# Date 2008-01-16 Time 06:43:43 PST -0800 (1200494623.28 s)
#phil __OFF__

Command line arguments: "../1264.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11933
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1264

-------------------------------------------------------------------------------
  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: (72.0062, 46.6953, 88.5498, 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: (72.0062, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 1.99366
Completeness in resolution range: 0.935304
Completeness with d_max=infinity: 0.932632

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3688
                             d_min =   1.9937

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: (72.0062, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3688 1.99366
Completeness in resolution range: 0.935304
Completeness with d_max=infinity: 0.932632

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3693 -  4.2674 [2202/2229]  1981   221  10.0%
  bin  2:  4.2674 -  3.3992 [2118/2138]  1906   212  10.0%
  bin  3:  3.3992 -  2.9731 [2084/2103]  1878   206   9.9%
  bin  4:  2.9731 -  2.7029 [2069/2099]  1859   210  10.1%
  bin  5:  2.7029 -  2.5100 [2057/2076]  1859   198   9.6%
  bin  6:  2.5100 -  2.3626 [2055/2080]  1842   213  10.4%
  bin  7:  2.3626 -  2.2446 [2032/2060]  1826   206  10.1%
  bin  8:  2.2446 -  2.1472 [2015/2051]  1813   202  10.0%
  bin  9:  2.1472 -  2.0647 [2033/2075]  1836   197   9.7%
  bin 10:  2.0647 -  1.9937 [ 924/2033]   830    94  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1264/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2166
        3.04 -     3.66: 4590
        3.66 -     4.28: 8855
        4.28 -     4.90: 12144
  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 341 " - " O   HOH Z 207 "  2.171 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.171 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 324 " - " O   HOH Z 374 "  2.323 3.040 -x,y-1/2,-z+1/2
  ... (remaining 27761 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_1264/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1264/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 = 72.00625 46.69535 88.54975 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 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4521   r_free= 0.4425   ksol= 0.00   Bsol= 0.00   scale= 0.884    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.261543                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.7604 0.99   1426  158 0.3579 0.3353       6.542      6.4458|
|  2:  4.7604 -  3.7972 0.99   1381  155 0.3791 0.3924      6.7876      6.8093|
|  3:  3.7972 -  3.3228 0.99   1342  144 0.4257 0.3769       6.643      6.5575|
|  4:  3.3228 -  3.0215 0.99   1345  156 0.4354 0.4484      6.4778      6.4748|
|  5:  3.0215 -  2.8063 0.99   1333  149 0.4891 0.4719      6.3466      6.3557|
|  6:  2.8063 -  2.6417 0.99   1332  147 0.4663 0.4805      6.2309      6.1892|
|  7:  2.6417 -  2.5100 0.99   1324  138 0.4959 0.4485      6.2225      6.1657|
|  8:  2.5100 -  2.4012 0.98   1302  153 0.5080 0.4856      6.1676       6.179|
|  9:  2.4012 -  2.3091 0.98   1302  144 0.5031 0.5107      6.1033       6.168|
| 10:  2.3091 -  2.2296 1.00   1323  151 0.5197 0.4800       6.087      6.0504|
| 11:  2.2296 -  2.1601 0.98   1307  139 0.4934 0.5057      6.0252      6.0324|
| 12:  2.1601 -  2.0985 0.98   1293  144 0.5194 0.5005      5.9294      5.9663|
| 13:  2.0985 -  2.0434 0.96   1259  139 0.5030 0.5240       5.869      5.7967|
| 14:  2.0434 -  1.9937 0.28    361   42 0.4836 0.5447      5.8236      5.8622|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.7604  1426   158  0.75  30.01   0.82     0.78      57164.97|
|  2:  4.7604 -  3.7972  1381   155  0.76  29.83   0.90     0.84      84941.61|
|  3:  3.7972 -  3.3228  1342   144  0.65  39.73   0.90     0.81      92624.34|
|  4:  3.3228 -  3.0215  1345   156  0.56  46.65   0.89     0.72      86647.78|
|  5:  3.0215 -  2.8063  1333   149  0.46  55.13   0.88     0.63      72216.94|
|  6:  2.8063 -  2.6417  1332   147  0.42  58.37   0.90     0.56      64998.20|
|  7:  2.6417 -  2.5100  1324   138  0.41  58.98   0.89     0.54      59871.29|
|  8:  2.5100 -  2.4012  1302   153  0.39  60.72   0.87     0.54      54880.04|
|  9:  2.4012 -  2.3091  1302   144  0.39  60.61   0.91     0.56      50996.12|
| 10:  2.3091 -  2.2296  1323   151  0.38  61.84   0.92     0.54      46445.64|
| 11:  2.2296 -  2.1601  1307   139  0.36  63.09   0.93     0.52      45546.97|
| 12:  2.1601 -  2.0985  1293   144  0.32  66.22   0.91     0.49      42393.91|
| 13:  2.0985 -  2.0434  1259   139  0.28  69.23   0.90     0.43      38623.95|
| 14:  2.0434 -  1.9937   361    42  0.26  70.58   0.95     0.35      33289.40|
|alpha:            min =        0.35 max =            0.84 mean =         0.61|
|beta:             min =    33289.40 max =        92624.34 mean =     61036.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.88|
|phase err.(test): min =        0.00 max =           89.69 mean =        53.51|
|-----------------------------------------------------------------------------|

============================== 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 = 14.129885             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.997   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.282843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.804   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      194 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1972 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1813 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2777 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4567 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4288 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5535 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6609 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.141 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    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 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4521   r_free= 0.4425   ksol= 0.00   Bsol= 0.00   scale= 0.884    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.261543                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4417   r_free= 0.4359   ksol= 0.31   Bsol= 67.68   scale= 0.935   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,-3.30,4.67,-0.00,0.00,0.00); trace/3= 1.08                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.251049                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.294239             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.763   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.089203              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.304   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4417      final r-factor (work) = 0.2932          |
| start r-factor (free) = 0.4359      final r-factor (free) = 0.3227          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.5781 = 12.29 * 0.50 * 6.2494 + 1.00 * 0.1623                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.5598 = 12.29 * 0.50 * 6.0866 + 1.00 * 0.1448                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2932      final r-factor (work) = 0.2694          |
| start r-factor (free) = 0.3227      final r-factor (free) = 0.3268          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6363 = 1.09 * 1.00 * 6.0866 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4937 = 1.09 * 1.00 * 5.8870 + 1.00 * 0.0816                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.13   17.19    None  None   None       |
|    all(noH): 2823   0      0.00    98.13   17.19    None  None   None       |
|    Sol.    : 438    0      1.85    65.02   38.66    None  None   None       |
|    Mac.    : 2385   0      0.00    98.13   13.25    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 -   9.813:  899   |   5:    49.067 -  58.880:   91        |
|      1:     9.813 -  19.627: 1091   |   6:    58.880 -  68.694:   13        |
|      2:    19.627 -  29.440:  398   |   7:    68.694 -  78.507:    0        |
|      3:    29.440 -  39.254:  177   |   8:    78.507 -  88.321:    0        |
|      4:    39.254 -  49.067:  153   |   9:    88.321 -  98.134:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2694 r_free = 0.3268             target_work(ml) = 5.893         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2689 r_free = 0.3262             target_work(ml) = 5.893         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2689   r_free= 0.3262   ksol= 0.31   Bsol= 67.68   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,-3.30,4.67,-0.00,0.00,0.00); trace/3= 1.08                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.892647                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2667   r_free= 0.3256   ksol= 0.34   Bsol= 77.02   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-2.68,1.74,-0.00,0.00,0.00); trace/3= -0.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.893067                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.754045              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.968   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.148263              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.957   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2667      final r-factor (work) = 0.1929          |
| start r-factor (free) = 0.3256      final r-factor (free) = 0.2450          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0962 = 5.75 * 0.50 * 5.8920 + 1.00 * 0.1448                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6842 = 5.75 * 0.50 * 5.7715 + 1.00 * 0.0795                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1929      final r-factor (work) = 0.1708          |
| start r-factor (free) = 0.2450      final r-factor (free) = 0.2323          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6424 = 1.15 * 1.00 * 5.7715 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3957 = 1.15 * 1.00 * 5.5569 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.32  18.57    None  None   None       |
|    all(noH): 2823   0      0.00    102.32  18.57    None  None   None       |
|    Sol.    : 438    0      3.10    102.32  46.56    None  None   None       |
|    Mac.    : 2385   0      0.00    89.81   13.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.233: 1091   |   5:    51.162 -  61.395:  100        |
|      1:    10.233 -  20.465: 1025   |   6:    61.395 -  71.627:   73        |
|      2:    20.465 -  30.697:  252   |   7:    71.627 -  81.860:   34        |
|      3:    30.697 -  40.930:  113   |   8:    81.860 -  92.092:   19        |
|      4:    40.930 -  51.162:  113   |   9:    92.092 - 102.325:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1708 r_free = 0.2323             target_work(ml) = 5.530         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1707 r_free = 0.2321             target_work(ml) = 5.529         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1707   r_free= 0.2321   ksol= 0.34   Bsol= 77.02   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-2.68,1.74,-0.00,0.00,0.00); trace/3= -0.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.529406                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1704   r_free= 0.2319   ksol= 0.35   Bsol= 87.92   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.20,-2.29,0.54,-0.00,0.00,0.00); trace/3= -0.99                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.527243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.620299              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.249  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.436127              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.529  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1704      final r-factor (work) = 0.1481          |
| start r-factor (free) = 0.2319      final r-factor (free) = 0.2004          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3601 = 2.62 * 0.50 * 5.5571 + 1.00 * 0.0795                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2251 = 2.62 * 0.50 * 5.4685 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1481      final r-factor (work) = 0.1427          |
| start r-factor (free) = 0.2004      final r-factor (free) = 0.1922          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3998 = 0.44 * 1.00 * 5.4685 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3571 = 0.44 * 1.00 * 5.3764 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.83  18.02    None  None   None       |
|    all(noH): 2823   0      0.00    102.83  18.02    None  None   None       |
|    Sol.    : 438    0      4.73    102.83  45.46    None  None   None       |
|    Mac.    : 2385   0      0.00    86.83   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.283: 1123   |   5:    51.414 -  61.696:   88        |
|      1:    10.283 -  20.566: 1040   |   6:    61.696 -  71.979:   70        |
|      2:    20.566 -  30.848:  231   |   7:    71.979 -  82.262:   32        |
|      3:    30.848 -  41.131:  119   |   8:    82.262 -  92.545:   13        |
|      4:    41.131 -  51.414:  101   |   9:    92.545 - 102.827:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1427 r_free = 0.1922             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1425 r_free = 0.1921             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1425   r_free= 0.1921   ksol= 0.35   Bsol= 87.92   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.20,-2.29,0.54,-0.00,0.00,0.00); trace/3= -0.99                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.353795                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1429   r_free= 0.1919   ksol= 0.33   Bsol= 80.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-2.22,0.08,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.354621                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.632805              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.477  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.272211              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.468  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1429      final r-factor (work) = 0.1337          |
| start r-factor (free) = 0.1919      final r-factor (free) = 0.1814          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4505 = 1.63 * 0.50 * 5.3772 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4054 = 1.63 * 0.50 * 5.3271 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1337      final r-factor (work) = 0.1327          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1786          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4622 = 0.27 * 1.00 * 5.3271 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4526 = 0.27 * 1.00 * 5.2972 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.62    102.52  17.54    None  None   None       |
|    all(noH): 2823   0      0.62    102.52  17.54    None  None   None       |
|    Sol.    : 438    0      5.06    102.52  43.49    None  None   None       |
|    Mac.    : 2385   0      0.62    83.14   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.619 -  10.809: 1243   |   5:    51.569 -  61.759:   80        |
|      1:    10.809 -  20.999:  967   |   6:    61.759 -  71.949:   68        |
|      2:    20.999 -  31.189:  218   |   7:    71.949 -  82.139:   22        |
|      3:    31.189 -  41.379:  118   |   8:    82.139 -  92.329:   10        |
|      4:    41.379 -  51.569:   93   |   9:    92.329 - 102.519:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1327 r_free = 0.1786             target_work(ml) = 5.289         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1326 r_free = 0.1786             target_work(ml) = 5.288         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1786   ksol= 0.33   Bsol= 80.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.45,-2.22,0.08,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.288074                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1787   ksol= 0.32   Bsol= 70.64   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-2.31,-0.23,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.288087                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.768418              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.264  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.639681              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.711  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1326      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1787      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0369 = 3.77 * 0.50 * 5.2969 + 1.00 * 0.0564                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9731 = 3.77 * 0.50 * 5.2478 + 1.00 * 0.0853                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1207      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3674 = 0.64 * 1.00 * 5.2478 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3467 = 0.64 * 1.00 * 5.2141 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.43  17.47    None  None   None       |
|    all(noH): 2823   0      0.00    108.43  17.47    None  None   None       |
|    Sol.    : 438    0      5.03    108.43  43.37    None  None   None       |
|    Mac.    : 2385   0      0.00    85.17   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.843: 1269   |   5:    54.215 -  65.058:   98        |
|      1:    10.843 -  21.686:  968   |   6:    65.058 -  75.901:   38        |
|      2:    21.686 -  32.529:  195   |   7:    75.901 -  86.744:   20        |
|      3:    32.529 -  43.372:  141   |   8:    86.744 -  97.587:    6        |
|      4:    43.372 -  54.215:   84   |   9:    97.587 - 108.430:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1695             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1696             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1696   ksol= 0.32   Bsol= 70.64   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-2.31,-0.23,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212116                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.7604 0.99   1426  158 0.0972 0.1379      5.3829      5.5971|
|  2:  4.7604 -  3.7972 0.99   1381  155 0.0853 0.1118      5.4494      5.6446|
|  3:  3.7972 -  3.3228 0.99   1342  144 0.1117 0.1685      5.5131      5.8632|
|  4:  3.3228 -  3.0215 0.99   1345  156 0.1301 0.1800       5.512      5.6972|
|  5:  3.0215 -  2.8063 0.99   1333  149 0.1491 0.1816       5.408      5.6108|
|  6:  2.8063 -  2.6417 0.99   1332  147 0.1356 0.2003      5.2778      5.5106|
|  7:  2.6417 -  2.5100 0.99   1324  138 0.1342 0.1726      5.2312      5.3771|
|  8:  2.5100 -  2.4012 0.98   1302  153 0.1279 0.1787      5.1398      5.4019|
|  9:  2.4012 -  2.3091 0.98   1302  144 0.1300 0.2108      5.1166      5.4084|
| 10:  2.3091 -  2.2296 1.00   1323  151 0.1209 0.1729      5.0085      5.2359|
| 11:  2.2296 -  2.1601 0.98   1307  139 0.1217 0.1888       5.004      5.3622|
| 12:  2.1601 -  2.0985 0.98   1293  144 0.1250 0.1971      4.9362      5.2076|
| 13:  2.0985 -  2.0434 0.96   1259  139 0.1193 0.1766      4.8442      5.0619|
| 14:  2.0434 -  1.9937 0.28    361   42 0.1089 0.1827      4.7343      5.0043|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.7604  1426   158  0.94   9.29   0.97     0.94       7539.06|
|  2:  4.7604 -  3.7972  1381   155  0.95   8.28   1.00     0.98       9551.93|
|  3:  3.7972 -  3.3228  1342   144  0.93  12.24   1.02     1.02      11298.58|
|  4:  3.3228 -  3.0215  1345   156  0.91  15.16   1.00     0.98      11778.83|
|  5:  3.0215 -  2.8063  1333   149  0.89  17.51   0.99     0.97       9655.22|
|  6:  2.8063 -  2.6417  1332   147  0.89  17.65   0.97     0.95       8040.54|
|  7:  2.6417 -  2.5100  1324   138  0.90  16.79   0.99     0.95       7184.64|
|  8:  2.5100 -  2.4012  1302   153  0.89  17.05   0.98     0.95       6119.19|
|  9:  2.4012 -  2.3091  1302   144  0.89  17.35   0.98     0.93       5869.31|
| 10:  2.3091 -  2.2296  1323   151  0.89  16.83   0.98     0.95       4930.50|
| 11:  2.2296 -  2.1601  1307   139  0.89  17.06   0.97     0.92       4839.81|
| 12:  2.1601 -  2.0985  1293   144  0.89  17.22   0.98     0.98       4486.16|
| 13:  2.0985 -  2.0434  1259   139  0.88  18.48   0.97     0.95       3957.09|
| 14:  2.0434 -  1.9937   361    42  0.91  15.59   0.94     0.92       3033.55|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     3033.55 max =        11778.83 mean =      7281.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.87 mean =        15.38|
|phase err.(test): min =        0.00 max =           89.14 mean =        14.76|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1695   ksol= 0.32   Bsol= 70.65   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,-2.11,-0.13,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212214                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.37 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1695   ksol= 0.32   Bsol= 70.65   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,-2.11,-0.13,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.212214                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3693 -  4.7604 0.99   1426  158 0.0972 0.1379      5.3832      5.5978|
|  2:  4.7604 -  3.7972 0.99   1381  155 0.0853 0.1118      5.4496      5.6447|
|  3:  3.7972 -  3.3228 0.99   1342  144 0.1116 0.1685       5.513      5.8634|
|  4:  3.3228 -  3.0215 0.99   1345  156 0.1301 0.1801       5.512      5.6972|
|  5:  3.0215 -  2.8063 0.99   1333  149 0.1490 0.1815       5.408      5.6105|
|  6:  2.8063 -  2.6417 0.99   1332  147 0.1356 0.2005       5.278      5.5113|
|  7:  2.6417 -  2.5100 0.99   1324  138 0.1342 0.1725      5.2315      5.3772|
|  8:  2.5100 -  2.4012 0.98   1302  153 0.1278 0.1787      5.1399       5.402|
|  9:  2.4012 -  2.3091 0.98   1302  144 0.1300 0.2111      5.1168      5.4092|
| 10:  2.3091 -  2.2296 1.00   1323  151 0.1209 0.1726      5.0084      5.2341|
| 11:  2.2296 -  2.1601 0.98   1307  139 0.1217 0.1887      5.0039      5.3619|
| 12:  2.1601 -  2.0985 0.98   1293  144 0.1250 0.1972      4.9358       5.208|
| 13:  2.0985 -  2.0434 0.96   1259  139 0.1193 0.1769      4.8445      5.0623|
| 14:  2.0434 -  1.9937 0.28    361   42 0.1089 0.1827      4.7352      5.0052|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.3693 -  4.7604  1426   158  0.94   9.30   0.97     0.94       7546.21|
|  2:  4.7604 -  3.7972  1381   155  0.95   8.29   1.00     0.98       9556.50|
|  3:  3.7972 -  3.3228  1342   144  0.93  12.24   1.02     1.02      11297.87|
|  4:  3.3228 -  3.0215  1345   156  0.91  15.16   1.00     0.98      11778.51|
|  5:  3.0215 -  2.8063  1333   149  0.89  17.52   0.99     0.97       9660.71|
|  6:  2.8063 -  2.6417  1332   147  0.89  17.66   0.98     0.95       8043.79|
|  7:  2.6417 -  2.5100  1324   138  0.90  16.80   0.99     0.96       7188.97|
|  8:  2.5100 -  2.4012  1302   153  0.89  17.06   0.99     0.96       6122.78|
|  9:  2.4012 -  2.3091  1302   144  0.89  17.36   0.99     0.94       5872.95|
| 10:  2.3091 -  2.2296  1323   151  0.89  16.82   0.99     0.96       4925.62|
| 11:  2.2296 -  2.1601  1307   139  0.89  17.05   0.98     0.92       4830.92|
| 12:  2.1601 -  2.0985  1293   144  0.89  17.21   0.99     0.99       4481.68|
| 13:  2.0985 -  2.0434  1259   139  0.88  18.49   0.98     0.96       3960.00|
| 14:  2.0434 -  1.9937   361    42  0.91  15.64   0.95     0.92       3040.30|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     3040.30 max =        11778.51 mean =      7283.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.87 mean =        15.38|
|phase err.(test): min =        0.00 max =           89.14 mean =        14.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.375)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.43  17.47    None  None   None       |
|    all(noH): 2823   0      0.00    108.43  17.47    None  None   None       |
|    Sol.    : 438    0      5.04    108.43  43.37    None  None   None       |
|    Mac.    : 2385   0      0.00    85.18   12.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.846: 1269   |   5:    54.218 -  65.061:   98        |
|      1:    10.846 -  21.689:  968   |   6:    65.061 -  75.904:   38        |
|      2:    21.689 -  32.532:  195   |   7:    75.904 -  86.747:   20        |
|      3:    32.532 -  43.375:  141   |   8:    86.747 -  97.590:    6        |
|      4:    43.375 -  54.218:   84   |   9:    97.590 - 108.432:    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)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.490 - 4.447
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 315
   mapped sites are within: 0.722 - 4.447

peak=   11.178 closest distance to " O  BHOH Z  74 " =    1.119
peak=    5.664 closest distance to " O   HOH Z 222 " =    1.378
peak=    5.278 closest distance to " NE2 GLN A  11 " =    1.124
peak=    5.276 closest distance to " CB  GLN A 223 " =    1.509
peak=    4.965 closest distance to " O   HOH Z 232 " =    2.186
peak=    4.943 closest distance to " CG  PRO A  54 " =    1.297
peak=    4.900 closest distance to " CB  SER A  63 " =    1.318
peak=    4.827 closest distance to " O   HOH Z 298 " =    2.341
peak=    4.787 closest distance to " CB  ARG A 190 " =    1.607
peak=    4.767 closest distance to " O   HOH Z 369 " =    2.081
peak=    4.760 closest distance to " CZ  PHE A 218 " =    1.102
peak=    4.614 closest distance to " O   HOH Z 144 " =    1.851
peak=    4.559 closest distance to " O   HOH Z 126 " =    1.579
peak=    4.463 closest distance to " CB  SER A 212 " =    1.208
peak=    4.461 closest distance to " CB  ASN A 148 " =    1.452
peak=    4.380 closest distance to " CD  ARG A 159 " =    0.840
peak=    4.360 closest distance to " O   HOH Z 183 " =    1.763
peak=    4.360 closest distance to " O   HOH Z 423 " =    1.612
peak=    4.323 closest distance to " NH1AARG A 145 " =    1.257
peak=    4.301 closest distance to " CB  ASP A 124 " =    0.841
peak=    4.281 closest distance to " CZ3 TRP A 266 " =    1.103
peak=    4.277 closest distance to " CB  LEU A 228 " =    1.105
peak=    4.258 closest distance to " O   HOH Z   7 " =    1.335
peak=    4.248 closest distance to " O   HOH Z 287 " =    2.046
peak=    4.244 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.188 closest distance to " CB  GLN A 183 " =    1.288
peak=    4.146 closest distance to " CD2 TRP A 179 " =    1.284
peak=    4.135 closest distance to " CB  TRP A 266 " =    1.016
peak=    4.128 closest distance to " O   HOH Z 425 " =    1.409
peak=    4.113 closest distance to " CG2 THR A 221 " =    0.944
peak=    4.104 closest distance to " CB  PRO A  54 " =    0.996
peak=    4.102 closest distance to " CB  GLU A 277 " =    3.805
peak=    4.093 closest distance to " O   PRO A 198 " =    1.566
peak=    4.087 closest distance to " O   HOH Z 290 " =    1.293
peak=    4.076 closest distance to " CA  ARG A 195 " =    1.324
peak=    4.072 closest distance to " O   HOH Z 188 " =    2.730
peak=    4.059 closest distance to " CG  LEU A 167 " =    1.259
peak=    4.021 closest distance to " ND2 ASN A 187 " =    1.451
peak=    4.012 closest distance to " CE  LYS A  76 " =    0.898
peak=    4.001 closest distance to " CB  ASN A 142 " =    0.924
peak=    4.001 closest distance to " O   HOH Z 406 " =    1.749
peak=    3.978 closest distance to " CA  TYR A  30 " =    1.079
peak=    3.977 closest distance to " O   HOH Z  88 " =    3.992
peak=    3.948 closest distance to " CB  ARG A 275 " =    1.041
peak=    3.943 closest distance to " O   HOH Z 427 " =    3.053
peak=    3.943 closest distance to " CG  PRO A 198 " =    1.275
peak=    3.915 closest distance to " CB  GLU A 128 " =    0.970
peak=    3.909 closest distance to " CA  VAL A 125 " =    1.235
peak=    3.904 closest distance to " O   HOH Z  69 " =    0.907
peak=    3.889 closest distance to " CB  ASP A 140 " =    0.915
peak=    3.879 closest distance to " O   HOH Z 207 " =    0.949
peak=    3.856 closest distance to " CG  PRO A  90 " =    1.390
peak=    3.855 closest distance to " O   HOH Z 180 " =    2.091
peak=    3.854 closest distance to " O   HOH Z 394 " =    3.957
peak=    3.816 closest distance to " O   HOH Z 111 " =    1.725
peak=    3.815 closest distance to " O   HOH Z  21 " =    1.750
peak=    3.805 closest distance to " O   HOH Z 185 " =    2.055
peak=    3.801 closest distance to " CD1 LEU A 300 " =    1.156
peak=    3.800 closest distance to " CG  GLU A  37 " =    1.007
peak=    3.799 closest distance to " O   HOH Z 411 " =    3.437
peak=    3.799 closest distance to " O   HOH Z 285 " =    2.233
peak=    3.798 closest distance to " CB  MET A  40 " =    0.751
peak=    3.789 closest distance to " O   HOH Z 265 " =    1.971
peak=    3.785 closest distance to " O   HOH Z 214 " =    2.540
peak=    3.780 closest distance to " CD  ARG A  66 " =    2.248
peak=    3.766 closest distance to " CB  VAL A 265 " =    1.322
peak=    3.758 closest distance to " CA  ALA A  51 " =    0.940
peak=    3.756 closest distance to " CA  ALA A 158 " =    1.156
peak=    3.746 closest distance to " CB  TYR A 169 " =    0.781
peak=    3.743 closest distance to " CG  PRO A 243 " =    1.060
peak=    3.742 closest distance to " O   HOH Z 303 " =    2.360
peak=    3.739 closest distance to " CA  MET A  40 " =    1.310
peak=    3.734 closest distance to " O   HOH Z  80 " =    1.775
peak=    3.733 closest distance to " O   HOH Z 126 " =    2.080
peak=    3.732 closest distance to " O   HOH Z 184 " =    1.641
peak=    3.729 closest distance to " CA  ARG A 102 " =    1.159
peak=    3.729 closest distance to " OG  SER A  62 " =    2.975
peak=    3.729 closest distance to " O   HOH Z  53 " =    2.460
peak=    3.725 closest distance to " O   HOH Z  58 " =    1.761
peak=    3.723 closest distance to " CD ALYS A 290 " =    0.989
peak=    3.722 closest distance to " O   HOH Z 158 " =    2.948
peak=    3.722 closest distance to " O   HOH Z 156 " =    2.854
peak=    3.720 closest distance to " O   HOH Z 167 " =    1.769
peak=    3.716 closest distance to " O   HOH Z 368 " =    2.052
peak=    3.704 closest distance to " CD  LYS A 166 " =    1.458
peak=    3.702 closest distance to " O   HOH Z 193 " =    2.215
peak=    3.699 closest distance to " O   HOH Z 298 " =    4.122
peak=    3.682 closest distance to " O   TYR A 116 " =    1.252
peak=    3.679 closest distance to " O   HOH Z 116 " =    1.895
peak=    3.672 closest distance to " CD  ARG A 269 " =    0.900
peak=    3.672 closest distance to " N   ASN A 127 " =    1.359
peak=    3.665 closest distance to " CB  ASN A  39 " =    0.983
peak=    3.657 closest distance to " CA  TYR A 116 " =    1.410
peak=    3.647 closest distance to " O   HOH Z 148 " =    3.527
peak=    3.645 closest distance to " CA  THR A 264 " =    0.918
peak=    3.643 closest distance to " NE2 HIS A 207 " =    1.230
peak=    3.628 closest distance to " NZ  LYS A 117 " =    2.997
peak=    3.619 closest distance to " CB  ARG A  79 " =    1.514
peak=    3.618 closest distance to " CB  LEU A 237 " =    0.798
peak=    3.608 closest distance to " O   HOH Z 145 " =    1.762
peak=    3.596 closest distance to " CG2 VAL A 257 " =    0.803
peak=    3.596 closest distance to " O   HOH Z  61 " =    1.695
peak=    3.595 closest distance to " O   HOH Z   9 " =    1.936
peak=    3.585 closest distance to " O   HOH Z 325 " =    2.316
peak=    3.583 closest distance to " OE1 GLN A 240 " =    1.647
peak=    3.581 closest distance to " O   HOH Z 362 " =    2.799
peak=    3.576 closest distance to " CB  GLU A  46 " =    0.944
peak=    3.567 closest distance to " CB  SER A  97 " =    1.022
peak=    3.564 closest distance to " CG AARG A 275 " =    1.271
peak=    3.561 closest distance to " O   SER A  87 " =    2.372
peak=    3.553 closest distance to " O   HOH Z 359 " =    1.529
peak=    3.552 closest distance to " O   HOH Z 238 " =    3.524
peak=    3.548 closest distance to " CB  ALA A 104 " =    0.799
peak=    3.544 closest distance to " NZ  LYS A 119 " =    2.964
peak=    3.540 closest distance to " CB  TYR A 116 " =    0.850
peak=    3.535 closest distance to " CA  SER A  87 " =    0.934
peak=    3.530 closest distance to " CA  ALA A 160 " =    0.968
peak=    3.527 closest distance to " O   MET A 105 " =    1.781
peak=    3.526 closest distance to " CA  ALA A 154 " =    1.117
peak=    3.519 closest distance to " CB  ASN A 285 " =    0.940
peak=    3.518 closest distance to " CA  PRO A  54 " =    1.399
peak=    3.516 closest distance to " O   HOH Z 313 " =    1.965
peak=    3.508 closest distance to " O   HOH Z 422 " =    2.781
peak=    3.508 closest distance to " O   HOH Z  49 " =    0.966
peak=    3.507 closest distance to " O   HOH Z 222 " =    2.288
peak=    3.507 closest distance to " CB  GLU A 152 " =    1.272
peak=    3.502 closest distance to " O   HOH Z 106 " =    4.285
peak=    3.499 closest distance to " CG BARG A 275 " =    1.522
peak=    3.498 closest distance to " CG2 ILE A  20 " =    1.366
peak=    3.495 closest distance to " CB  SER A 210 " =    0.887
peak=    3.493 closest distance to " O   HOH Z 218 " =    1.482
peak=    3.493 closest distance to " N   SER A 271 " =    0.920
peak=    3.484 closest distance to " O   HOH Z 316 " =    3.133
peak=    3.483 closest distance to " OD1 ASN A 217 " =    1.403
peak=    3.482 closest distance to " CB  VAL A 202 " =    1.551
peak=    3.479 closest distance to " O   HOH Z 234 " =    3.959
peak=    3.476 closest distance to " CB  ARG A 138 " =    0.998
peak=    3.465 closest distance to " O   HOH Z 346 " =    1.749
peak=    3.464 closest distance to " NH1 ARG A  56 " =    1.164
peak=    3.461 closest distance to " O   THR A 182 " =    1.420
peak=    3.457 closest distance to " O   HOH Z 116 " =    3.524
peak=    3.453 closest distance to " O   HOH Z   2 " =    1.642
peak=    3.452 closest distance to " O   HOH Z 112 " =    1.199
peak=    3.450 closest distance to " OG1 THR A 264 " =    0.805
peak=    3.443 closest distance to " O   HOH Z 332 " =    1.584
peak=    3.443 closest distance to " CA  GLU A  46 " =    0.965
peak=    3.441 closest distance to " O   HOH Z 213 " =    2.217
peak=    3.436 closest distance to " O   THR A 251 " =    1.255
peak=    3.435 closest distance to " CB  SER A   3 " =    1.580
peak=    3.434 closest distance to " O   HOH Z 171 " =    4.083
peak=    3.422 closest distance to " O   HOH Z 409 " =    2.629
peak=    3.418 closest distance to " CA  ASN A 127 " =    1.120
peak=    3.414 closest distance to " N   PHE A 130 " =    1.244
peak=    3.410 closest distance to " O   HOH Z 166 " =    3.909
peak=    3.405 closest distance to " CB  TYR A  30 " =    1.181
peak=    3.400 closest distance to " N   ARG A 156 " =    1.371
peak=    3.398 closest distance to " O   HOH Z 251 " =    1.682
peak=    3.398 closest distance to " CG1 VAL A 153 " =    1.009
peak=    3.395 closest distance to " CA  ARG A  36 " =    1.240
peak=    3.391 closest distance to " O   HOH Z 250 " =    1.388
peak=    3.388 closest distance to " OG  SER A 135 " =    1.235
peak=    3.383 closest distance to " CA  GLY A 241 " =    0.815
peak=    3.378 closest distance to " O   HOH Z  61 " =    1.616
peak=    3.375 closest distance to " O   HOH Z 272 " =    1.741
peak=    3.374 closest distance to " CB  SER A 216 " =    1.020
peak=    3.372 closest distance to " O   HOH Z  40 " =    1.804
peak=    3.371 closest distance to " O   HOH Z 302 " =    1.863
peak=    3.370 closest distance to " O   HOH Z 132 " =    2.540
peak=    3.363 closest distance to " O   HOH Z 128 " =    1.553
peak=    3.363 closest distance to " CG1 ILE A  20 " =    1.411
peak=    3.360 closest distance to " O   HOH Z   1 " =    1.935
peak=    3.351 closest distance to " CA  ILE A 263 " =    1.063
peak=    3.346 closest distance to " CB  TRP A 150 " =    1.055
peak=    3.345 closest distance to " CB  SER A 276 " =    1.074
peak=    3.345 closest distance to " O   HOH Z 145 " =    1.674
peak=    3.339 closest distance to " CA  MET A 105 " =    0.962
peak=    3.336 closest distance to " CA  ARG A 139 " =    1.151
peak=    3.335 closest distance to " OG  SER A  28 " =    1.716
peak=    3.335 closest distance to " O   HOH Z 207 " =    2.537
peak=    3.334 closest distance to " CE  MET A 113 " =    1.848
peak=    3.332 closest distance to " CA  ILE A 234 " =    1.138
peak=    3.329 closest distance to " CB  ALA A 114 " =    0.925
peak=    3.326 closest distance to " NH2 ARG A 156 " =    1.162
peak=    3.325 closest distance to " CA  ASN A  74 " =    1.365
peak=    3.324 closest distance to " O   ASN A  74 " =    1.486
peak=    3.323 closest distance to " CG1 ILE A  33 " =    1.189
peak=    3.321 closest distance to " O   HOH Z 104 " =    2.220
peak=    3.321 closest distance to " CG2 VAL A 197 " =    1.133
peak=    3.320 closest distance to " CG  PHE A 204 " =    0.869
peak=    3.320 closest distance to " CB  ALA A  34 " =    1.165
peak=    3.319 closest distance to " ND1 HIS A  81 " =    1.953
peak=    3.317 closest distance to " CA  ALA A 129 " =    1.208
peak=    3.316 closest distance to " CE3 TRP A  85 " =    0.949
peak=    3.313 closest distance to " CA  TRP A  92 " =    1.202
peak=    3.312 closest distance to " NE  ARG A  79 " =    1.045
peak=    3.312 closest distance to " N   TYR A  15 " =    0.830
peak=    3.310 closest distance to " OD2 ASP A 286 " =    3.330
peak=    3.305 closest distance to " N   GLU A 152 " =    1.479
peak=    3.304 closest distance to " O   THR A 220 " =    1.262
peak=    3.301 closest distance to " O   HOH Z 273 " =    2.580
peak=    3.300 closest distance to " O   HOH Z 213 " =    3.123
peak=    3.295 closest distance to " O   HOH Z 193 " =    1.719
peak=    3.289 closest distance to " O   HOH Z 273 " =    1.143
peak=    3.289 closest distance to " O   HOH Z 371 " =    2.987
peak=    3.289 closest distance to " O   HOH Z  78 " =    2.055
peak=    3.286 closest distance to " O   HOH Z 391 " =    2.926
peak=    3.285 closest distance to " OE2 GLU A  53 " =    2.105
peak=    3.284 closest distance to " CA  ALA A 160 " =    1.369
peak=    3.282 closest distance to " CA  ASP A 124 " =    0.745
peak=    3.281 closest distance to " CB  ILE A 120 " =    1.331
peak=    3.281 closest distance to " O   HOH Z  78 " =    1.508
peak=    3.280 closest distance to " OE2 GLU A  53 " =    1.579
peak=    3.279 closest distance to " O   HOH Z 298 " =    2.462
peak=    3.279 closest distance to " CG2 THR A  29 " =    1.446
peak=    3.278 closest distance to " O   HOH Z  63 " =    1.673
peak=    3.277 closest distance to " CD1 ILE A  33 " =    1.720
peak=    3.277 closest distance to " O   HOH Z 189 " =    3.498
peak=    3.274 closest distance to " CG2 ILE A 151 " =    0.891
peak=    3.272 closest distance to " O   HOH Z 193 " =    2.032
peak=    3.270 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.268 closest distance to " O   HOH Z  90 " =    2.484
peak=    3.266 closest distance to " OH  TYR A 186 " =    1.111
peak=    3.265 closest distance to " CG  GLN A 144 " =    0.883
peak=    3.262 closest distance to " OG BSER A  99 " =    2.297
peak=    3.260 closest distance to " CB  ALA A 248 " =    1.027
peak=    3.254 closest distance to " O  BHOH Z 338 " =    2.428
peak=    3.253 closest distance to " O   HOH Z 272 " =    2.712
peak=    3.251 closest distance to " O   HOH Z 154 " =    2.218
peak=    3.248 closest distance to " CD  ARG A 195 " =    3.511
peak=    3.236 closest distance to " CA  ARG A 156 " =    1.076
peak=    3.233 closest distance to " O   HOH Z 240 " =    2.354
peak=    3.233 closest distance to " ND2 ASN A 127 " =    1.217
peak=    3.233 closest distance to " CB  ALA A  43 " =    0.780
peak=    3.232 closest distance to " CG1 ILE A 151 " =    1.130
peak=    3.229 closest distance to " O   HOH Z  10 " =    1.858
peak=    3.228 closest distance to " O   HOH Z 216 " =    4.163
peak=    3.227 closest distance to " CB  PRO A  90 " =    1.126
peak=    3.226 closest distance to " O   HOH Z 299 " =    4.447
peak=    3.226 closest distance to " O   TRP A  70 " =    1.521
peak=    3.224 closest distance to " OD1 ASN A  69 " =    2.588
peak=    3.224 closest distance to " CA  THR A 221 " =    0.970
peak=    3.222 closest distance to " CD2 PHE A  59 " =    1.854
peak=    3.220 closest distance to " O   HOH Z 258 " =    2.066
peak=    3.217 closest distance to " CB  GLU A  37 " =    0.997
peak=    3.216 closest distance to " CB  MET A  47 " =    1.158
peak=    3.216 closest distance to " CB  LEU A  96 " =    1.582
peak=    3.210 closest distance to " O   HOH Z 383 " =    1.861
peak=    3.210 closest distance to " CB  LYS A 193 " =    1.010
peak=    3.208 closest distance to " CB  PRO A 243 " =    1.210
peak=    3.205 closest distance to " CD1 ILE A 199 " =    1.026
peak=    3.202 closest distance to " O   PRO A 213 " =    1.472
peak=    3.201 closest distance to " O   HOH Z 345 " =    3.591
peak=    3.197 closest distance to " O   HOH Z   9 " =    1.404
peak=    3.190 closest distance to " CB  ARG A 102 " =    0.876
peak=    3.189 closest distance to " N   SER A 135 " =    1.465
peak=    3.186 closest distance to " NE AARG A 275 " =    1.512
peak=    3.182 closest distance to " CA  SER A  26 " =    1.008
peak=    3.182 closest distance to " CB  TYR A  30 " =    1.309
peak=    3.182 closest distance to " CB  LEU A 300 " =    0.957
peak=    3.180 closest distance to " CG  ARG A 159 " =    0.886
peak=    3.179 closest distance to " CB  SER A 288 " =    1.291
peak=    3.178 closest distance to " O   PHE A 192 " =    1.423
peak=    3.176 closest distance to " O   HOH Z 287 " =    2.241
peak=    3.176 closest distance to " CB  ARG A  79 " =    0.959
peak=    3.173 closest distance to " O   HOH Z 271 " =    2.879
peak=    3.172 closest distance to " O   HOH Z 172 " =    3.408
peak=    3.171 closest distance to " O   HOH Z 417 " =    3.576
peak=    3.170 closest distance to " NH1 ARG A 138 " =    1.081
peak=    3.165 closest distance to " ND2 ASN A  69 " =    1.373
peak=    3.162 closest distance to " O   HOH Z 368 " =    3.734
peak=    3.160 closest distance to " CB  ALA A 242 " =    0.847
peak=    3.157 closest distance to " CB  TYR A  15 " =    0.865
peak=    3.156 closest distance to " OE1 GLN A  11 " =    2.188
peak=    3.155 closest distance to " CD2 TYR A 186 " =    1.134
peak=    3.155 closest distance to " CB  ALA A 299 " =    0.856
peak=    3.153 closest distance to " O   HOH Z 423 " =    2.593
peak=    3.152 closest distance to " O   HOH Z 207 " =    1.799
peak=    3.151 closest distance to " CA  ASP A 162 " =    1.029
peak=    3.151 closest distance to " CA  ALA A 184 " =    1.143
peak=    3.151 closest distance to " O   HOH Z 124 " =    1.861
peak=    3.150 closest distance to " OD2 ASP A  65 " =    3.079
peak=    3.150 closest distance to " CA  GLN A  94 " =    0.722
peak=    3.147 closest distance to " CB  HIS A  86 " =    0.936
peak=    3.134 closest distance to " OE1 GLU A 236 " =    1.063
peak=    3.133 closest distance to " O   THR A  18 " =    1.915
peak=    3.131 closest distance to " CB  ARG A 156 " =    1.094
peak=    3.130 closest distance to " CE2 TYR A 186 " =    0.874
peak=    3.129 closest distance to " O   HOH Z  57 " =    1.368
peak=    3.128 closest distance to " N   VAL A 296 " =    1.815
peak=    3.128 closest distance to " CG  ARG A 138 " =    1.191
peak=    3.126 closest distance to " CA  ALA A 295 " =    1.111
peak=    3.121 closest distance to " O   HOH Z 281 " =    2.401
peak=    3.119 closest distance to " OG  SER A  62 " =    3.102
peak=    3.116 closest distance to " O   HOH Z 227 " =    1.990
peak=    3.113 closest distance to " CA  ILE A 106 " =    0.860
peak=    3.108 closest distance to " O   HOH Z  97 " =    1.478
peak=    3.106 closest distance to " O   HOH Z 356 " =    2.998
peak=    3.101 closest distance to " CB  THR A  31 " =    1.522
peak=    3.101 closest distance to " CB  ALA A 100 " =    1.314
peak=    3.087 closest distance to " CA  ARG A 159 " =    1.419
peak=    3.083 closest distance to " O   HOH Z 357 " =    2.680
peak=    3.072 closest distance to " CB  HIS A 108 " =    0.753
peak=    3.072 closest distance to " NH2AARG A 145 " =    1.213
peak=    3.071 closest distance to " CD1 LEU A  96 " =    0.727
peak=    3.070 closest distance to " NE2 GLN A  58 " =    4.309
peak=    3.067 closest distance to " O   LEU A 300 " =    1.512
peak=    3.066 closest distance to " OE1 GLN A  55 " =    1.322
peak=    3.063 closest distance to " CG2 ILE A 234 " =    0.878
peak=    3.038 closest distance to " O   HOH Z 119 " =    3.343
peak=    3.034 closest distance to " O   HOH Z 156 " =    2.961
peak=    3.015 closest distance to " CB  SER A  62 " =    0.828

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.261 - 5.897
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 223
   mapped sites are within: 0.709 - 5.897

peak=   -4.529 closest distance to " CB  PRO A 243 " =    2.649
peak=   -4.522 closest distance to " O   HOH Z 377 " =    1.888
peak=   -4.383 closest distance to " OE1 GLN A 223 " =    2.406
peak=   -4.366 closest distance to " O   PRO A 198 " =    1.288
peak=   -4.265 closest distance to " CG1 VAL A 250 " =    2.641
peak=   -4.254 closest distance to " CD  ARG A  14 " =    3.583
peak=   -4.110 closest distance to " O   HOH Z 216 " =    1.158
peak=   -4.075 closest distance to " O   HOH Z  73 " =    2.162
peak=   -4.056 closest distance to " N   ALA A  43 " =    2.674
peak=   -4.022 closest distance to " O   HOH Z 231 " =    2.163
peak=   -3.955 closest distance to " CD  ARG A 156 " =    2.169
peak=   -3.955 closest distance to " CG1 VAL A 112 " =    2.583
peak=   -3.930 closest distance to " CE2 TYR A  30 " =    2.644
peak=   -3.928 closest distance to " OD1 ASP A 171 " =    1.697
peak=   -3.928 closest distance to " OE1 GLN A  88 " =    1.134
peak=   -3.927 closest distance to " CD2 LEU A 143 " =    2.595
peak=   -3.888 closest distance to " O   HOH Z 111 " =    1.615
peak=   -3.863 closest distance to " CD  GLN A  88 " =    0.904
peak=   -3.862 closest distance to " O   HOH Z 103 " =    1.702
peak=   -3.854 closest distance to " CD2 TYR A 293 " =    1.895
peak=   -3.851 closest distance to " CB  HIS A  86 " =    1.153
peak=   -3.842 closest distance to " CD  GLN A  58 " =    0.916
peak=   -3.839 closest distance to " CG2 ILE A  49 " =    2.845
peak=   -3.829 closest distance to " C   ASN A 285 " =    2.579
peak=   -3.820 closest distance to " CB  ALA A  43 " =    2.710
peak=   -3.797 closest distance to " O   HOH Z  38 " =    1.317
peak=   -3.783 closest distance to " CB  ASP A 286 " =    2.046
peak=   -3.781 closest distance to " O   HOH Z 359 " =    3.117
peak=   -3.771 closest distance to " O   HOH Z  69 " =    1.669
peak=   -3.767 closest distance to " CD1 PHE A  59 " =    2.041
peak=   -3.753 closest distance to " O   HOH Z 357 " =    2.047
peak=   -3.746 closest distance to " O   HOH Z 407 " =    3.234
peak=   -3.744 closest distance to " O   HOH Z 275 " =    1.778
peak=   -3.740 closest distance to " O   HOH Z 114 " =    1.231
peak=   -3.738 closest distance to " O   HOH Z  52 " =    1.435
peak=   -3.718 closest distance to " O   HOH Z 145 " =    0.709
peak=   -3.699 closest distance to " CA  GLY A 241 " =    2.374
peak=   -3.686 closest distance to " O   ALA A  10 " =    1.791
peak=   -3.685 closest distance to " O   HOH Z 290 " =    1.312
peak=   -3.681 closest distance to " OG  SER A  97 " =    2.300
peak=   -3.676 closest distance to " CD2 LEU A 237 " =    2.932
peak=   -3.669 closest distance to " OG BSER A 134 " =    1.502
peak=   -3.665 closest distance to " CZ3 TRP A 179 " =    1.140
peak=   -3.661 closest distance to " O   HOH Z 207 " =    1.242
peak=   -3.658 closest distance to " O   HOH Z 196 " =    2.374
peak=   -3.656 closest distance to " CB  ASP A  27 " =    2.519
peak=   -3.656 closest distance to " O   PRO A 163 " =    2.046
peak=   -3.655 closest distance to " CG  GLU A  53 " =    1.348
peak=   -3.641 closest distance to " O   HOH Z 232 " =    1.902
peak=   -3.633 closest distance to " O   HOH Z  60 " =    1.224
peak=   -3.613 closest distance to " O   HOH Z 389 " =    2.025
peak=   -3.608 closest distance to " O   GLY A 211 " =    1.328
peak=   -3.605 closest distance to " O   VAL A 189 " =    2.631
peak=   -3.603 closest distance to " O   HOH Z 198 " =    1.904
peak=   -3.588 closest distance to " CB  ALA A 129 " =    2.466
peak=   -3.587 closest distance to " CG  MET A 105 " =    0.983
peak=   -3.585 closest distance to " O   HOH Z 118 " =    1.027
peak=   -3.583 closest distance to " O   VAL A 125 " =    2.271
peak=   -3.581 closest distance to " N   THR A  52 " =    1.686
peak=   -3.569 closest distance to " O   PHE A 218 " =    1.528
peak=   -3.567 closest distance to " CE2 PHE A  61 " =    2.750
peak=   -3.564 closest distance to " O   HOH Z 426 " =    1.586
peak=   -3.550 closest distance to " O   HOH Z 231 " =    0.903
peak=   -3.544 closest distance to " O   HOH Z 128 " =    2.812
peak=   -3.533 closest distance to " O   HOH Z 337 " =    1.451
peak=   -3.533 closest distance to " C   ALA A 158 " =    1.621
peak=   -3.521 closest distance to " O   HOH Z  11 " =    2.235
peak=   -3.521 closest distance to " CA  GLY A 241 " =    2.999
peak=   -3.520 closest distance to " O   HOH Z  51 " =    1.662
peak=   -3.514 closest distance to " NH2AARG A 275 " =    5.758
peak=   -3.512 closest distance to " O   HOH Z  53 " =    1.700
peak=   -3.507 closest distance to " O   VAL A  67 " =    2.872
peak=   -3.486 closest distance to " CG2 THR A  52 " =    3.167
peak=   -3.480 closest distance to " CG  ARG A 269 " =    2.460
peak=   -3.479 closest distance to " CA  VAL A  67 " =    3.058
peak=   -3.474 closest distance to " NZ  LYS A 166 " =    1.199
peak=   -3.471 closest distance to " CD  GLN A  55 " =    1.057
peak=   -3.468 closest distance to " ND2 ASN A 249 " =    2.262
peak=   -3.463 closest distance to " CE BMET A  47 " =    1.708
peak=   -3.462 closest distance to " O   HOH Z  65 " =    1.149
peak=   -3.462 closest distance to " O   HOH Z 394 " =    1.603
peak=   -3.460 closest distance to " O   GLY A  17 " =    1.227
peak=   -3.452 closest distance to " O   GLN A 240 " =    2.598
peak=   -3.452 closest distance to " O   HOH Z 174 " =    2.517
peak=   -3.449 closest distance to " CG2 THR A 178 " =    2.287
peak=   -3.446 closest distance to " O   HOH Z 368 " =    1.754
peak=   -3.441 closest distance to " CB  TRP A  85 " =    2.525
peak=   -3.432 closest distance to " O   HOH Z   9 " =    1.747
peak=   -3.429 closest distance to " OG  SER A  62 " =    4.529
peak=   -3.429 closest distance to " O   ASN A 187 " =    1.628
peak=   -3.420 closest distance to " ND2 ASN A  45 " =    2.120
peak=   -3.419 closest distance to " C   LEU A 222 " =    0.957
peak=   -3.416 closest distance to " CA  GLY A  98 " =    2.050
peak=   -3.414 closest distance to " CG  PRO A 163 " =    2.309
peak=   -3.407 closest distance to " N   THR A 157 " =    1.633
peak=   -3.406 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.405 closest distance to " O   HOH Z 281 " =    2.690
peak=   -3.402 closest distance to " CE1 PHE A  38 " =    2.758
peak=   -3.402 closest distance to " NH2 ARG A  79 " =    1.625
peak=   -3.396 closest distance to " CE  MET A 105 " =    2.474
peak=   -3.395 closest distance to " ND2 ASN A  60 " =    3.926
peak=   -3.382 closest distance to " O   HOH Z 166 " =    1.737
peak=   -3.376 closest distance to " CE2 PHE A 218 " =    2.453
peak=   -3.373 closest distance to " OG ASER A 134 " =    1.287
peak=   -3.371 closest distance to " CA  GLY A 133 " =    2.244
peak=   -3.371 closest distance to " NH2BARG A 275 " =    1.915
peak=   -3.370 closest distance to " CB  ALA A 291 " =    2.200
peak=   -3.368 closest distance to " CD1 LEU A 101 " =    2.329
peak=   -3.367 closest distance to " O   HOH Z 106 " =    2.039
peak=   -3.362 closest distance to " O   HOH Z 357 " =    2.039
peak=   -3.361 closest distance to " O   HOH Z 318 " =    1.905
peak=   -3.360 closest distance to " C   LEU A 143 " =    1.333
peak=   -3.357 closest distance to " CB  ALA A  10 " =    2.213
peak=   -3.355 closest distance to " NE2 GLN A  11 " =    1.639
peak=   -3.351 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.347 closest distance to " O   HOH Z 421 " =    3.149
peak=   -3.346 closest distance to " CA  GLY A 203 " =    2.468
peak=   -3.344 closest distance to " OD1 ASN A 148 " =    1.564
peak=   -3.344 closest distance to " CG2 ILE A 263 " =    2.430
peak=   -3.344 closest distance to " O   HOH Z 116 " =    4.309
peak=   -3.344 closest distance to " CE1 PHE A 225 " =    2.026
peak=   -3.342 closest distance to " C   HIS A 108 " =    1.114
peak=   -3.335 closest distance to " CB  PRO A  54 " =    2.559
peak=   -3.334 closest distance to " N   SER A 141 " =    1.931
peak=   -3.331 closest distance to " OG  SER A  87 " =    1.432
peak=   -3.329 closest distance to " O   HOH Z  99 " =    0.828
peak=   -3.327 closest distance to " CG1 VAL A 112 " =    2.587
peak=   -3.322 closest distance to " OG  SER A  28 " =    2.263
peak=   -3.320 closest distance to " OH  TYR A 172 " =    1.826
peak=   -3.317 closest distance to " O   HOH Z 351 " =    1.542
peak=   -3.313 closest distance to " O   HOH Z  11 " =    1.768
peak=   -3.310 closest distance to " CG1 VAL A 125 " =    1.809
peak=   -3.309 closest distance to " O   HOH Z 115 " =    1.463
peak=   -3.309 closest distance to " O   HOH Z 241 " =    1.472
peak=   -3.308 closest distance to " CB  ASN A  39 " =    2.286
peak=   -3.307 closest distance to " CB  ASP A 132 " =    2.293
peak=   -3.306 closest distance to " ND2 ASN A  69 " =    1.819
peak=   -3.301 closest distance to " O   HOH Z 198 " =    1.337
peak=   -3.297 closest distance to " CG2 VAL A 202 " =    2.438
peak=   -3.297 closest distance to " CD2 HIS A 207 " =    2.201
peak=   -3.292 closest distance to " O   HOH Z 298 " =    2.483
peak=   -3.283 closest distance to " CZ  PHE A 130 " =    1.196
peak=   -3.276 closest distance to " CD  LYS A 289 " =    2.286
peak=   -3.273 closest distance to " O   ILE A 109 " =    2.619
peak=   -3.273 closest distance to " O   HOH Z 313 " =    1.875
peak=   -3.272 closest distance to " O   HOH Z 275 " =    1.634
peak=   -3.267 closest distance to " CG  LEU A 282 " =    2.503
peak=   -3.267 closest distance to " O   SER A 210 " =    1.858
peak=   -3.265 closest distance to " SG BCYS A 201 " =    2.237
peak=   -3.264 closest distance to " CA  GLY A 241 " =    3.204
peak=   -3.261 closest distance to " O   GLY A  80 " =    2.581
peak=   -3.260 closest distance to " O   HOH Z  70 " =    2.138
peak=   -3.259 closest distance to " CG2 VAL A 189 " =    1.992
peak=   -3.258 closest distance to " O   HOH Z 411 " =    5.257
peak=   -3.252 closest distance to " O   HOH Z 131 " =    4.073
peak=   -3.248 closest distance to " CG1 VAL A 112 " =    3.055
peak=   -3.246 closest distance to " O   HOH Z 252 " =    3.941
peak=   -3.244 closest distance to " CB  PHE A 130 " =    1.261
peak=   -3.242 closest distance to " OG BSER A 134 " =    1.874
peak=   -3.241 closest distance to " CB  ALA A 100 " =    2.209
peak=   -3.240 closest distance to " SG BCYS A 201 " =    1.035
peak=   -3.240 closest distance to " O   HOH Z 177 " =    1.864
peak=   -3.239 closest distance to " SD  MET A 105 " =    2.603
peak=   -3.234 closest distance to " CG  TRP A 266 " =    1.708
peak=   -3.228 closest distance to " O   HOH Z  10 " =    1.522
peak=   -3.226 closest distance to " OE1 GLN A  77 " =    1.010
peak=   -3.226 closest distance to " O   HOH Z 171 " =    1.438
peak=   -3.225 closest distance to " O   HOH Z 133 " =    1.361
peak=   -3.225 closest distance to " O   HOH Z 390 " =    2.070
peak=   -3.223 closest distance to " O   HOH Z 118 " =    1.969
peak=   -3.220 closest distance to " O   SER A 135 " =    1.543
peak=   -3.217 closest distance to " CG2 ILE A 151 " =    2.659
peak=   -3.206 closest distance to " CE3 TRP A  70 " =    1.784
peak=   -3.205 closest distance to " CD1 LEU A 228 " =    2.383
peak=   -3.197 closest distance to " O   ARG A  56 " =    1.865
peak=   -3.193 closest distance to " O   HOH Z 266 " =    5.400
peak=   -3.192 closest distance to " OD2 ASP A  50 " =    1.725
peak=   -3.187 closest distance to " O   HOH Z 323 " =    1.522
peak=   -3.185 closest distance to " ND2 ASN A  45 " =    1.392
peak=   -3.184 closest distance to " O   HOH Z 166 " =    1.487
peak=   -3.184 closest distance to " CD1 LEU A   5 " =    2.610
peak=   -3.182 closest distance to " O   HOH Z 189 " =    2.519
peak=   -3.181 closest distance to " CB  PRO A 163 " =    2.488
peak=   -3.175 closest distance to " O   HOH Z 191 " =    5.897
peak=   -3.173 closest distance to " CG  MET A 188 " =    1.233
peak=   -3.168 closest distance to " O   HOH Z  32 " =    1.542
peak=   -3.165 closest distance to " NE2 GLN A 240 " =    1.574
peak=   -3.164 closest distance to " O   GLY A 203 " =    2.448
peak=   -3.164 closest distance to " O   HOH Z  85 " =    2.282
peak=   -3.158 closest distance to " CB  ASP A 132 " =    2.257
peak=   -3.156 closest distance to " O   HOH Z 374 " =    1.854
peak=   -3.154 closest distance to " C   ASP A 272 " =    2.523
peak=   -3.148 closest distance to " N   LYS A 166 " =    1.858
peak=   -3.146 closest distance to " O   HOH Z 128 " =    4.218
peak=   -3.145 closest distance to " O   HOH Z 193 " =    1.422
peak=   -3.144 closest distance to " N   GLY A  35 " =    1.545
peak=   -3.144 closest distance to " CD1 ILE A 199 " =    2.699
peak=   -3.142 closest distance to " OD2 ASP A 171 " =    1.950
peak=   -3.140 closest distance to " CB  TYR A  15 " =    2.340
peak=   -3.138 closest distance to " O   HOH Z 326 " =    5.060
peak=   -3.132 closest distance to " OH  TYR A 247 " =    1.750
peak=   -3.129 closest distance to " OE2 GLU A 152 " =    1.259
peak=   -3.122 closest distance to " O   HOH Z 219 " =    4.258
peak=   -3.110 closest distance to " CB  CYS A 254 " =    2.165
peak=   -3.109 closest distance to " O   HOH Z 198 " =    1.916
peak=   -3.105 closest distance to " O   HOH Z 154 " =    1.891
peak=   -3.104 closest distance to " O   HOH Z 368 " =    1.896
peak=   -3.098 closest distance to " CG  PRO A 163 " =    1.829
peak=   -3.096 closest distance to " O   HOH Z 353 " =    2.157
peak=   -3.093 closest distance to " O   HOH Z  71 " =    1.775
peak=   -3.092 closest distance to " O   HOH Z  22 " =    2.080
peak=   -3.089 closest distance to " CA  GLY A 287 " =    1.351
peak=   -3.087 closest distance to " O   HOH Z 371 " =    1.266
peak=   -3.082 closest distance to " N   ASP A 191 " =    1.211
peak=   -3.081 closest distance to " O   HOH Z   9 " =    2.639
peak=   -3.073 closest distance to " CZ  PHE A  38 " =    2.064
peak=   -3.069 closest distance to " CA  SER A 135 " =    1.216
peak=   -3.068 closest distance to " O   VAL A 189 " =    1.693
peak=   -3.061 closest distance to " O   HOH Z   1 " =    1.415
peak=   -3.039 closest distance to " O   HOH Z 364 " =    2.470

================= 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    :  0.4521 0.4425   6.261543e+00   6.244356e+00
   1_bss:  0.4417 0.4359   6.251049e+00   6.234870e+00
   1_xyz:  0.2932 0.3227   5.939938e+00   6.015879e+00
   1_adp:  0.2694 0.3268   5.893121e+00   6.028664e+00
   1_occ:  0.2689 0.3262   5.892647e+00   6.029265e+00
   2_bss:  0.2667 0.3256   5.893067e+00   6.030329e+00
   2_xyz:  0.1929 0.2450   5.612748e+00   5.794382e+00
   2_adp:  0.1708 0.2323   5.530193e+00   5.743258e+00
   2_occ:  0.1707 0.2321   5.529406e+00   5.742774e+00
   3_bss:  0.1704 0.2319   5.527243e+00   5.740503e+00
   3_xyz:  0.1481 0.2004   5.391874e+00   5.613018e+00
   3_adp:  0.1427 0.1922   5.354450e+00   5.570336e+00
   3_occ:  0.1425 0.1921   5.353795e+00   5.569771e+00
   4_bss:  0.1429 0.1919   5.354621e+00   5.569477e+00
   4_xyz:  0.1337 0.1814   5.299083e+00   5.518369e+00
   4_adp:  0.1327 0.1786   5.288569e+00   5.503138e+00
   4_occ:  0.1326 0.1786   5.288074e+00   5.502628e+00
   5_bss:  0.1326 0.1787   5.288087e+00   5.502837e+00
   5_xyz:  0.1207 0.1700   5.219971e+00   5.458179e+00
   5_adp:  0.1192 0.1695   5.212205e+00   5.454477e+00
   5_occ:  0.1191 0.1696   5.212116e+00   5.454500e+00
   5_bss:  0.1190 0.1695   5.212214e+00   5.454603e+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:  0.310  67.680   1.871  -3.304   4.674  -0.000   0.000   0.000
   1_xyz:  0.310  67.680   1.871  -3.304   4.674  -0.000   0.000   0.000
   1_adp:  0.310  67.680   1.871  -3.304   4.674  -0.000   0.000   0.000
   1_occ:  0.310  67.680   1.871  -3.304   4.674  -0.000   0.000   0.000
   2_bss:  0.339  77.024  -0.573  -2.683   1.735  -0.000   0.000   0.000
   2_xyz:  0.339  77.024  -0.573  -2.683   1.735  -0.000   0.000   0.000
   2_adp:  0.339  77.024  -0.573  -2.683   1.735  -0.000   0.000   0.000
   2_occ:  0.339  77.024  -0.573  -2.683   1.735  -0.000   0.000   0.000
   3_bss:  0.345  87.925  -1.202  -2.293   0.539  -0.000   0.000   0.000
   3_xyz:  0.345  87.925  -1.202  -2.293   0.539  -0.000   0.000   0.000
   3_adp:  0.345  87.925  -1.202  -2.293   0.539  -0.000   0.000   0.000
   3_occ:  0.345  87.925  -1.202  -2.293   0.539  -0.000   0.000   0.000
   4_bss:  0.334  80.001  -1.446  -2.219   0.084  -0.000   0.000   0.000
   4_xyz:  0.334  80.001  -1.446  -2.219   0.084  -0.000   0.000   0.000
   4_adp:  0.334  80.001  -1.446  -2.219   0.084  -0.000   0.000   0.000
   4_occ:  0.334  80.001  -1.446  -2.219   0.084  -0.000   0.000   0.000
   5_bss:  0.323  70.645  -1.688  -2.307  -0.234  -0.000  -0.000  -0.000
   5_xyz:  0.323  70.645  -1.688  -2.307  -0.234  -0.000  -0.000  -0.000
   5_adp:  0.323  70.645  -1.688  -2.307  -0.234  -0.000  -0.000  -0.000
   5_occ:  0.323  70.645  -1.688  -2.307  -0.234  -0.000  -0.000  -0.000
   5_bss:  0.323  70.648  -1.529  -2.111  -0.133  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.841 0.4717  0.6105    61036.907
   1_bss:  52.718 0.4856  0.6604    59326.798
   1_xyz:  33.415 0.7203  0.9334    27881.831
   1_adp:  34.364 0.7086  0.9179    28945.179
   1_occ:  34.447 0.7075  0.9161    28979.543
   2_bss:  34.326 0.7091  0.8705    29014.578
   2_xyz:  24.441 0.8167  0.9595    15531.003
   2_adp:  22.709 0.8349  0.9637    13953.465
   2_occ:  22.697 0.8350  0.9635    13923.918
   3_bss:  22.608 0.8358  0.9478    13817.560
   3_xyz:  19.184 0.8690  0.9681    10260.417
   3_adp:  18.086 0.8796  0.9681     9454.907
   3_occ:  18.073 0.8797  0.9682     9440.160
   4_bss:  18.064 0.8798  0.9613     9428.433
   4_xyz:  16.849 0.8908  0.9660     8341.323
   4_adp:  16.434 0.8948  0.9644     8110.503
   4_occ:  16.426 0.8949  0.9645     8101.180
   5_bss:  16.429 0.8949  0.9572     8102.959
   5_xyz:  15.426 0.9034  0.9632     7359.711
   5_adp:  15.317 0.9045  0.9587     7284.748
   5_occ:  15.317 0.9045  0.9586     7281.933
   5_bss:  15.320 0.9045  0.9637     7283.306
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6231e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6231e-01
   1_xyz:   1.543  0.013  0.098 16.328  0.006  4.121   1.4478e-01
   1_adp:   1.543  0.013  0.098 16.328  0.006  4.121   1.4478e-01
   1_occ:   1.543  0.013  0.098 16.328  0.006  4.121   1.4478e-01
   2_bss:   1.543  0.013  0.098 16.328  0.006  4.121   1.4478e-01
   2_xyz:   1.203  0.009  0.087 14.814  0.005  4.116   7.9468e-02
   2_adp:   1.203  0.009  0.087 14.814  0.005  4.116   7.9468e-02
   2_occ:   1.203  0.009  0.087 14.814  0.005  4.116   7.9468e-02
   3_bss:   1.203  0.009  0.087 14.814  0.005  4.116   7.9468e-02
   3_xyz:   1.005  0.008  0.071 14.629  0.003  4.127   6.0598e-02
   3_adp:   1.005  0.008  0.071 14.629  0.003  4.127   6.0598e-02
   3_occ:   1.005  0.008  0.071 14.629  0.003  4.127   6.0598e-02
   4_bss:   1.005  0.008  0.071 14.629  0.003  4.127   6.0598e-02
   4_xyz:   0.975  0.007  0.073 14.232  0.003  4.116   5.6381e-02
   4_adp:   0.975  0.007  0.073 14.232  0.003  4.116   5.6381e-02
   4_occ:   0.975  0.007  0.073 14.232  0.003  4.116   5.6381e-02
   5_bss:   0.975  0.007  0.073 14.232  0.003  4.116   5.6381e-02
   5_xyz:   1.194  0.012  0.085 14.664  0.004  4.124   8.5257e-02
   5_adp:   1.194  0.012  0.085 14.664  0.004  4.124   8.5257e-02
   5_occ:   1.194  0.012  0.085 14.664  0.004  4.124   8.5257e-02
   5_bss:   1.194  0.012  0.085 14.664  0.004  4.124   8.5257e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4450e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4450e-01
   1_xyz:  11.281  0.114  0.324 83.177  0.053  2.068   2.7138e-01
   1_adp:  11.281  0.114  0.324 83.177  0.053  2.068   2.7138e-01
   1_occ:  11.281  0.114  0.324 83.177  0.053  2.068   2.7138e-01
   2_bss:  11.281  0.114  0.324 83.177  0.053  2.068   2.7138e-01
   2_xyz:   7.119  0.046  0.262 80.409  0.046  2.267   5.3921e-02
   2_adp:   7.119  0.046  0.262 80.409  0.046  2.267   5.3921e-02
   2_occ:   7.119  0.046  0.262 80.409  0.046  2.267   5.3921e-02
   3_bss:   7.119  0.046  0.262 80.409  0.046  2.267   5.3921e-02
   3_xyz:   9.096  0.043  0.243 83.126  0.042  2.342   4.8144e-02
   3_adp:   9.096  0.043  0.243 83.126  0.042  2.342   4.8144e-02
   3_occ:   9.096  0.043  0.243 83.126  0.042  2.342   4.8144e-02
   4_bss:   9.096  0.043  0.243 83.126  0.042  2.342   4.8144e-02
   4_xyz:   8.099  0.039  0.235 81.135  0.035  2.432   4.5482e-02
   4_adp:   8.099  0.039  0.235 81.135  0.035  2.432   4.5482e-02
   4_occ:   8.099  0.039  0.235 81.135  0.035  2.432   4.5482e-02
   5_bss:   8.099  0.039  0.235 81.135  0.035  2.432   4.5482e-02
   5_xyz:   8.511  0.061  0.270 82.586  0.038  2.310   6.9335e-02
   5_adp:   8.511  0.061  0.270 82.586  0.038  2.310   6.9335e-02
   5_occ:   8.511  0.061  0.270 82.586  0.038  2.310   6.9335e-02
   5_bss:   8.511  0.061  0.270 82.586  0.038  2.310   6.9335e-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:  98.13   0.00  17.19  98.13   0.00  13.25  65.02   1.85  38.66
   1_occ:  98.13   0.00  17.19  98.13   0.00  13.25  65.02   1.85  38.66
   2_bss:  98.13   0.00  17.19  98.13   0.00  13.25  65.02   1.85  38.66
   2_xyz:  98.13   0.00  17.19  98.13   0.00  13.25  65.02   1.85  38.66
   2_adp: 102.32   0.00  18.57  89.81   0.00  13.43 102.32   3.10  46.56
   2_occ: 102.32   0.00  18.57  89.81   0.00  13.43 102.32   3.10  46.56
   3_bss: 102.32   0.00  18.57  89.81   0.00  13.43 102.32   3.10  46.56
   3_xyz: 102.32   0.00  18.57  89.81   0.00  13.43 102.32   3.10  46.56
   3_adp: 102.83   0.00  18.02  86.83   0.00  12.98 102.83   4.73  45.46
   3_occ: 102.83   0.00  18.02  86.83   0.00  12.98 102.83   4.73  45.46
   4_bss: 102.83   0.00  18.02  86.83   0.00  12.98 102.83   4.73  45.46
   4_xyz: 102.83   0.00  18.02  86.83   0.00  12.98 102.83   4.73  45.46
   4_adp: 102.52   0.62  17.54  83.14   0.62  12.77 102.52   5.06  43.49
   4_occ: 102.52   0.62  17.54  83.14   0.62  12.77 102.52   5.06  43.49
   5_bss: 102.52   0.62  17.54  83.14   0.62  12.77 102.52   5.06  43.49
   5_xyz: 102.52   0.62  17.54  83.14   0.62  12.77 102.52   5.06  43.49
   5_adp: 108.43   0.00  17.47  85.17   0.00  12.71 108.43   5.03  43.37
   5_occ: 108.43   0.00  17.47  85.17   0.00  12.71 108.43   5.03  43.37
   5_bss: 108.43   0.00  17.47  85.18   0.00  12.71 108.43   5.04  43.37
------------------------------------------------------------------------
 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:    1.450    0.022    0.462
   1_adp:    1.450    0.022    0.462
   1_occ:    1.450    0.022    0.462
   2_bss:    1.450    0.022    0.462
   2_xyz:    1.393    0.022    0.582
   2_adp:    1.393    0.022    0.582
   2_occ:    1.393    0.022    0.582
   3_bss:    1.393    0.022    0.582
   3_xyz:    1.348    0.051    0.641
   3_adp:    1.348    0.051    0.641
   3_occ:    1.348    0.051    0.641
   4_bss:    1.348    0.051    0.641
   4_xyz:    1.417    0.028    0.666
   4_adp:    1.417    0.028    0.666
   4_occ:    1.417    0.028    0.666
   5_bss:    1.417    0.028    0.666
   5_xyz:    1.388    0.037    0.685
   5_adp:    1.388    0.037    0.685
   5_occ:    1.388    0.037    0.685
   5_bss:    1.388    0.037    0.685
------------------------------------------------------------------------

CPU time actual refinement: 354.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1264/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_1264/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1264/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1264/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1264/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.59 
  Macro-tasks:
    bulk solvent and scale       = 54.35  
    individual site refinement   = 140.54 
    weights calculation          = 29.73  
    collect and process          = 6.63   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 231.38 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 109.94 
    alpha_beta                      = 8.20   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 117.88 
    fmodel                         = 8.96   
    r_factors                      = 0.32   
    phase_errors                   = 10.90  
    foms                           = 0.35   
    TOTAL for micro-tasks          = 259.54 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.014 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    631 calls, 109.69 s
gradients_fft:          576 calls, 104.57 s

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

# Date 2008-01-16 Time 06:49:50 PST -0800 (1200494990.39 s)
Start R-work = 0.4521, R-free = 0.4425 (no bulk solvent and anisotropic scale)
Final R-work = 0.1397, R-free = 0.1866 (no bulk solvent and anisotropic scale)

Start R-work = 0.4417, R-free = 0.4359
Final R-work = 0.1190, R-free = 0.1695