# Date 2008-01-16 Time 05:40:22 PST -0800 (1200490822.35 s)
#phil __OFF__

Command line arguments: "../829.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28088
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 829

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.8686, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.9913
Completeness in resolution range: 0.955235
Completeness with d_max=infinity: 0.952263

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9913

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.9913
Completeness in resolution range: 0.955235
Completeness with d_max=infinity: 0.952263

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2606 [2154/2182]  1939   215  10.0%
  bin  2:  4.2606 -  3.3946 [2063/2086]  1855   208  10.1%
  bin  3:  3.3946 -  2.9692 [2047/2069]  1842   205  10.0%
  bin  4:  2.9692 -  2.6995 [2019/2038]  1824   195   9.7%
  bin  5:  2.6995 -  2.5069 [2021/2050]  1811   210  10.4%
  bin  6:  2.5069 -  2.3597 [1976/2017]  1789   187   9.5%
  bin  7:  2.3597 -  2.2419 [1986/2021]  1783   203  10.2%
  bin  8:  2.2419 -  2.1446 [1996/2034]  1794   202  10.1%
  bin  9:  2.1446 -  2.0623 [1981/2013]  1788   193   9.7%
  bin 10:  2.0623 -  1.9913 [1346/1997]  1205   141  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_829/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.78 -     2.41: 13
        2.41 -     3.03: 2078
        3.03 -     3.65: 4597
        3.65 -     4.28: 8972
        4.28 -     4.90: 12396
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.781 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.794 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.870 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.072 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28051 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_829/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_829/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.8686 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3827   r_free= 0.3673   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.184476                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7519 0.99   1395  154 0.3174 0.3425      6.4416      6.4308|
|  2:  4.7519 -  3.7916 0.99   1356  148 0.3174 0.3346      6.6722      6.6612|
|  3:  3.7916 -  3.3182 0.99   1318  155 0.3431 0.3053      6.5349      6.4685|
|  4:  3.3182 -  3.0175 0.99   1315  138 0.3583 0.3337      6.3965      6.2918|
|  5:  3.0175 -  2.8027 0.99   1294  147 0.3868 0.3540      6.2704      6.2649|
|  6:  2.8027 -  2.6384 0.98   1295  149 0.4140 0.3700      6.1952      6.0525|
|  7:  2.6384 -  2.5069 0.99   1298  142 0.4168 0.3536      6.1649       6.051|
|  8:  2.5069 -  2.3983 0.99   1282  143 0.4274 0.4224       6.095       6.094|
|  9:  2.3983 -  2.3063 0.98   1298  137 0.4401 0.4160       6.059       6.092|
| 10:  2.3063 -  2.2269 0.98   1265  146 0.4278 0.4273      6.0293      6.0241|
| 11:  2.2269 -  2.1575 0.98   1269  140 0.4336 0.3595      5.9815      5.9138|
| 12:  2.1575 -  2.0960 0.99   1262  141 0.4239 0.4516      5.9088      5.9608|
| 13:  2.0960 -  2.0410 0.97   1266  138 0.4393 0.4155      5.8203      5.8071|
| 14:  2.0410 -  1.9913 0.56    717   81 0.4029 0.4092      5.7378      5.6906|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7519  1395   154  0.74  30.47   0.85     0.77      57661.44|
|  2:  4.7519 -  3.7916  1356   148  0.79  27.37   0.94     0.86      67180.32|
|  3:  3.7916 -  3.3182  1318   155  0.74  31.94   0.94     0.88      66954.38|
|  4:  3.3182 -  3.0175  1315   138  0.70  35.26   0.95     0.86      56948.47|
|  5:  3.0175 -  2.8027  1294   147  0.66  39.32   0.94     0.83      46096.56|
|  6:  2.8027 -  2.6384  1295   149  0.65  40.09   0.94     0.82      38117.27|
|  7:  2.6384 -  2.5069  1298   142  0.64  40.53   0.96     0.82      35056.02|
|  8:  2.5069 -  2.3983  1282   143  0.59  44.84   0.95     0.79      35924.83|
|  9:  2.3983 -  2.3063  1298   137  0.57  46.52   0.94     0.77      35440.13|
| 10:  2.3063 -  2.2269  1265   146  0.57  46.74   0.98     0.77      33484.56|
| 11:  2.2269 -  2.1575  1269   140  0.58  46.23   0.98     0.80      30386.24|
| 12:  2.1575 -  2.0960  1262   141  0.57  46.69   1.00     0.81      28226.39|
| 13:  2.0960 -  2.0410  1266   138  0.55  48.68   0.96     0.78      24706.03|
| 14:  2.0410 -  1.9913   717    81  0.56  47.46   1.00     0.75      20334.88|
|alpha:            min =        0.75 max =            0.88 mean =         0.81|
|beta:             min =    20334.88 max =        67180.32 mean =     42180.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.99 mean =        40.49|
|phase err.(test): min =        0.00 max =           89.91 mean =        40.54|
|-----------------------------------------------------------------------------|

============================== 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 = 5.321486              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.579   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.097553              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.475   (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 |  1.781 -  2.093:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.093 -  2.405:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.405 -  2.717:      144 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.717 -  3.029:     1934 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.029 -  3.341:     1861 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.341 -  3.653:     2736 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.653 -  3.964:     4636 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.964 -  4.276:     4336 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.276 -  4.588:     5638 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.588 -  4.900:     6758 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.781 |       0.202 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.127)------------------------------------------|
|    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 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3827   r_free= 0.3673   ksol= 0.00   Bsol= 0.00   scale= 0.931    |
|                                                                             |
| 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:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.184476                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3679   r_free= 0.3529   ksol= 0.30   Bsol= 34.99   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,5.37,-1.65,0.00,-0.00,-0.00); trace/3= 0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.164354                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.909401              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.365   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.569112              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.340   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3679      final r-factor (work) = 0.2800          |
| start r-factor (free) = 0.3529      final r-factor (free) = 0.3056          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3015 = 4.91 * 0.50 * 6.1663 + 1.00 * 0.1652                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7714 = 4.91 * 0.50 * 5.9782 + 1.00 * 0.0967                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2800      final r-factor (work) = 0.2560          |
| start r-factor (free) = 0.3056      final r-factor (free) = 0.3156          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4082 = 0.57 * 1.00 * 5.9782 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3546 = 0.57 * 1.00 * 5.8737 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.127)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.23   17.10    None  None   None       |
|    all(noH): 2823   0      0.00    90.23   17.10    None  None   None       |
|    Sol.    : 438    0      1.72    90.23   36.14    None  None   None       |
|    Mac.    : 2385   0      0.00    76.46   13.60    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 -   9.023:  868   |   5:    45.115 -  54.138:   87        |
|      1:     9.023 -  18.046: 1050   |   6:    54.138 -  63.161:   45        |
|      2:    18.046 -  27.069:  404   |   7:    63.161 -  72.184:   21        |
|      3:    27.069 -  36.092:  200   |   8:    72.184 -  81.207:   12        |
|      4:    36.092 -  45.115:  135   |   9:    81.207 -  90.230:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2560 r_free = 0.3156             target_work(ml) = 5.881         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2558 r_free = 0.3153             target_work(ml) = 5.880         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2558   r_free= 0.3153   ksol= 0.30   Bsol= 34.99   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.00,5.37,-1.65,0.00,-0.00,-0.00); trace/3= 0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.880438                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2542   r_free= 0.3126   ksol= 0.32   Bsol= 59.07   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,2.10,-0.97,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.877600                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.077193              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.585   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.314732              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.313  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2542      final r-factor (work) = 0.2046          |
| start r-factor (free) = 0.3126      final r-factor (free) = 0.2501          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1321 = 3.08 * 0.50 * 5.8725 + 1.00 * 0.0967                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9573 = 3.08 * 0.50 * 5.7808 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2046      final r-factor (work) = 0.1940          |
| start r-factor (free) = 0.2501      final r-factor (free) = 0.2394          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8312 = 0.31 * 1.00 * 5.7808 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7903 = 0.31 * 1.00 * 5.6387 + 1.00 * 0.0156                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.127)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.03   16.88    None  None   None       |
|    all(noH): 2823   0      0.00    90.03   16.88    None  None   None       |
|    Sol.    : 438    0      3.99    90.03   37.80    None  None   None       |
|    Mac.    : 2385   0      0.00    79.17   13.04    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 -   9.003:  939   |   5:    45.014 -  54.017:  107        |
|      1:     9.003 -  18.006: 1071   |   6:    54.017 -  63.020:   45        |
|      2:    18.006 -  27.009:  330   |   7:    63.020 -  72.023:   29        |
|      3:    27.009 -  36.011:  172   |   8:    72.023 -  81.026:    9        |
|      4:    36.011 -  45.014:  119   |   9:    81.026 -  90.028:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1940 r_free = 0.2394             target_work(ml) = 5.624         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1938 r_free = 0.2396             target_work(ml) = 5.624         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1938   r_free= 0.2396   ksol= 0.32   Bsol= 59.07   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,2.10,-0.97,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.623706                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1936   r_free= 0.2389   ksol= 0.32   Bsol= 62.11   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.65,-0.78,0.00,-0.00,-0.00); trace/3= -0.65                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.623001                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.719685              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.951   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334502              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.351   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1936      final r-factor (work) = 0.1485          |
| start r-factor (free) = 0.2389      final r-factor (free) = 0.1885          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7307 = 2.72 * 0.50 * 5.6388 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5375 = 2.72 * 0.50 * 5.4993 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1485      final r-factor (work) = 0.1395          |
| start r-factor (free) = 0.1885      final r-factor (free) = 0.1818          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8499 = 0.33 * 1.00 * 5.4993 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0200 = 0.33 * 1.00 * 5.3427 + 1.00 * 0.2329                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.127)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.80   16.64    None  None   None       |
|    all(noH): 2823   0      0.00    88.80   16.64    None  None   None       |
|    Sol.    : 438    0      4.44    88.80   38.68    None  None   None       |
|    Mac.    : 2385   0      0.00    80.57   12.60    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 -   8.880:  950   |   5:    44.400 -  53.280:  113        |
|      1:     8.880 -  17.760: 1103   |   6:    53.280 -  62.160:   54        |
|      2:    17.760 -  26.640:  287   |   7:    62.160 -  71.040:   31        |
|      3:    26.640 -  35.520:  151   |   8:    71.040 -  79.921:    9        |
|      4:    35.520 -  44.400:  122   |   9:    79.921 -  88.801:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1395 r_free = 0.1818             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1393 r_free = 0.1816             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1816   ksol= 0.32   Bsol= 62.11   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.82,0.65,-0.78,0.00,-0.00,-0.00); trace/3= -0.65                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.324026                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1396   r_free= 0.1819   ksol= 0.32   Bsol= 60.80   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-0.36,-0.77,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.325018                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.728487              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.748  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.479818              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.851   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1396      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1819      final r-factor (free) = 0.1699          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6784 = 1.73 * 0.50 * 5.3446 + 1.00 * 0.0593                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6191 = 1.73 * 0.50 * 5.2832 + 1.00 * 0.0531                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1699      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1882 = 2.48 * 1.00 * 5.2832 + 1.00 * 0.0869                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9831 = 2.48 * 1.00 * 5.2305 + 1.00 * 0.0123                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.127)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.33  17.03    None  None   None       |
|    all(noH): 2823   0      0.00    102.33  17.03    None  None   None       |
|    Sol.    : 438    0      4.63    96.85   42.43    None  None   None       |
|    Mac.    : 2385   0      0.00    102.33  12.36    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: 1250   |   5:    51.167 -  61.401:   90        |
|      1:    10.233 -  20.467:  969   |   6:    61.401 -  71.634:   61        |
|      2:    20.467 -  30.700:  192   |   7:    71.634 -  81.867:   23        |
|      3:    30.700 -  40.934:  121   |   8:    81.867 -  92.101:    9        |
|      4:    40.934 -  51.167:  104   |   9:    92.101 - 102.334:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1228 r_free = 0.1685             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1228 r_free = 0.1685             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1685   ksol= 0.32   Bsol= 60.80   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-0.36,-0.77,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.223638                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1685   ksol= 0.32   Bsol= 65.79   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-0.52,-0.51,-0.00,-0.00,-0.00); trace/3= -0.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.223467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.736802              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.550  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.635078              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.589   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2105 = 2.74 * 0.50 * 5.2305 + 1.00 * 0.0531                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1734 = 2.74 * 0.50 * 5.1926 + 1.00 * 0.0678                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3098 = 0.64 * 1.00 * 5.1926 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2946 = 0.64 * 1.00 * 5.1704 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.127)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.91  16.51    None  None   None       |
|    all(noH): 2823   0      0.00    106.91  16.51    None  None   None       |
|    Sol.    : 438    0      4.67    96.13   40.99    None  None   None       |
|    Mac.    : 2385   0      0.00    106.91  12.01    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 -  10.691: 1396   |   5:    53.455 -  64.146:   80        |
|      1:    10.691 -  21.382:  857   |   6:    64.146 -  74.837:   35        |
|      2:    21.382 -  32.073:  198   |   7:    74.837 -  85.528:   16        |
|      3:    32.073 -  42.764:  120   |   8:    85.528 -  96.219:    6        |
|      4:    42.764 -  53.455:  112   |   9:    96.219 - 106.910:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1615             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1615             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1615   ksol= 0.32   Bsol= 65.79   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-0.52,-0.51,-0.00,-0.00,-0.00); trace/3= -0.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.164928                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7519 0.99   1395  154 0.0968 0.1287      5.3632      5.5314|
|  2:  4.7519 -  3.7916 0.99   1356  148 0.0822 0.1040      5.3998      5.5857|
|  3:  3.7916 -  3.3182 0.99   1318  155 0.1025 0.1503       5.454      5.8456|
|  4:  3.3182 -  3.0175 0.99   1315  138 0.1254 0.1641      5.4788       5.649|
|  5:  3.0175 -  2.8027 0.99   1294  147 0.1356 0.1833      5.3656      5.5628|
|  6:  2.8027 -  2.6384 0.98   1295  149 0.1295 0.1977      5.2644      5.4852|
|  7:  2.6384 -  2.5069 0.99   1298  142 0.1260 0.1691      5.1815      5.4269|
|  8:  2.5069 -  2.3983 0.99   1282  143 0.1197 0.1801      5.1003      5.3242|
|  9:  2.3983 -  2.3063 0.98   1298  137 0.1207 0.1768      5.0554      5.3452|
| 10:  2.3063 -  2.2269 0.98   1265  146 0.1163 0.1906      4.9972      5.2559|
| 11:  2.2269 -  2.1575 0.98   1269  140 0.1165 0.1783      4.9506      5.2638|
| 12:  2.1575 -  2.0960 0.99   1262  141 0.1125 0.1690      4.8951      5.1487|
| 13:  2.0960 -  2.0410 0.97   1266  138 0.1177 0.1819      4.8176      5.1206|
| 14:  2.0410 -  1.9913 0.56    717   81 0.1146 0.1799      4.7333      4.9431|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7519  1395   154  0.94   8.90   0.97     0.94       6976.02|
|  2:  4.7519 -  3.7916  1356   148  0.95   7.89   1.00     0.99       8538.49|
|  3:  3.7916 -  3.3182  1318   155  0.94  10.95   1.02     1.01      10047.63|
|  4:  3.3182 -  3.0175  1315   138  0.91  14.56   1.00     0.98      10963.88|
|  5:  3.0175 -  2.8027  1294   147  0.89  16.93   1.00     0.97       9147.60|
|  6:  2.8027 -  2.6384  1295   149  0.89  16.86   0.98     0.96       7890.90|
|  7:  2.6384 -  2.5069  1298   142  0.90  16.04   0.99     0.96       6492.03|
|  8:  2.5069 -  2.3983  1282   143  0.90  16.26   0.99     0.95       5868.43|
|  9:  2.3983 -  2.3063  1298   137  0.90  16.03   0.99     0.94       5203.45|
| 10:  2.3063 -  2.2269  1265   146  0.90  16.31   0.98     0.94       4834.97|
| 11:  2.2269 -  2.1575  1269   140  0.90  16.62   0.98     0.93       4423.63|
| 12:  2.1575 -  2.0960  1262   141  0.91  15.51   0.99     0.97       4096.71|
| 13:  2.0960 -  2.0410  1266   138  0.89  16.93   0.98     0.97       3608.60|
| 14:  2.0410 -  1.9913   717    81  0.90  16.15   0.95     0.91       2916.50|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2916.50 max =        10963.88 mean =      6652.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.59|
|phase err.(test): min =        0.00 max =           89.53 mean =        14.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1614   ksol= 0.32   Bsol= 65.79   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.52,-0.32,-0.00,-0.00,-0.00); trace/3= -0.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166535                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1614   ksol= 0.32   Bsol= 65.79   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,-0.52,-0.32,-0.00,-0.00,-0.00); trace/3= -0.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.166535                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7519 0.99   1395  154 0.0979 0.1262      5.3779      5.5336|
|  2:  4.7519 -  3.7916 0.99   1356  148 0.0834 0.1043      5.4094      5.5974|
|  3:  3.7916 -  3.3182 0.99   1318  155 0.1025 0.1504      5.4553      5.8411|
|  4:  3.3182 -  3.0175 0.99   1315  138 0.1252 0.1631      5.4761      5.6431|
|  5:  3.0175 -  2.8027 0.99   1294  147 0.1356 0.1828      5.3642      5.5596|
|  6:  2.8027 -  2.6384 0.98   1295  149 0.1295 0.1974      5.2637      5.4846|
|  7:  2.6384 -  2.5069 0.99   1298  142 0.1262 0.1694      5.1815      5.4285|
|  8:  2.5069 -  2.3983 0.99   1282  143 0.1196 0.1796      5.1008      5.3242|
|  9:  2.3983 -  2.3063 0.98   1298  137 0.1204 0.1766      5.0552      5.3447|
| 10:  2.3063 -  2.2269 0.98   1265  146 0.1163 0.1906       4.997      5.2561|
| 11:  2.2269 -  2.1575 0.98   1269  140 0.1164 0.1783      4.9501      5.2635|
| 12:  2.1575 -  2.0960 0.99   1262  141 0.1123 0.1697      4.8951      5.1506|
| 13:  2.0960 -  2.0410 0.97   1266  138 0.1177 0.1818       4.818      5.1199|
| 14:  2.0410 -  1.9913 0.56    717   81 0.1145 0.1795      4.7326      4.9418|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7519  1395   154  0.94   9.33   0.97     0.94       7272.13|
|  2:  4.7519 -  3.7916  1356   148  0.95   8.04   1.01     0.99       8728.87|
|  3:  3.7916 -  3.3182  1318   155  0.94  10.98   1.02     1.02      10092.85|
|  4:  3.3182 -  3.0175  1315   138  0.91  14.49   1.01     0.98      10862.96|
|  5:  3.0175 -  2.8027  1294   147  0.89  16.85   1.00     0.97       9084.04|
|  6:  2.8027 -  2.6384  1295   149  0.89  16.84   0.99     0.96       7877.87|
|  7:  2.6384 -  2.5069  1298   142  0.90  16.05   0.99     0.96       6498.06|
|  8:  2.5069 -  2.3983  1282   143  0.90  16.28   0.99     0.96       5879.50|
|  9:  2.3983 -  2.3063  1298   137  0.90  16.04   0.99     0.95       5209.73|
| 10:  2.3063 -  2.2269  1265   146  0.90  16.31   0.99     0.95       4830.55|
| 11:  2.2269 -  2.1575  1269   140  0.90  16.62   0.99     0.94       4423.77|
| 12:  2.1575 -  2.0960  1262   141  0.91  15.52   1.00     0.98       4102.00|
| 13:  2.0960 -  2.0410  1266   138  0.89  16.93   0.99     0.98       3609.61|
| 14:  2.0410 -  1.9913   717    81  0.90  16.14   0.96     0.92       2908.48|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2908.48 max =        10862.96 mean =      6682.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.63|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.10|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.127)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.91  16.51    None  None   None       |
|    all(noH): 2823   0      0.00    106.91  16.51    None  None   None       |
|    Sol.    : 438    0      4.67    96.13   40.99    None  None   None       |
|    Mac.    : 2385   0      0.00    106.91  12.01    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 -  10.694: 1396   |   5:    53.458 -  64.149:   80        |
|      1:    10.694 -  21.385:  857   |   6:    64.149 -  74.840:   35        |
|      2:    21.385 -  32.076:  198   |   7:    74.840 -  85.531:   16        |
|      3:    32.076 -  42.767:  120   |   8:    85.531 -  96.222:    6        |
|      4:    42.767 -  53.458:  112   |   9:    96.222 - 106.913:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.641 - 4.676
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 314
   mapped sites are within: 0.705 - 4.676

peak=    5.991 closest distance to " NH2 ARG A  56 " =    2.369
peak=    5.561 closest distance to " CB  SER A  63 " =    1.203
peak=    5.375 closest distance to " CB  GLN A 223 " =    1.415
peak=    5.370 closest distance to " O   HOH Z 210 " =    1.086
peak=    5.168 closest distance to " CG  PRO A  54 " =    1.274
peak=    4.934 closest distance to " O   HOH Z 403 " =    1.794
peak=    4.839 closest distance to " CB  GLN A 183 " =    1.284
peak=    4.746 closest distance to " O   HOH Z  15 " =    2.169
peak=    4.722 closest distance to " C   PRO A 198 " =    1.530
peak=    4.719 closest distance to " CG  PRO A 213 " =    1.210
peak=    4.686 closest distance to " O   HOH Z 134 " =    1.616
peak=    4.668 closest distance to " O   HOH Z  43 " =    2.150
peak=    4.633 closest distance to " O   HOH Z 232 " =    2.357
peak=    4.596 closest distance to " CB  ARG A 190 " =    1.711
peak=    4.557 closest distance to " CA  TYR A  30 " =    0.931
peak=    4.494 closest distance to " O   HOH Z  40 " =    1.924
peak=    4.477 closest distance to " CB  PRO A  54 " =    0.860
peak=    4.463 closest distance to " O   HOH Z 369 " =    2.296
peak=    4.453 closest distance to " CG1 ILE A  33 " =    1.247
peak=    4.388 closest distance to " CB  ARG A 275 " =    0.865
peak=    4.383 closest distance to " O   HOH Z 189 " =    2.297
peak=    4.370 closest distance to " O   HOH Z 298 " =    1.977
peak=    4.355 closest distance to " O   HOH Z 209 " =    2.415
peak=    4.326 closest distance to " O   HOH Z 234 " =    3.837
peak=    4.304 closest distance to " O   HOH Z  63 " =    1.970
peak=    4.277 closest distance to " O   HOH Z 433 " =    1.496
peak=    4.276 closest distance to " CD  ARG A 269 " =    0.932
peak=    4.275 closest distance to " O   HOH Z 402 " =    1.546
peak=    4.265 closest distance to " CB  GLU A 128 " =    1.154
peak=    4.241 closest distance to " CB  TYR A 169 " =    0.839
peak=    4.230 closest distance to " O   HOH Z  80 " =    1.727
peak=    4.181 closest distance to " O   SER A  87 " =    2.246
peak=    4.170 closest distance to " O   HOH Z 352 " =    1.901
peak=    4.169 closest distance to " CG  PRO A 198 " =    1.211
peak=    4.166 closest distance to " O   HOH Z  68 " =    2.031
peak=    4.159 closest distance to " CB  SER A 141 " =    1.045
peak=    4.155 closest distance to " CB  ARG A  79 " =    1.366
peak=    4.146 closest distance to " CB  GLU A 152 " =    1.152
peak=    4.124 closest distance to " O   HOH Z  20 " =    1.689
peak=    4.119 closest distance to " OD1 ASN A  69 " =    2.516
peak=    4.108 closest distance to " NH2BARG A 145 " =    2.088
peak=    4.088 closest distance to " O   HOH Z  97 " =    1.974
peak=    4.084 closest distance to " O   HOH Z 133 " =    2.481
peak=    4.078 closest distance to " NH2 ARG A 156 " =    1.209
peak=    4.066 closest distance to " CB  LEU A 228 " =    1.153
peak=    4.052 closest distance to " CG  PRO A  90 " =    1.105
peak=    4.044 closest distance to " O   HOH Z 412 " =    3.583
peak=    4.028 closest distance to " CG  ARG A  66 " =    2.586
peak=    4.026 closest distance to " CB  GLU A 277 " =    3.701
peak=    4.022 closest distance to " O   HOH Z 368 " =    2.073
peak=    4.021 closest distance to " O   HOH Z 128 " =    2.162
peak=    4.016 closest distance to " O   HOH Z  44 " =    1.922
peak=    4.015 closest distance to " CG  PRO A 280 " =    0.705
peak=    4.000 closest distance to " O   HOH Z 423 " =    1.915
peak=    3.997 closest distance to " O   HOH Z 265 " =    2.188
peak=    3.990 closest distance to " CA  ALA A  51 " =    0.985
peak=    3.987 closest distance to " CA  ARG A 195 " =    1.184
peak=    3.982 closest distance to " CA  ALA A  21 " =    1.395
peak=    3.972 closest distance to " O   HOH Z 361 " =    3.600
peak=    3.961 closest distance to " O   HOH Z 389 " =    2.036
peak=    3.956 closest distance to " O   ALA A 165 " =    1.299
peak=    3.955 closest distance to " NZ  LYS A 117 " =    3.120
peak=    3.949 closest distance to " CB  TRP A 179 " =    1.389
peak=    3.940 closest distance to " O   HOH Z 357 " =    2.083
peak=    3.918 closest distance to " O   HOH Z  59 " =    2.449
peak=    3.908 closest distance to " O   HOH Z 284 " =    2.980
peak=    3.908 closest distance to " CG2 THR A 221 " =    1.112
peak=    3.906 closest distance to " O   HOH Z 108 " =    2.821
peak=    3.869 closest distance to " O   HOH Z 418 " =    1.528
peak=    3.867 closest distance to " O   HOH Z  61 " =    1.549
peak=    3.859 closest distance to " O   HOH Z 163 " =    1.640
peak=    3.854 closest distance to " CD  LYS A 166 " =    1.371
peak=    3.830 closest distance to " CD2 TRP A 179 " =    1.356
peak=    3.827 closest distance to " O   HOH Z 374 " =    2.777
peak=    3.826 closest distance to " CB  VAL A 202 " =    1.502
peak=    3.826 closest distance to " O   HOH Z 193 " =    1.900
peak=    3.812 closest distance to " CG  PRO A 243 " =    1.177
peak=    3.809 closest distance to " CB  SER A   3 " =    1.353
peak=    3.762 closest distance to " CA  ASP A 191 " =    0.865
peak=    3.756 closest distance to " CB  TRP A 266 " =    0.954
peak=    3.750 closest distance to " O   HOH Z 426 " =    1.484
peak=    3.742 closest distance to " ND2 ASN A 187 " =    1.540
peak=    3.737 closest distance to " OG BSER A 164 " =    2.359
peak=    3.733 closest distance to " O   HOH Z 247 " =    1.419
peak=    3.730 closest distance to " CD1 LEU A 300 " =    1.187
peak=    3.725 closest distance to " O   HOH Z 132 " =    2.744
peak=    3.722 closest distance to " CB  ASP A 140 " =    0.904
peak=    3.721 closest distance to " O   HOH Z  78 " =    1.619
peak=    3.720 closest distance to " O   HOH Z 291 " =    1.522
peak=    3.715 closest distance to " NE2 GLN A  11 " =    1.105
peak=    3.714 closest distance to " O   THR A 251 " =    1.202
peak=    3.710 closest distance to " O   HOH Z 214 " =    2.510
peak=    3.697 closest distance to " O   HOH Z 421 " =    1.772
peak=    3.692 closest distance to " CB  ASN A  39 " =    0.892
peak=    3.690 closest distance to " O   HOH Z 102 " =    1.258
peak=    3.688 closest distance to " O   HOH Z 425 " =    1.305
peak=    3.687 closest distance to " C   ILE A 106 " =    1.892
peak=    3.680 closest distance to " O   HOH Z 279 " =    2.199
peak=    3.673 closest distance to " NZ  LYS A 117 " =    1.865
peak=    3.669 closest distance to " CB  ASN A 148 " =    1.294
peak=    3.662 closest distance to " O   HOH Z  49 " =    1.935
peak=    3.653 closest distance to " CB  SER A  62 " =    0.770
peak=    3.652 closest distance to " O   HOH Z 406 " =    1.542
peak=    3.650 closest distance to " CZ  PHE A 218 " =    1.096
peak=    3.642 closest distance to " CG2BVAL A  41 " =    0.862
peak=    3.639 closest distance to " O   HOH Z 180 " =    2.238
peak=    3.637 closest distance to " O   HOH Z  30 " =    1.249
peak=    3.636 closest distance to " O   HOH Z 371 " =    3.370
peak=    3.628 closest distance to " CA  ASN A 176 " =    1.498
peak=    3.622 closest distance to " O   HOH Z  21 " =    1.783
peak=    3.619 closest distance to " OE1 GLU A   2 " =    2.052
peak=    3.614 closest distance to " O   HOH Z 147 " =    1.785
peak=    3.612 closest distance to " CG1BVAL A  72 " =    1.784
peak=    3.611 closest distance to " C   SER A  32 " =    1.054
peak=    3.610 closest distance to " O   HOH Z 126 " =    1.582
peak=    3.605 closest distance to " O   HOH Z 185 " =    1.734
peak=    3.604 closest distance to " OE1 GLN A  11 " =    1.976
peak=    3.595 closest distance to " CA  ARG A  36 " =    1.112
peak=    3.592 closest distance to " O   ASN A  74 " =    1.603
peak=    3.591 closest distance to " O   HOH Z 365 " =    2.849
peak=    3.588 closest distance to " O   HOH Z 386 " =    2.224
peak=    3.586 closest distance to " NZ  LYS A 166 " =    3.070
peak=    3.580 closest distance to " O   HOH Z  88 " =    3.480
peak=    3.575 closest distance to " O   HOH Z 345 " =    1.654
peak=    3.574 closest distance to " O   HOH Z 346 " =    1.511
peak=    3.562 closest distance to " O   HOH Z 174 " =    2.416
peak=    3.559 closest distance to " O   HOH Z 432 " =    1.647
peak=    3.558 closest distance to " O   HOH Z 245 " =    1.391
peak=    3.553 closest distance to " CA  ALA A 160 " =    0.885
peak=    3.551 closest distance to " CA  ASP A 162 " =    1.184
peak=    3.539 closest distance to " O   HOH Z 316 " =    3.002
peak=    3.533 closest distance to " CB  ALA A  71 " =    1.322
peak=    3.532 closest distance to " O   HOH Z 435 " =    2.955
peak=    3.527 closest distance to " O   HOH Z 383 " =    2.134
peak=    3.527 closest distance to " O   HOH Z 303 " =    2.234
peak=    3.524 closest distance to " CB  ALA A 291 " =    1.323
peak=    3.523 closest distance to " N   ASN A  39 " =    1.379
peak=    3.504 closest distance to " O   HOH Z 287 " =    1.890
peak=    3.503 closest distance to " O   HOH Z 299 " =    4.477
peak=    3.491 closest distance to " O   HOH Z 387 " =    2.590
peak=    3.490 closest distance to " O   HOH Z 403 " =    1.554
peak=    3.480 closest distance to " CG  GLN A  58 " =    2.543
peak=    3.478 closest distance to " O   HOH Z 250 " =    1.420
peak=    3.477 closest distance to " O   HOH Z 344 " =    3.246
peak=    3.475 closest distance to " CB  ASN A 285 " =    0.929
peak=    3.466 closest distance to " O   HOH Z 402 " =    2.994
peak=    3.464 closest distance to " OG1 THR A 294 " =    2.415
peak=    3.456 closest distance to " CZ  PHE A  38 " =    1.351
peak=    3.455 closest distance to " O   HOH Z 126 " =    2.002
peak=    3.454 closest distance to " O   HOH Z 158 " =    2.953
peak=    3.452 closest distance to " O   ALA A 158 " =    1.225
peak=    3.452 closest distance to " O   HOH Z 145 " =    2.263
peak=    3.451 closest distance to " CG2 VAL A 197 " =    1.102
peak=    3.444 closest distance to " CA  ASP A 124 " =    0.737
peak=    3.443 closest distance to " CG AARG A 275 " =    1.146
peak=    3.443 closest distance to " CA  LYS A 117 " =    1.267
peak=    3.442 closest distance to " O   HOH Z 128 " =    2.149
peak=    3.438 closest distance to " O   HOH Z 214 " =    1.330
peak=    3.436 closest distance to " OG  SER A  62 " =    2.976
peak=    3.433 closest distance to " O   GLY A  57 " =    2.690
peak=    3.430 closest distance to " CD2 LEU A 297 " =    0.788
peak=    3.430 closest distance to " O   HOH Z 427 " =    3.031
peak=    3.429 closest distance to " O   HOH Z  19 " =    1.728
peak=    3.426 closest distance to " CB  ASN A 142 " =    1.192
peak=    3.423 closest distance to " O   HOH Z 124 " =    2.006
peak=    3.420 closest distance to " CA  ALA A 295 " =    1.144
peak=    3.418 closest distance to " O   HOH Z 144 " =    1.928
peak=    3.411 closest distance to " O   HOH Z 189 " =    2.907
peak=    3.411 closest distance to " CA  THR A 221 " =    0.957
peak=    3.408 closest distance to " O   HOH Z 345 " =    2.981
peak=    3.406 closest distance to " OD2 ASP A 286 " =    2.896
peak=    3.405 closest distance to " CA  VAL A 125 " =    1.315
peak=    3.403 closest distance to " O   HOH Z 130 " =    2.208
peak=    3.403 closest distance to " O   HOH Z 250 " =    1.726
peak=    3.402 closest distance to " O   HOH Z 261 " =    1.652
peak=    3.400 closest distance to " O   HOH Z 437 " =    1.431
peak=    3.397 closest distance to " O   ASP A 124 " =    1.557
peak=    3.396 closest distance to " O   HOH Z  66 " =    2.127
peak=    3.396 closest distance to " O   HOH Z 173 " =    2.259
peak=    3.394 closest distance to " CB  ARG A 139 " =    0.943
peak=    3.393 closest distance to " CD  ARG A 195 " =    0.937
peak=    3.383 closest distance to " CA  THR A 221 " =    1.443
peak=    3.382 closest distance to " CB  ASN A 187 " =    1.149
peak=    3.379 closest distance to " O   HOH Z 394 " =    1.669
peak=    3.375 closest distance to " O   HOH Z 197 " =    2.022
peak=    3.373 closest distance to " CB  MET A  40 " =    0.846
peak=    3.372 closest distance to " O   HOH Z 422 " =    2.546
peak=    3.363 closest distance to " O   HOH Z 155 " =    3.242
peak=    3.360 closest distance to " O   HOH Z 380 " =    1.768
peak=    3.359 closest distance to " CB  LEU A  83 " =    0.853
peak=    3.358 closest distance to " CB  ALA A 100 " =    1.353
peak=    3.350 closest distance to " O   HOH Z 419 " =    1.592
peak=    3.339 closest distance to " O   HOH Z 409 " =    3.084
peak=    3.339 closest distance to " O   HOH Z 427 " =    2.997
peak=    3.334 closest distance to " CE1 HIS A 115 " =    3.765
peak=    3.333 closest distance to " CG2 ILE A 120 " =    0.970
peak=    3.332 closest distance to " CE1 TYR A 186 " =    1.166
peak=    3.332 closest distance to " CA  VAL A  41 " =    0.863
peak=    3.329 closest distance to " O   HOH Z 150 " =    1.547
peak=    3.326 closest distance to " OD2 ASP A 298 " =    4.030
peak=    3.322 closest distance to " CB  TYR A 116 " =    1.077
peak=    3.322 closest distance to " O   HOH Z 142 " =    1.465
peak=    3.321 closest distance to " CD  ARG A  66 " =    2.667
peak=    3.317 closest distance to " OG  SER A 276 " =    1.509
peak=    3.317 closest distance to " CB  PRO A 198 " =    1.027
peak=    3.311 closest distance to " CG2 VAL A  78 " =    0.943
peak=    3.309 closest distance to " O   HOH Z 358 " =    2.007
peak=    3.306 closest distance to " OG  SER A 245 " =    1.601
peak=    3.305 closest distance to " O   HOH Z 196 " =    1.191
peak=    3.304 closest distance to " CB  ALA A   9 " =    1.573
peak=    3.301 closest distance to " CG  MET A 185 " =    1.128
peak=    3.300 closest distance to " O   HOH Z  64 " =    2.296
peak=    3.295 closest distance to " O   HOH Z 227 " =    1.633
peak=    3.291 closest distance to " ND1 HIS A  81 " =    1.558
peak=    3.283 closest distance to " C   GLY A  80 " =    1.087
peak=    3.281 closest distance to " O   HOH Z  48 " =    1.474
peak=    3.281 closest distance to " CD1 LEU A  96 " =    0.762
peak=    3.280 closest distance to " O   HOH Z 295 " =    1.502
peak=    3.280 closest distance to " CG2 ILE A  20 " =    1.410
peak=    3.279 closest distance to " O   HOH Z 255 " =    1.788
peak=    3.277 closest distance to " O   HOH Z 133 " =    1.521
peak=    3.273 closest distance to " O   HOH Z   1 " =    2.672
peak=    3.271 closest distance to " NH2AARG A 275 " =    3.533
peak=    3.271 closest distance to " CG2AVAL A 121 " =    2.216
peak=    3.267 closest distance to " O   HOH Z 393 " =    3.365
peak=    3.260 closest distance to " O   HOH Z 124 " =    1.279
peak=    3.257 closest distance to " CZ3 TRP A  85 " =    0.953
peak=    3.253 closest distance to " CD  PRO A  54 " =    1.082
peak=    3.253 closest distance to " O   HOH Z 258 " =    2.214
peak=    3.248 closest distance to " O   HOH Z  54 " =    1.574
peak=    3.246 closest distance to " O   HOH Z  44 " =    3.216
peak=    3.245 closest distance to " O   HOH Z 299 " =    2.433
peak=    3.244 closest distance to " CB  THR A 157 " =    1.108
peak=    3.239 closest distance to " O   HOH Z 282 " =    2.053
peak=    3.237 closest distance to " CA  LEU A  83 " =    1.377
peak=    3.235 closest distance to " O   HOH Z 272 " =    1.914
peak=    3.234 closest distance to " O   HOH Z 434 " =    1.461
peak=    3.233 closest distance to " CD  ARG A 159 " =    0.850
peak=    3.232 closest distance to " O   HOH Z 109 " =    2.524
peak=    3.232 closest distance to " NH1AARG A 145 " =    1.189
peak=    3.229 closest distance to " CA  SER A  32 " =    1.607
peak=    3.224 closest distance to " CA  GLU A 152 " =    0.903
peak=    3.224 closest distance to " CA  ASP A 140 " =    1.225
peak=    3.221 closest distance to " O   HOH Z 327 " =    2.313
peak=    3.217 closest distance to " O   HOH Z 162 " =    1.628
peak=    3.217 closest distance to " O   HOH Z 421 " =    2.448
peak=    3.215 closest distance to " O   HOH Z 327 " =    1.626
peak=    3.213 closest distance to " CB  GLN A 103 " =    0.883
peak=    3.212 closest distance to " O   HOH Z 417 " =    3.114
peak=    3.209 closest distance to " N   ASP A 132 " =    1.193
peak=    3.203 closest distance to " CG  GLU A  37 " =    0.921
peak=    3.201 closest distance to " CB  ASN A 148 " =    1.617
peak=    3.200 closest distance to " CA  GLY A 241 " =    0.854
peak=    3.199 closest distance to " CA  ILE A  33 " =    1.533
peak=    3.197 closest distance to " O   HOH Z 118 " =    1.033
peak=    3.197 closest distance to " O   HOH Z 334 " =    1.453
peak=    3.195 closest distance to " O   HOH Z 327 " =    1.969
peak=    3.195 closest distance to " O   HOH Z 353 " =    2.779
peak=    3.193 closest distance to " O   THR A 220 " =    1.135
peak=    3.193 closest distance to " N   CYS A 260 " =    0.801
peak=    3.192 closest distance to " O   HOH Z 281 " =    4.676
peak=    3.191 closest distance to " C   TYR A 214 " =    1.427
peak=    3.189 closest distance to " O   HOH Z 156 " =    2.596
peak=    3.186 closest distance to " CA  ALA A 100 " =    1.039
peak=    3.176 closest distance to " CA  ASN A 217 " =    1.324
peak=    3.175 closest distance to " CG2 THR A  29 " =    1.428
peak=    3.172 closest distance to " CA  ILE A 106 " =    0.818
peak=    3.170 closest distance to " CD BLYS A 290 " =    1.004
peak=    3.167 closest distance to " O   HOH Z 130 " =    1.144
peak=    3.167 closest distance to " CA  SER A  87 " =    1.018
peak=    3.162 closest distance to " O   HOH Z 329 " =    3.667
peak=    3.158 closest distance to " NZ  LYS A  48 " =    1.263
peak=    3.157 closest distance to " CD1 ILE A 199 " =    0.995
peak=    3.155 closest distance to " CB  MET A  47 " =    0.993
peak=    3.152 closest distance to " CA  MET A  40 " =    1.082
peak=    3.149 closest distance to " O   HOH Z 355 " =    1.664
peak=    3.149 closest distance to " NE2 HIS A 115 " =    1.030
peak=    3.148 closest distance to " CG  GLN A  11 " =    1.239
peak=    3.147 closest distance to " O   HOH Z  88 " =    1.717
peak=    3.146 closest distance to " CB  PHE A 283 " =    0.708
peak=    3.145 closest distance to " CB  MET A 105 " =    1.064
peak=    3.142 closest distance to " CA  ALA A  84 " =    1.234
peak=    3.141 closest distance to " CA  ALA A 291 " =    0.859
peak=    3.141 closest distance to " CD  LYS A 119 " =    1.732
peak=    3.139 closest distance to " O   HOH Z 227 " =    1.665
peak=    3.133 closest distance to " O   HOH Z 166 " =    3.695
peak=    3.121 closest distance to " ND2 ASN A 110 " =    1.554
peak=    3.120 closest distance to " O   HOH Z  47 " =    2.620
peak=    3.118 closest distance to " O   HOH Z  88 " =    2.895
peak=    3.118 closest distance to " CB  VAL A 257 " =    0.879
peak=    3.117 closest distance to " CB  VAL A 265 " =    1.257
peak=    3.116 closest distance to " CD  ARG A 139 " =    1.299
peak=    3.115 closest distance to " OH  TYR A 116 " =    1.161
peak=    3.115 closest distance to " NE1 TRP A 266 " =    1.315
peak=    3.114 closest distance to " N   TRP A 150 " =    1.043
peak=    3.109 closest distance to " CE  LYS A 119 " =    1.095
peak=    3.108 closest distance to " CB  SER A 273 " =    0.810
peak=    3.101 closest distance to " CB  LEU A   5 " =    1.089
peak=    3.095 closest distance to " CA  MET A 105 " =    1.095
peak=    3.095 closest distance to " O   HOH Z 261 " =    2.027
peak=    3.092 closest distance to " O   HOH Z 423 " =    3.385
peak=    3.092 closest distance to " O   ASN A  74 " =    1.508
peak=    3.079 closest distance to " CB  ARG A 138 " =    0.980
peak=    3.064 closest distance to " O   HOH Z 377 " =    1.178
peak=    3.062 closest distance to " O   HOH Z 294 " =    1.519
peak=    3.054 closest distance to " O   HOH Z 104 " =    2.557
peak=    3.053 closest distance to " N   ASN A 127 " =    1.241
peak=    3.053 closest distance to " OD2 ASP A 200 " =    1.297
peak=    3.050 closest distance to " O   TRP A 274 " =    1.850
peak=    3.039 closest distance to " CB  GLN A 278 " =    0.992
peak=    3.039 closest distance to " CG2 VAL A 257 " =    0.790

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 227         
Filter by distance & map next to the model:
   mapped sites are within: 0.869 - 5.991
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 227 from: 227
   mapped sites are within: 0.869 - 5.991

peak=   -5.006 closest distance to " O   HOH Z 266 " =    4.799
peak=   -4.356 closest distance to " O   HOH Z  13 " =    1.743
peak=   -4.333 closest distance to " O   PRO A 163 " =    2.129
peak=   -4.318 closest distance to " CD  ARG A 156 " =    2.054
peak=   -4.298 closest distance to " O   HOH Z  10 " =    1.617
peak=   -4.175 closest distance to " OXT GLY A 302 " =    2.971
peak=   -4.153 closest distance to " CB  PRO A 243 " =    2.682
peak=   -4.089 closest distance to " O   VAL A  67 " =    2.740
peak=   -4.024 closest distance to " O   HOH Z 166 " =    1.758
peak=   -3.989 closest distance to " O   HOH Z 283 " =    2.192
peak=   -3.967 closest distance to " CG1 VAL A 250 " =    2.714
peak=   -3.945 closest distance to " CA  ASP A 298 " =    1.050
peak=   -3.944 closest distance to " NH2 ARG A  66 " =    1.649
peak=   -3.940 closest distance to " CE2 TYR A  30 " =    2.691
peak=   -3.937 closest distance to " CD  GLN A 223 " =    1.349
peak=   -3.904 closest distance to " CD  GLN A  58 " =    1.101
peak=   -3.895 closest distance to " CD1 PHE A  59 " =    1.948
peak=   -3.877 closest distance to " O   VAL A  67 " =    2.914
peak=   -3.854 closest distance to " O   HOH Z 196 " =    2.268
peak=   -3.847 closest distance to " O   HOH Z 231 " =    2.380
peak=   -3.842 closest distance to " O   HOH Z 292 " =    4.567
peak=   -3.841 closest distance to " O   HOH Z 234 " =    4.340
peak=   -3.837 closest distance to " CG2 ILE A 263 " =    2.343
peak=   -3.832 closest distance to " O   PRO A 198 " =    1.336
peak=   -3.825 closest distance to " OD1 ASN A 148 " =    1.570
peak=   -3.822 closest distance to " C   HIS A 108 " =    1.126
peak=   -3.819 closest distance to " N   ALA A  43 " =    2.708
peak=   -3.819 closest distance to " O   HOH Z 377 " =    1.150
peak=   -3.812 closest distance to " OG  SER A  97 " =    2.229
peak=   -3.808 closest distance to " CB  PHE A 208 " =    2.335
peak=   -3.802 closest distance to " OD1 ASP A 191 " =    1.667
peak=   -3.802 closest distance to " CD  ARG A  14 " =    3.463
peak=   -3.794 closest distance to " CD1 LEU A 101 " =    2.527
peak=   -3.777 closest distance to " O   HOH Z 377 " =    2.162
peak=   -3.774 closest distance to " O   HOH Z  52 " =    1.606
peak=   -3.757 closest distance to " CH2 TRP A 179 " =    1.217
peak=   -3.740 closest distance to " CA  SER A 276 " =    1.534
peak=   -3.733 closest distance to " C   SER A 206 " =    1.521
peak=   -3.729 closest distance to " O   PHE A 218 " =    1.514
peak=   -3.726 closest distance to " OE1 GLN A 223 " =    2.352
peak=   -3.720 closest distance to " O   HOH Z 407 " =    3.595
peak=   -3.693 closest distance to " C   ASN A 285 " =    2.376
peak=   -3.686 closest distance to " O   HOH Z  71 " =    1.681
peak=   -3.674 closest distance to " O   HOH Z 252 " =    4.050
peak=   -3.666 closest distance to " CG  ASP A 132 " =    2.431
peak=   -3.656 closest distance to " CB  ALA A 161 " =    2.636
peak=   -3.652 closest distance to " CG  GLU A  53 " =    1.481
peak=   -3.640 closest distance to " ND2 ASN A  45 " =    1.790
peak=   -3.634 closest distance to " O   HOH Z 210 " =    0.877
peak=   -3.628 closest distance to " ND2 ASN A 187 " =    1.660
peak=   -3.627 closest distance to " ND2 ASN A  45 " =    1.140
peak=   -3.622 closest distance to " O   HOH Z 111 " =    1.468
peak=   -3.610 closest distance to " CD1 LEU A  25 " =    2.449
peak=   -3.610 closest distance to " O   HOH Z 394 " =    1.522
peak=   -3.590 closest distance to " O   SER A 210 " =    1.882
peak=   -3.589 closest distance to " CG2 ILE A  49 " =    2.717
peak=   -3.587 closest distance to " O   HOH Z 353 " =    2.312
peak=   -3.586 closest distance to " CD2 LEU A 300 " =    2.819
peak=   -3.581 closest distance to " O   HOH Z 185 " =    2.470
peak=   -3.575 closest distance to " O   HOH Z 165 " =    1.982
peak=   -3.568 closest distance to " CD  ARG A 139 " =    1.631
peak=   -3.560 closest distance to " N   GLN A  58 " =    1.495
peak=   -3.559 closest distance to " O   HOH Z 422 " =    1.407
peak=   -3.555 closest distance to " CD2 PHE A 225 " =    1.271
peak=   -3.538 closest distance to " O   HOH Z 150 " =    1.166
peak=   -3.532 closest distance to " NE2 GLN A 103 " =    1.714
peak=   -3.532 closest distance to " O   HOH Z  19 " =    2.085
peak=   -3.522 closest distance to " CB  ALA A  10 " =    2.118
peak=   -3.521 closest distance to " O   HOH Z 290 " =    1.092
peak=   -3.520 closest distance to " O   TRP A  92 " =    1.900
peak=   -3.518 closest distance to " O   HOH Z 351 " =    1.558
peak=   -3.517 closest distance to " O   HOH Z 150 " =    1.816
peak=   -3.510 closest distance to " O   ALA A  34 " =    2.494
peak=   -3.508 closest distance to " C   THR A 279 " =    1.109
peak=   -3.501 closest distance to " CG  ARG A 269 " =    2.375
peak=   -3.499 closest distance to " CD1 LEU A 228 " =    2.351
peak=   -3.498 closest distance to " O   HOH Z 426 " =    1.765
peak=   -3.492 closest distance to " OD1 ASN A 187 " =    1.726
peak=   -3.491 closest distance to " CG  ASP A 231 " =    0.869
peak=   -3.485 closest distance to " O   HOH Z 117 " =    4.475
peak=   -3.477 closest distance to " OE2 GLU A   2 " =    1.411
peak=   -3.472 closest distance to " OG BSER A 210 " =    1.260
peak=   -3.470 closest distance to " O   SER A 276 " =    1.627
peak=   -3.455 closest distance to " O   HOH Z 200 " =    1.356
peak=   -3.454 closest distance to " ND2 ASN A 249 " =    2.182
peak=   -3.452 closest distance to " O   ALA A  10 " =    1.732
peak=   -3.452 closest distance to " CE  MET A  93 " =    1.296
peak=   -3.451 closest distance to " CA  GLY A 133 " =    2.357
peak=   -3.450 closest distance to " OG  SER A  62 " =    1.552
peak=   -3.449 closest distance to " CE BMET A  47 " =    2.162
peak=   -3.445 closest distance to " O   ASN A 301 " =    1.338
peak=   -3.439 closest distance to " N   THR A 235 " =    1.305
peak=   -3.435 closest distance to " O   HOH Z 372 " =    2.526
peak=   -3.435 closest distance to " O   HOH Z 298 " =    2.735
peak=   -3.434 closest distance to " O   HOH Z  38 " =    1.494
peak=   -3.429 closest distance to " CB  PHE A 192 " =    1.904
peak=   -3.429 closest distance to " O   HOH Z 197 " =    2.021
peak=   -3.426 closest distance to " O   HOH Z 126 " =    1.982
peak=   -3.424 closest distance to " CA  GLY A 203 " =    2.237
peak=   -3.417 closest distance to " O   HOH Z 145 " =    2.037
peak=   -3.415 closest distance to " O   HOH Z  11 " =    1.858
peak=   -3.407 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.407 closest distance to " CB  ALA A 291 " =    2.371
peak=   -3.400 closest distance to " C   ALA A 158 " =    1.344
peak=   -3.396 closest distance to " CZ  PHE A  38 " =    1.949
peak=   -3.394 closest distance to " OD1 ASN A  39 " =    2.245
peak=   -3.393 closest distance to " O   GLY A  80 " =    2.636
peak=   -3.392 closest distance to " CG2 VAL A 189 " =    2.210
peak=   -3.389 closest distance to " O   HOH Z  37 " =    1.859
peak=   -3.384 closest distance to " O   ALA A   1 " =    1.982
peak=   -3.384 closest distance to " CE2 PHE A  61 " =    2.584
peak=   -3.384 closest distance to " OG BSER A 134 " =    1.288
peak=   -3.380 closest distance to " CG  ARG A 219 " =    2.501
peak=   -3.374 closest distance to " OG BSER A 210 " =    2.172
peak=   -3.374 closest distance to " OD2 ASP A 171 " =    1.887
peak=   -3.367 closest distance to " CG  PRO A 243 " =    1.723
peak=   -3.364 closest distance to " CD  ARG A 195 " =    5.063
peak=   -3.359 closest distance to " O   HOH Z  15 " =    1.506
peak=   -3.358 closest distance to " CD  GLN A  58 " =    1.345
peak=   -3.355 closest distance to " O   HOH Z 118 " =    3.594
peak=   -3.353 closest distance to " CD2 LEU A 167 " =    1.788
peak=   -3.352 closest distance to " ND2 ASN A  60 " =    1.581
peak=   -3.348 closest distance to " NH2 ARG A  66 " =    5.733
peak=   -3.348 closest distance to " O   HOH Z   6 " =    1.604
peak=   -3.347 closest distance to " O   HOH Z 283 " =    5.987
peak=   -3.347 closest distance to " NH2 ARG A  79 " =    2.036
peak=   -3.346 closest distance to " CZ3 TRP A 274 " =    2.435
peak=   -3.345 closest distance to " ND2BASN A 224 " =    1.893
peak=   -3.342 closest distance to " O   HOH Z 418 " =    1.291
peak=   -3.339 closest distance to " CB  ALA A 131 " =    2.324
peak=   -3.321 closest distance to " O   HOH Z 198 " =    2.263
peak=   -3.317 closest distance to " N   ALA A 248 " =    1.833
peak=   -3.316 closest distance to " CZ  TYR A 169 " =    1.836
peak=   -3.315 closest distance to " O   HOH Z 177 " =    1.756
peak=   -3.314 closest distance to " NH1 ARG A 195 " =    2.708
peak=   -3.313 closest distance to " CB  PRO A 163 " =    2.707
peak=   -3.306 closest distance to " O   HOH Z 136 " =    1.889
peak=   -3.301 closest distance to " O   HOH Z 150 " =    2.124
peak=   -3.300 closest distance to " CD1 LEU A 167 " =    2.081
peak=   -3.298 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.295 closest distance to " CB  CYS A 254 " =    2.558
peak=   -3.295 closest distance to " O   HOH Z 384 " =    2.164
peak=   -3.291 closest distance to " CA  GLY A  98 " =    2.192
peak=   -3.282 closest distance to " OH  TYR A 169 " =    0.998
peak=   -3.278 closest distance to " C   LEU A 143 " =    1.144
peak=   -3.277 closest distance to " O   HOH Z 409 " =    4.799
peak=   -3.268 closest distance to " O   VAL A 125 " =    2.187
peak=   -3.268 closest distance to " O   HOH Z 311 " =    3.675
peak=   -3.268 closest distance to " CD1 TRP A 179 " =    1.070
peak=   -3.266 closest distance to " O   HOH Z 171 " =    2.159
peak=   -3.265 closest distance to " O   HOH Z 414 " =    1.651
peak=   -3.260 closest distance to " O   VAL A 189 " =    2.594
peak=   -3.259 closest distance to " O   VAL A 174 " =    2.133
peak=   -3.257 closest distance to " O   HOH Z 128 " =    2.536
peak=   -3.257 closest distance to " O   HOH Z 393 " =    1.572
peak=   -3.255 closest distance to " O   HOH Z  91 " =    2.143
peak=   -3.254 closest distance to " OG BSER A 134 " =    1.874
peak=   -3.252 closest distance to " N   ALA A 226 " =    2.077
peak=   -3.245 closest distance to " O   HOH Z 166 " =    1.859
peak=   -3.235 closest distance to " O   HOH Z 264 " =    1.755
peak=   -3.232 closest distance to " CB  ASP A 162 " =    2.760
peak=   -3.231 closest distance to " CA  VAL A 197 " =    0.988
peak=   -3.226 closest distance to " CB  ALA A   9 " =    2.661
peak=   -3.220 closest distance to " O   HOH Z 222 " =    1.311
peak=   -3.218 closest distance to " CE3 TRP A 150 " =    2.070
peak=   -3.218 closest distance to " O   SER A  26 " =    1.524
peak=   -3.218 closest distance to " O   HOH Z  43 " =    1.444
peak=   -3.212 closest distance to " OE2 GLU A 152 " =    2.340
peak=   -3.208 closest distance to " O   HOH Z 252 " =    3.721
peak=   -3.207 closest distance to " CG1 VAL A  78 " =    2.705
peak=   -3.205 closest distance to " O   ALA A 160 " =    1.477
peak=   -3.205 closest distance to " CB  TRP A  85 " =    2.411
peak=   -3.205 closest distance to " NE2 GLN A  88 " =    1.898
peak=   -3.204 closest distance to " NH2 ARG A  66 " =    4.128
peak=   -3.198 closest distance to " CD2 PHE A  61 " =    2.058
peak=   -3.198 closest distance to " OG  SER A  87 " =    1.567
peak=   -3.198 closest distance to " NE2 GLN A 223 " =    1.273
peak=   -3.197 closest distance to " O   ASN A 187 " =    1.585
peak=   -3.195 closest distance to " OD2 ASP A 171 " =    2.332
peak=   -3.192 closest distance to " CD2 PHE A  59 " =    2.448
peak=   -3.190 closest distance to " O   ALA A  34 " =    2.112
peak=   -3.185 closest distance to " O   HOH Z 113 " =    2.227
peak=   -3.182 closest distance to " O   HOH Z 191 " =    5.854
peak=   -3.174 closest distance to " O   GLY A 196 " =    1.088
peak=   -3.171 closest distance to " O   HOH Z 236 " =    1.555
peak=   -3.170 closest distance to " O   HOH Z  56 " =    1.212
peak=   -3.168 closest distance to " OD1 ASP A 171 " =    1.531
peak=   -3.167 closest distance to " OG  SER A  26 " =    1.402
peak=   -3.162 closest distance to " O   HOH Z 134 " =    2.314
peak=   -3.160 closest distance to " CB  PHE A  16 " =    2.595
peak=   -3.159 closest distance to " O   HOH Z 423 " =    2.358
peak=   -3.154 closest distance to " CD2 TYR A 293 " =    1.937
peak=   -3.152 closest distance to " N   THR A  52 " =    1.679
peak=   -3.152 closest distance to " NH2 ARG A  66 " =    5.991
peak=   -3.148 closest distance to " O   HOH Z  90 " =    1.925
peak=   -3.148 closest distance to " NH2 ARG A 159 " =    2.348
peak=   -3.146 closest distance to " O   HOH Z 265 " =    2.220
peak=   -3.145 closest distance to " O   SER A 135 " =    1.572
peak=   -3.145 closest distance to " C   GLU A  46 " =    0.987
peak=   -3.143 closest distance to " NE2 GLN A 194 " =    1.825
peak=   -3.139 closest distance to " CD1 TYR A 247 " =    2.197
peak=   -3.138 closest distance to " CG1 VAL A 112 " =    2.586
peak=   -3.137 closest distance to " CH2 TRP A 177 " =    1.963
peak=   -3.136 closest distance to " O   HOH Z 361 " =    3.378
peak=   -3.131 closest distance to " NE2 GLN A  58 " =    1.156
peak=   -3.130 closest distance to " CB  ALA A  43 " =    2.532
peak=   -3.127 closest distance to " NE2 GLN A 223 " =    1.130
peak=   -3.127 closest distance to " N   LEU A 281 " =    1.814
peak=   -3.127 closest distance to " O   HOH Z 392 " =    1.412
peak=   -3.125 closest distance to " O   HOH Z 149 " =    1.824
peak=   -3.124 closest distance to " O   HOH Z 385 " =    3.826
peak=   -3.123 closest distance to " CG  TRP A 266 " =    1.861
peak=   -3.122 closest distance to " O   HOH Z  11 " =    1.910
peak=   -3.097 closest distance to " O   HOH Z 389 " =    1.679
peak=   -3.097 closest distance to " ND2 ASN A  69 " =    1.530
peak=   -3.088 closest distance to " OG ASER A 134 " =    1.257
peak=   -3.087 closest distance to " O   HOH Z  40 " =    2.975
peak=   -3.072 closest distance to " O   HOH Z 424 " =    2.954
peak=   -3.068 closest distance to " O   ARG A  24 " =    2.146
peak=   -3.062 closest distance to " O   HOH Z 198 " =    1.604
peak=   -3.061 closest distance to " C   ALA A 242 " =    2.026
peak=   -3.041 closest distance to " CG  ASN A 301 " =    2.053
peak=   -3.033 closest distance to " O   HOH Z  78 " =    1.770
peak=   -3.030 closest distance to " SD  MET A 188 " =    2.460
peak=   -3.017 closest distance to " O   HOH Z  97 " =    1.614
peak=   -3.006 closest distance to " O   HOH Z 111 " =    3.809
peak=   -3.003 closest distance to " CG1 VAL A 112 " =    3.059

================= 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    :  0.3827 0.3673   6.184476e+00   6.148737e+00
   1_bss:  0.3679 0.3529   6.164354e+00   6.124996e+00
   1_xyz:  0.2800 0.3056   5.931281e+00   6.001269e+00
   1_adp:  0.2560 0.3156   5.881440e+00   6.019350e+00
   1_occ:  0.2558 0.3153   5.880438e+00   6.019007e+00
   2_bss:  0.2542 0.3126   5.877600e+00   6.016175e+00
   2_xyz:  0.2046 0.2501   5.662209e+00   5.820200e+00
   2_adp:  0.1940 0.2394   5.624179e+00   5.786208e+00
   2_occ:  0.1938 0.2396   5.623706e+00   5.786014e+00
   3_bss:  0.1936 0.2389   5.623001e+00   5.783530e+00
   3_xyz:  0.1485 0.1885   5.374768e+00   5.571450e+00
   3_adp:  0.1395 0.1818   5.324819e+00   5.532837e+00
   3_occ:  0.1393 0.1816   5.324026e+00   5.531898e+00
   4_bss:  0.1396 0.1819   5.325018e+00   5.530688e+00
   4_xyz:  0.1274 0.1699   5.249590e+00   5.466749e+00
   4_adp:  0.1228 0.1685   5.223770e+00   5.451809e+00
   4_occ:  0.1228 0.1685   5.223638e+00   5.451756e+00
   5_bss:  0.1226 0.1685   5.223467e+00   5.451861e+00
   5_xyz:  0.1142 0.1637   5.174241e+00   5.422463e+00
   5_adp:  0.1132 0.1615   5.164903e+00   5.411001e+00
   5_occ:  0.1132 0.1615   5.164928e+00   5.411311e+00
   5_bss:  0.1134 0.1614   5.166535e+00   5.411415e+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:  0.295  34.989  -3.003   5.369  -1.651   0.000  -0.000  -0.000
   1_xyz:  0.295  34.989  -3.003   5.369  -1.651   0.000  -0.000  -0.000
   1_adp:  0.295  34.989  -3.003   5.369  -1.651   0.000  -0.000  -0.000
   1_occ:  0.295  34.989  -3.003   5.369  -1.651   0.000  -0.000  -0.000
   2_bss:  0.319  59.071  -2.112   2.098  -0.972   0.000  -0.000  -0.000
   2_xyz:  0.319  59.071  -2.112   2.098  -0.972   0.000  -0.000  -0.000
   2_adp:  0.319  59.071  -2.112   2.098  -0.972   0.000  -0.000  -0.000
   2_occ:  0.319  59.071  -2.112   2.098  -0.972   0.000  -0.000  -0.000
   3_bss:  0.319  62.110  -1.823   0.649  -0.779   0.000  -0.000  -0.000
   3_xyz:  0.319  62.110  -1.823   0.649  -0.779   0.000  -0.000  -0.000
   3_adp:  0.319  62.110  -1.823   0.649  -0.779   0.000  -0.000  -0.000
   3_occ:  0.319  62.110  -1.823   0.649  -0.779   0.000  -0.000  -0.000
   4_bss:  0.324  60.797  -1.908  -0.365  -0.767  -0.000  -0.000  -0.000
   4_xyz:  0.324  60.797  -1.908  -0.365  -0.767  -0.000  -0.000  -0.000
   4_adp:  0.324  60.797  -1.908  -0.365  -0.767  -0.000  -0.000  -0.000
   4_occ:  0.324  60.797  -1.908  -0.365  -0.767  -0.000  -0.000  -0.000
   5_bss:  0.325  65.788  -1.639  -0.523  -0.514  -0.000  -0.000  -0.000
   5_xyz:  0.325  65.788  -1.639  -0.523  -0.514  -0.000  -0.000  -0.000
   5_adp:  0.325  65.788  -1.639  -0.523  -0.514  -0.000  -0.000  -0.000
   5_occ:  0.325  65.788  -1.639  -0.523  -0.514  -0.000  -0.000  -0.000
   5_bss:  0.325  65.790  -1.411  -0.525  -0.323  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.491 0.6400  0.8105    42181.856
   1_bss:  39.519 0.6499  0.8240    38575.000
   1_xyz:  33.013 0.7248  0.8969    26798.219
   1_adp:  33.987 0.7129  0.8695    27968.419
   1_occ:  33.966 0.7131  0.8694    27921.339
   2_bss:  33.479 0.7189  0.8650    27537.611
   2_xyz:  25.415 0.8065  0.9455    16293.513
   2_adp:  23.892 0.8233  0.9481    15027.340
   2_occ:  23.888 0.8233  0.9480    15012.502
   3_bss:  23.758 0.8246  0.9400    14897.923
   3_xyz:  18.101 0.8793  0.9765     9135.535
   3_adp:  17.167 0.8881  0.9730     8532.414
   3_occ:  17.143 0.8883  0.9731     8517.418
   4_bss:  17.105 0.8886  0.9615     8489.255
   4_xyz:  15.719 0.9007  0.9681     7407.659
   4_adp:  15.358 0.9039  0.9622     7181.552
   4_occ:  15.355 0.9039  0.9622     7180.850
   5_bss:  15.352 0.9040  0.9668     7186.138
   5_xyz:  14.768 0.9087  0.9684     6768.851
   5_adp:  14.528 0.9108  0.9609     6648.464
   5_occ:  14.531 0.9108  0.9609     6653.179
   5_bss:  14.574 0.9104  0.9657     6683.013
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6520e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6520e-01
   1_xyz:   1.382  0.010  0.085 15.474  0.005  4.114   9.6734e-02
   1_adp:   1.382  0.010  0.085 15.474  0.005  4.114   9.6734e-02
   1_occ:   1.382  0.010  0.085 15.474  0.005  4.114   9.6734e-02
   2_bss:   1.382  0.010  0.085 15.474  0.005  4.114   9.6734e-02
   2_xyz:   1.100  0.007  0.071 14.138  0.004  4.127   6.2929e-02
   2_adp:   1.100  0.007  0.071 14.138  0.004  4.127   6.2929e-02
   2_occ:   1.100  0.007  0.071 14.138  0.004  4.127   6.2929e-02
   3_bss:   1.100  0.007  0.071 14.138  0.004  4.127   6.2929e-02
   3_xyz:   1.002  0.007  0.070 14.450  0.003  4.115   5.9319e-02
   3_adp:   1.002  0.007  0.070 14.450  0.003  4.115   5.9319e-02
   3_occ:   1.002  0.007  0.070 14.450  0.003  4.115   5.9319e-02
   4_bss:   1.002  0.007  0.070 14.450  0.003  4.115   5.9319e-02
   4_xyz:   0.956  0.006  0.071 14.135  0.003  4.121   5.3120e-02
   4_adp:   0.956  0.006  0.071 14.135  0.003  4.121   5.3120e-02
   4_occ:   0.956  0.006  0.071 14.135  0.003  4.121   5.3120e-02
   5_bss:   0.956  0.006  0.071 14.135  0.003  4.121   5.3120e-02
   5_xyz:   1.075  0.009  0.078 14.601  0.004  4.126   6.7834e-02
   5_adp:   1.075  0.009  0.078 14.601  0.004  4.126   6.7834e-02
   5_occ:   1.075  0.009  0.078 14.601  0.004  4.126   6.7834e-02
   5_bss:   1.075  0.009  0.078 14.601  0.004  4.126   6.7834e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.781   2.4271e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.781   2.4271e-01
   1_xyz:  10.117  0.079  0.480 88.116  0.027  2.182   9.7730e-02
   1_adp:  10.117  0.079  0.480 88.116  0.027  2.182   9.7730e-02
   1_occ:  10.117  0.079  0.480 88.116  0.027  2.182   9.7730e-02
   2_bss:  10.117  0.079  0.480 88.116  0.027  2.182   9.7730e-02
   2_xyz:   7.095  0.037  0.222 87.664  0.052  2.368   9.7485e-02
   2_adp:   7.095  0.037  0.222 87.664  0.052  2.368   9.7485e-02
   2_occ:   7.095  0.037  0.222 87.664  0.052  2.368   9.7485e-02
   3_bss:   7.095  0.037  0.222 87.664  0.052  2.368   9.7485e-02
   3_xyz:   7.293  0.055  0.243 84.392  0.023  2.315   4.5754e-02
   3_adp:   7.293  0.055  0.243 84.392  0.023  2.315   4.5754e-02
   3_occ:   7.293  0.055  0.243 84.392  0.023  2.315   4.5754e-02
   4_bss:   7.293  0.055  0.243 84.392  0.023  2.315   4.5754e-02
   4_xyz:   7.176  0.040  0.233 81.446  0.034  2.397   4.1492e-02
   4_adp:   7.176  0.040  0.233 81.446  0.034  2.397   4.1492e-02
   4_occ:   7.176  0.040  0.233 81.446  0.034  2.397   4.1492e-02
   5_bss:   7.176  0.040  0.233 81.446  0.034  2.397   4.1492e-02
   5_xyz:   8.161  0.045  0.262 82.028  0.030  2.309   4.8741e-02
   5_adp:   8.161  0.045  0.262 82.028  0.030  2.309   4.8741e-02
   5_occ:   8.161  0.045  0.262 82.028  0.030  2.309   4.8741e-02
   5_bss:   8.161  0.045  0.262 82.028  0.030  2.309   4.8741e-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:  90.23   0.00  17.10  76.46   0.00  13.60  90.23   1.72  36.14
   1_occ:  90.23   0.00  17.10  76.46   0.00  13.60  90.23   1.72  36.14
   2_bss:  90.23   0.00  17.10  76.46   0.00  13.60  90.23   1.72  36.14
   2_xyz:  90.23   0.00  17.10  76.46   0.00  13.60  90.23   1.72  36.14
   2_adp:  90.03   0.00  16.88  79.17   0.00  13.04  90.03   3.99  37.80
   2_occ:  90.03   0.00  16.88  79.17   0.00  13.04  90.03   3.99  37.80
   3_bss:  90.03   0.00  16.88  79.17   0.00  13.04  90.03   3.99  37.80
   3_xyz:  90.03   0.00  16.88  79.17   0.00  13.04  90.03   3.99  37.80
   3_adp:  88.80   0.00  16.64  80.57   0.00  12.60  88.80   4.44  38.68
   3_occ:  88.80   0.00  16.64  80.57   0.00  12.60  88.80   4.44  38.68
   4_bss:  88.80   0.00  16.64  80.57   0.00  12.60  88.80   4.44  38.68
   4_xyz:  88.80   0.00  16.64  80.57   0.00  12.60  88.80   4.44  38.68
   4_adp: 102.33   0.00  17.03 102.33   0.00  12.36  96.85   4.63  42.43
   4_occ: 102.33   0.00  17.03 102.33   0.00  12.36  96.85   4.63  42.43
   5_bss: 102.33   0.00  17.03 102.33   0.00  12.36  96.85   4.63  42.43
   5_xyz: 102.33   0.00  17.03 102.33   0.00  12.36  96.85   4.63  42.43
   5_adp: 106.91   0.00  16.51 106.91   0.00  12.01  96.13   4.67  40.99
   5_occ: 106.91   0.00  16.51 106.91   0.00  12.01  96.13   4.67  40.99
   5_bss: 106.91   0.00  16.51 106.91   0.00  12.01  96.13   4.67  40.99
------------------------------------------------------------------------
 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:    1.697    0.019    0.309
   1_adp:    1.697    0.019    0.309
   1_occ:    1.697    0.019    0.309
   2_bss:    1.697    0.019    0.309
   2_xyz:    1.111    0.032    0.416
   2_adp:    1.111    0.032    0.416
   2_occ:    1.111    0.032    0.416
   3_bss:    1.111    0.032    0.416
   3_xyz:    1.230    0.027    0.559
   3_adp:    1.230    0.027    0.559
   3_occ:    1.230    0.027    0.559
   4_bss:    1.230    0.027    0.559
   4_xyz:    1.273    0.053    0.588
   4_adp:    1.273    0.053    0.588
   4_occ:    1.273    0.053    0.588
   5_bss:    1.273    0.053    0.588
   5_xyz:    1.267    0.029    0.617
   5_adp:    1.267    0.029    0.617
   5_occ:    1.267    0.029    0.617
   5_bss:    1.267    0.029    0.617
------------------------------------------------------------------------

CPU time actual refinement: 335.11


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_829/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_829/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_829/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_829/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_829/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.96 
  Macro-tasks:
    bulk solvent and scale       = 39.06  
    individual site refinement   = 143.46 
    weights calculation          = 29.43  
    collect and process          = 6.61   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 218.67 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 105.83 
    alpha_beta                      = 8.25   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 116.44 
    fmodel                         = 6.63   
    r_factors                      = 0.15   
    phase_errors                   = 11.06  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 252.15 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.702 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    640 calls, 105.50 s
gradients_fft:          585 calls, 102.57 s

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

# Date 2008-01-16 Time 05:46:09 PST -0800 (1200491169.79 s)
Start R-work = 0.3827, R-free = 0.3673 (no bulk solvent and anisotropic scale)
Final R-work = 0.1311, R-free = 0.1771 (no bulk solvent and anisotropic scale)

Start R-work = 0.3679, R-free = 0.3529
Final R-work = 0.1134, R-free = 0.1614