " CE  MET A  93 " =    1.261
peak=   -3.136 closest distance to " O   HOH Z 139 " =    2.932
peak=   -3.135 closest distance to " O   ALA A 161 " =    1.631
peak=   -3.133 closest distance to " O   GLU A 152 " =    1.390
peak=   -3.132 closest distance to " CG1 VAL A 125 " =    2.327
peak=   -3.130 closest distance to " CD2 TYR A 293 " =    2.076
peak=   -3.128 closest distance to " CB  TRP A  85 " =    2.471
peak=   -3.127 closest distance to " C   MET A 188 " =    1.555
peak=   -3.103 closest distance to " O   HOH Z 283 " =    5.760
peak=   -3.100 closest distance to " N   TYR A  68 " =    3.147
peak=   -3.099 closest distance to " O   HOH Z 298 " =    2.603
peak=   -3.099 closest distance to " CD1 LEU A  83 " =    2.459
peak=   -3.090 closest distance to " CD2 LEU A 237 " =    2.188
peak=   -3.087 closest distance to " ND2 ASN A  60 " =    1.428
peak=   -3.080 closest distance to " O   ALA A 292 " =    1.972
peak=   -3.080 closest distance to " O   HOH Z  89 " =    3.041
peak=   -3.076 closest distance to " O   HOH Z  77 " =    2.089
peak=   -3.058 closest distance to " O   PRO A 198 " =    1.334
peak=   -3.058 closest distance to " CB  CYS A 201 " =    2.640
peak=   -3.051 closest distance to " CG2 THR A 221 " =    2.271
peak=   -3.048 closest distance to " O   HOH Z 350 " =    1.988
peak=   -3.028 closest distance to " O   HOH Z  97 " =    1.692

================= 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    :  0.2747 0.2679   5.917538e+00   5.893026e+00
   1_bss:  0.2581 0.2509   5.885612e+00   5.850752e+00
   1_xyz:  0.1600 0.1762   5.405029e+00   5.502483e+00
   1_adp:  0.1453 0.1796   5.344258e+00   5.522305e+00
   1_occ:  0.1448 0.1794   5.342883e+00   5.521257e+00
   2_bss:  0.1440 0.1784   5.337227e+00   5.514077e+00
   2_xyz:  0.1201 0.1576   5.184012e+00   5.393132e+00
   2_adp:  0.1183 0.1541   5.165621e+00   5.372742e+00
   2_occ:  0.1181 0.1540   5.164860e+00   5.372322e+00
   3_bss:  0.1179 0.1538   5.163292e+00   5.371293e+00
   3_xyz:  0.1126 0.1526   5.135331e+00   5.361642e+00
   3_adp:  0.1111 0.1532   5.131188e+00   5.366167e+00
   3_occ:  0.1110 0.1533   5.131230e+00   5.366506e+00
   4_bss:  0.1114 0.1529   5.133010e+00   5.366732e+00
   4_xyz:  0.1078 0.1548   5.120558e+00   5.371932e+00
   4_adp:  0.1068 0.1567   5.121382e+00   5.379286e+00
   4_occ:  0.1068 0.1568   5.121516e+00   5.379693e+00
   5_bss:  0.1066 0.1567   5.121363e+00   5.379591e+00
   5_xyz:  0.1060 0.1577   5.121432e+00   5.385021e+00
   5_adp:  0.1060 0.1576   5.120584e+00   5.384850e+00
   5_occ:  0.1060 0.1576   5.120713e+00   5.385158e+00
   5_bss:  0.1059 0.1576   5.120823e+00   5.385255e+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:  0.314  45.592  -3.270   0.843  -1.490   0.000  -0.000  -0.000
   1_xyz:  0.314  45.592  -3.270   0.843  -1.490   0.000  -0.000  -0.000
   1_adp:  0.314  45.592  -3.270   0.843  -1.490   0.000  -0.000  -0.000
   1_occ:  0.314  45.592  -3.270   0.843  -1.490   0.000  -0.000  -0.000
   2_bss:  0.326  51.939  -3.129  -1.269  -1.612  -0.000  -0.000  -0.000
   2_xyz:  0.326  51.939  -3.129  -1.269  -1.612  -0.000  -0.000  -0.000
   2_adp:  0.326  51.939  -3.129  -1.269  -1.612  -0.000  -0.000  -0.000
   2_occ:  0.326  51.939  -3.129  -1.269  -1.612  -0.000  -0.000  -0.000
   3_bss:  0.326  51.939  -2.742  -1.690  -1.404  -0.000  -0.000  -0.000
   3_xyz:  0.326  51.939  -2.742  -1.690  -1.404  -0.000  -0.000  -0.000
   3_adp:  0.326  51.939  -2.742  -1.690  -1.404  -0.000  -0.000  -0.000
   3_occ:  0.326  51.939  -2.742  -1.690  -1.404  -0.000  -0.000  -0.000
   4_bss:  0.326  51.939  -2.550  -1.778  -1.270  -0.000  -0.000  -0.000
   4_xyz:  0.326  51.939  -2.550  -1.778  -1.270  -0.000  -0.000  -0.000
   4_adp:  0.326  51.939  -2.550  -1.778  -1.270  -0.000  -0.000  -0.000
   4_occ:  0.326  51.939  -2.550  -1.778  -1.270  -0.000  -0.000  -0.000
   5_bss:  0.320  51.939  -2.226  -1.540  -1.002  -0.000  -0.000  -0.000
   5_xyz:  0.320  51.939  -2.226  -1.540  -1.002  -0.000  -0.000  -0.000
   5_adp:  0.320  51.939  -2.226  -1.540  -1.002  -0.000  -0.000  -0.000
   5_occ:  0.320  51.939  -2.226  -1.540  -1.002  -0.000  -0.000  -0.000
   5_bss:  0.320  51.942  -1.958  -1.312  -0.747  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  26.907 0.7954  0.9603    20765.889
   1_bss:  25.584 0.8075  0.9277    17537.241
   1_xyz:  16.355 0.8961  0.9910     7997.913
   1_adp:  16.914 0.8906  0.9830     8254.314
   1_occ:  16.902 0.8906  0.9829     8235.509
   2_bss:  16.713 0.8924  0.9624     8127.535
   2_xyz:  14.204 0.9132  0.9732     6333.849
   2_adp:  13.729 0.9172  0.9709     6133.494
   2_occ:  13.723 0.9173  0.9709     6123.060
   3_bss:  13.697 0.9175  0.9739     6115.596
   3_xyz:  13.428 0.9198  0.9752     6002.429
   3_adp:  13.505 0.9193  0.9694     6052.355
   3_occ:  13.512 0.9192  0.9692     6054.607
   4_bss:  13.518 0.9192  0.9717     6064.237
   4_xyz:  13.630 0.9181  0.9715     6129.571
   4_adp:  13.793 0.9169  0.9639     6194.942
   4_occ:  13.798 0.9168  0.9638     6200.409
   5_bss:  13.798 0.9168  0.9735     6198.538
   5_xyz:  13.856 0.9165  0.9732     6276.701
   5_adp:  13.852 0.9165  0.9656     6264.990
   5_occ:  13.855 0.9165  0.9656     6268.006
   5_bss:  13.858 0.9164  0.9745     6269.719
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6060e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6060e-01
   1_xyz:   1.045  0.007  0.068 15.153  0.004  4.114   6.0690e-02
   1_adp:   1.045  0.007  0.068 15.153  0.004  4.114   6.0690e-02
   1_occ:   1.045  0.007  0.068 15.153  0.004  4.114   6.0690e-02
   2_bss:   1.045  0.007  0.068 15.153  0.004  4.114   6.0690e-02
   2_xyz:   0.946  0.006  0.071 14.802  0.004  4.120   5.4236e-02
   2_adp:   0.946  0.006  0.071 14.802  0.004  4.120   5.4236e-02
   2_occ:   0.946  0.006  0.071 14.802  0.004  4.120   5.4236e-02
   3_bss:   0.946  0.006  0.071 14.802  0.004  4.120   5.4236e-02
   3_xyz:   0.958  0.007  0.073 14.870  0.004  4.123   5.6156e-02
   3_adp:   0.958  0.007  0.073 14.870  0.004  4.123   5.6156e-02
   3_occ:   0.958  0.007  0.073 14.870  0.004  4.123   5.6156e-02
   4_bss:   0.958  0.007  0.073 14.870  0.004  4.123   5.6156e-02
   4_xyz:   1.039  0.008  0.080 14.987  0.004  4.125   6.5094e-02
   4_adp:   1.039  0.008  0.080 14.987  0.004  4.125   6.5094e-02
   4_occ:   1.039  0.008  0.080 14.987  0.004  4.125   6.5094e-02
   5_bss:   1.039  0.008  0.080 14.987  0.004  4.125   6.5094e-02
   5_xyz:   1.034  0.009  0.079 14.967  0.004  4.125   6.5315e-02
   5_adp:   1.034  0.009  0.079 14.967  0.004  4.125   6.5315e-02
   5_occ:   1.034  0.009  0.079 14.967  0.004  4.125   6.5315e-02
   5_bss:   1.034  0.009  0.079 14.967  0.004  4.125   6.5315e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4133e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4133e-01
   1_xyz:   7.512  0.043  0.242 84.259  0.027  2.340   6.0833e-02
   1_adp:   7.512  0.043  0.242 84.259  0.027  2.340   6.0833e-02
   1_occ:   7.512  0.043  0.242 84.259  0.027  2.340   6.0833e-02
   2_bss:   7.512  0.043  0.242 84.259  0.027  2.340   6.0833e-02
   2_xyz:   6.534  0.042  0.216 83.667  0.040  2.375   3.5897e-02
   2_adp:   6.534  0.042  0.216 83.667  0.040  2.375   3.5897e-02
   2_occ:   6.534  0.042  0.216 83.667  0.040  2.375   3.5897e-02
   3_bss:   6.534  0.042  0.216 83.667  0.040  2.375   3.5897e-02
   3_xyz:   7.110  0.039  0.234 82.633  0.035  2.368   3.9948e-02
   3_adp:   7.110  0.039  0.234 82.633  0.035  2.368   3.9948e-02
   3_occ:   7.110  0.039  0.234 82.633  0.035  2.368   3.9948e-02
   4_bss:   7.110  0.039  0.234 82.633  0.035  2.368   3.9948e-02
   4_xyz:   7.519  0.044  0.254 82.285  0.038  2.326   4.7188e-02
   4_adp:   7.519  0.044  0.254 82.285  0.038  2.326   4.7188e-02
   4_occ:   7.519  0.044  0.254 82.285  0.038  2.326   4.7188e-02
   5_bss:   7.519  0.044  0.254 82.285  0.038  2.326   4.7188e-02
   5_xyz:   7.349  0.049  0.253 82.365  0.037  2.330   4.9022e-02
   5_adp:   7.349  0.049  0.253 82.365  0.037  2.330   4.9022e-02
   5_occ:   7.349  0.049  0.253 82.365  0.037  2.330   4.9022e-02
   5_bss:   7.349  0.049  0.253 82.365  0.037  2.330   4.9022e-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:  73.28   1.47  16.80  73.28   1.47  12.94  70.49   5.83  37.82
   1_occ:  73.28   1.47  16.80  73.28   1.47  12.94  70.49   5.83  37.82
   2_bss:  73.28   1.47  16.80  73.28   1.47  12.94  70.49   5.83  37.82
   2_xyz:  73.28   1.47  16.80  73.28   1.47  12.94  70.49   5.83  37.82
   2_adp:  74.26   2.45  16.44  74.26   2.45  12.73  67.86   5.39  36.65
   2_occ:  74.26   2.45  16.44  74.26   2.45  12.73  67.86   5.39  36.65
   3_bss:  74.26   2.45  16.44  74.26   2.45  12.73  67.86   5.39  36.65
   3_xyz:  74.26   2.45  16.44  74.26   2.45  12.73  67.86   5.39  36.65
   3_adp:  76.66   1.15  16.49  76.66   1.15  12.64  67.68   5.78  37.49
   3_occ:  76.66   1.15  16.49  76.66   1.15  12.64  67.68   5.78  37.49
   4_bss:  76.66   1.15  16.49  76.66   1.15  12.64  67.68   5.78  37.49
   4_xyz:  76.66   1.15  16.49  76.66   1.15  12.64  67.68   5.78  37.49
   4_adp:  94.80   0.00  16.87  94.80   0.00  12.68  79.56   5.67  39.67
   4_occ:  94.80   0.00  16.87  94.80   0.00  12.68  79.56   5.67  39.67
   5_bss:  94.80   0.00  16.87  94.80   0.00  12.68  79.56   5.67  39.67
   5_xyz:  94.80   0.00  16.87  94.80   0.00  12.68  79.56   5.67  39.67
   5_adp:  96.91   0.00  16.68  96.91   0.00  12.48  80.88   5.51  39.57
   5_occ:  96.91   0.00  16.68  96.91   0.00  12.48  80.88   5.51  39.57
   5_bss:  96.92   0.00  16.68  96.92   0.00  12.48  80.88   5.51  39.58
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.106    0.011    0.267
   1_adp:    1.106    0.011    0.267
   1_occ:    1.106    0.011    0.267
   2_bss:    1.106    0.011    0.267
   2_xyz:    0.790    0.026    0.300
   2_adp:    0.790    0.026    0.300
   2_occ:    0.790    0.026    0.300
   3_bss:    0.790    0.026    0.300
   3_xyz:    0.821    0.025    0.326
   3_adp:    0.821    0.025    0.326
   3_occ:    0.821    0.025    0.326
   4_bss:    0.821    0.025    0.326
   4_xyz:    0.857    0.012    0.338
   4_adp:    0.857    0.012    0.338
   4_occ:    0.857    0.012    0.338
   5_bss:    0.857    0.012    0.338
   5_xyz:    1.036    0.016    0.344
   5_adp:    1.036    0.016    0.344
   5_occ:    1.036    0.016    0.344
   5_bss:    1.036    0.016    0.344
------------------------------------------------------------------------

CPU time actual refinement: 313.91


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_686/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_686/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_686/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_686/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_686/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 313.76 
  Macro-tasks:
    bulk solvent and scale       = 38.66  
    individual site refinement   = 129.33 
    weights calculation          = 28.63  
    collect and process          = 6.62   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 203.35 
  Micro-tasks:
    mask                            = 1.19   
    f_calc                          = 98.08  
    alpha_beta                      = 7.69   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 107.68 
    fmodel                         = 6.39   
    r_factors                      = 0.21   
    phase_errors                   = 11.41  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 234.04 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.459 micro seconds
Total CPU time: 5.45 minutes
from_scatterers_fft:    633 calls, 97.80 s
gradients_fft:          578 calls, 94.25 s

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

# Date 2008-01-16 Time 05:24:44 PST -0800 (1200489884.57 s)
Start R-work = 0.2747, R-free = 0.2679 (no bulk solvent and anisotropic scale)
Final R-work = 0.1274, R-free = 0.1743 (no bulk solvent and anisotropic scale)

Start R-work = 0.2581, R-free = 0.2509
Final R-work = 0.1059, R-free = 0.1576