# Date 2008-01-16 Time 05:13:40 PST -0800 (1200489220.64 s)
#phil __OFF__

Command line arguments: "../646.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10727
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 646

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.4607, 87.6859, 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: (70.25, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.98246
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.951708

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   1.9825

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.98246
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.951708

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2422 [2155/2179]  1936   219  10.2%
  bin  2:  4.2422 -  3.3797 [2062/2082]  1857   205   9.9%
  bin  3:  3.3797 -  2.9562 [2046/2065]  1843   203   9.9%
  bin  4:  2.9562 -  2.6876 [2022/2052]  1820   202  10.0%
  bin  5:  2.6876 -  2.4958 [2009/2028]  1808   201  10.0%
  bin  6:  2.4958 -  2.3493 [2002/2027]  1798   204  10.2%
  bin  7:  2.3493 -  2.2320 [2005/2033]  1806   199   9.9%
  bin  8:  2.2320 -  2.1351 [1970/2006]  1773   197  10.0%
  bin  9:  2.1351 -  2.0532 [1961/2003]  1771   190   9.7%
  bin 10:  2.0532 -  1.9825 [1357/2045]  1218   139  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_646/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 23
        2.42 -     3.04: 2183
        3.04 -     3.66: 4685
        3.66 -     4.28: 9007
        4.28 -     4.90: 12342
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.857 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.889 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.989 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.136 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28235 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_646/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_646/model_refine_001.geo

CPU time processing inputs: 9.43


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.4607 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3487   r_free= 0.3431   ksol= 0.00   Bsol= 0.00   scale= 0.958    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.104030                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7317 0.99   1396  154 0.2939 0.2738      6.3921      6.2803|
|  2:  4.7317 -  3.7752 0.99   1348  153 0.2681 0.2784       6.477      6.4584|
|  3:  3.7752 -  3.3037 0.99   1316  141 0.2978 0.2839      6.4082        6.42|
|  4:  3.3037 -  3.0043 0.99   1312  151 0.3229 0.3560       6.297        6.37|
|  5:  3.0043 -  2.7904 0.99   1306  145 0.3692 0.2964      6.1734       6.047|
|  6:  2.7904 -  2.6268 0.99   1301  142 0.3570 0.3849      6.0628      6.0179|
|  7:  2.6268 -  2.4958 0.99   1285  144 0.3685 0.3359      6.0523      6.0033|
|  8:  2.4958 -  2.3876 0.98   1279  142 0.3881 0.4000      6.0516      6.0685|
|  9:  2.3876 -  2.2961 0.98   1284  144 0.3922 0.3962      5.9779      5.9924|
| 10:  2.2961 -  2.2171 1.00   1290  141 0.4118 0.3713      5.9945      5.9041|
| 11:  2.2171 -  2.1480 0.98   1281  139 0.4212 0.4291      5.9418      5.9595|
| 12:  2.1480 -  2.0867 0.98   1254  144 0.4114 0.3857      5.8701      5.8591|
| 13:  2.0867 -  2.0319 0.99   1287  141 0.4146 0.4079       5.758      5.7543|
| 14:  2.0319 -  1.9825 0.53    691   78 0.4117 0.4444      5.7972      5.7109|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7317  1396   154  0.81  24.11   0.86     0.83      37696.96|
|  2:  4.7317 -  3.7752  1348   153  0.84  22.36   0.96     0.92      48106.40|
|  3:  3.7752 -  3.3037  1316   141  0.80  26.85   0.98     0.94      49671.69|
|  4:  3.3037 -  3.0043  1312   151  0.76  30.47   0.97     0.92      44308.21|
|  5:  3.0043 -  2.7904  1306   145  0.70  35.25   0.98     0.88      35169.31|
|  6:  2.7904 -  2.6268  1301   142  0.69  36.13   0.97     0.85      31386.18|
|  7:  2.6268 -  2.4958  1285   144  0.67  38.01   0.99     0.84      30304.57|
|  8:  2.4958 -  2.3876  1279   142  0.66  39.13   0.98     0.84      29506.91|
|  9:  2.3876 -  2.2961  1284   144  0.66  39.56   1.01     0.85      27668.35|
| 10:  2.2961 -  2.2171  1290   141  0.64  41.07   1.01     0.86      26352.87|
| 11:  2.2171 -  2.1480  1281   139  0.62  42.85   0.99     0.88      26821.69|
| 12:  2.1480 -  2.0867  1254   144  0.60  44.26   1.03     0.86      25690.13|
| 13:  2.0867 -  2.0319  1287   141  0.57  46.73   0.99     0.83      22619.11|
| 14:  2.0319 -  1.9825   691    78  0.62  43.07   1.05     0.80      18152.52|
|alpha:            min =        0.80 max =            0.94 mean =         0.87|
|beta:             min =    18152.52 max =        49671.69 mean =     33021.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           90.00 mean =        36.02|
|phase err.(test): min =        0.00 max =           89.70 mean =        35.97|
|-----------------------------------------------------------------------------|

============================== 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 = 5.587203              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.237   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.767944              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.960   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1988 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1852 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2833 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4616 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4391 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5649 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6693 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.201 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3487   r_free= 0.3431   ksol= 0.00   Bsol= 0.00   scale= 0.958    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.104030                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3344   r_free= 0.3314   ksol= 0.33   Bsol= 50.57   scale= 0.975   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,-0.19,2.28,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.085762                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.686410              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.161   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.405576              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.756   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3344      final r-factor (work) = 0.1884          |
| start r-factor (free) = 0.3314      final r-factor (free) = 0.2172          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4153 = 4.69 * 0.50 * 6.0819 + 1.00 * 0.1643                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6279 = 4.69 * 0.50 * 5.7843 + 1.00 * 0.0742                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1884      final r-factor (work) = 0.1705          |
| start r-factor (free) = 0.2172      final r-factor (free) = 0.2238          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3521 = 0.41 * 1.00 * 5.7843 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2357 = 0.41 * 1.00 * 5.4886 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.74    79.64   17.22    None  None   None       |
|    all(noH): 2823   0      0.74    79.64   17.22    None  None   None       |
|    Sol.    : 438    0      3.74    79.64   40.08    None  None   None       |
|    Mac.    : 2385   0      0.74    68.28   13.03    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:     0.735 -   8.625:  672   |   5:    40.186 -  48.076:  109        |
|      1:     8.625 -  16.516: 1258   |   6:    48.076 -  55.966:   79        |
|      2:    16.516 -  24.406:  372   |   7:    55.966 -  63.857:   57        |
|      3:    24.406 -  32.296:  144   |   8:    63.857 -  71.747:   19        |
|      4:    32.296 -  40.186:  107   |   9:    71.747 -  79.637:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1705 r_free = 0.2238             target_work(ml) = 5.503         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1703 r_free = 0.2235             target_work(ml) = 5.502         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1703   r_free= 0.2235   ksol= 0.33   Bsol= 50.57   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.26,-0.19,2.28,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.501600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1680   r_free= 0.2205   ksol= 0.34   Bsol= 59.27   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.02,-0.17,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.495150                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.632901              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.159  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.175387              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.857  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1680      final r-factor (work) = 0.1302          |
| start r-factor (free) = 0.2205      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3155 = 2.63 * 0.50 * 5.5006 + 1.00 * 0.0742                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1538 = 2.63 * 0.50 * 5.3900 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1302      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1761      final r-factor (free) = 0.1673          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9550 = 0.18 * 1.00 * 5.3900 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9286 = 0.18 * 1.00 * 5.2508 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    76.18   16.89    None  None   None       |
|    all(noH): 2823   0      1.21    76.18   16.89    None  None   None       |
|    Sol.    : 438    0      6.29    76.18   39.00    None  None   None       |
|    Mac.    : 2385   0      1.21    67.97   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.210 -   8.707:  674   |   5:    38.693 -  46.190:  102        |
|      1:     8.707 -  16.204: 1288   |   6:    46.190 -  53.687:   94        |
|      2:    16.204 -  23.700:  343   |   7:    53.687 -  61.183:   56        |
|      3:    23.700 -  31.197:  130   |   8:    61.183 -  68.680:   22        |
|      4:    31.197 -  38.693:  106   |   9:    68.680 -  76.177:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1249 r_free = 0.1673             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1247 r_free = 0.1672             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1672   ksol= 0.34   Bsol= 59.27   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.02,-0.17,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.224373                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1669   ksol= 0.34   Bsol= 59.27   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.38,-0.56,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222354                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.552308              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.632  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.765681              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.208  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1326 = 1.55 * 0.50 * 5.2495 + 1.00 * 0.0582                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0866 = 1.55 * 0.50 * 5.1981 + 1.00 * 0.0520                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9877 = 0.77 * 1.00 * 5.1981 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9647 = 0.77 * 1.00 * 5.1658 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.69    78.49   17.14    None  None   None       |
|    all(noH): 2823   0      0.69    78.49   17.14    None  None   None       |
|    Sol.    : 438    0      4.02    77.62   40.47    None  None   None       |
|    Mac.    : 2385   0      0.69    78.49   12.85    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:     0.688 -   8.468:  680   |   5:    39.588 -  47.368:   97        |
|      1:     8.468 -  16.248: 1295   |   6:    47.368 -  55.148:   88        |
|      2:    16.248 -  24.028:  322   |   7:    55.148 -  62.928:   66        |
|      3:    24.028 -  31.808:  137   |   8:    62.928 -  70.708:   28        |
|      4:    31.808 -  39.588:   96   |   9:    70.708 -  78.488:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1594             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1595             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1595   ksol= 0.34   Bsol= 59.27   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.38,-0.56,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.167379                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1593   ksol= 0.33   Bsol= 59.27   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.35,-0.59,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166836                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.163063              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.994  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.003741              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.941  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6386 = 2.16 * 0.50 * 5.1654 + 1.00 * 0.0520                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6282 = 2.16 * 0.50 * 5.1476 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1761 = 1.00 * 1.00 * 5.1476 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1674 = 1.00 * 1.00 * 5.1383 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.34    86.38   17.07    None  None   None       |
|    all(noH): 2823   0      0.34    86.38   17.07    None  None   None       |
|    Sol.    : 438    0      4.33    82.35   40.55    None  None   None       |
|    Mac.    : 2385   0      0.34    86.38   12.76    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:     0.336 -   8.941:  841   |   5:    43.360 -  51.965:   94        |
|      1:     8.941 -  17.546: 1227   |   6:    51.965 -  60.570:   77        |
|      2:    17.546 -  26.151:  278   |   7:    60.570 -  69.175:   39        |
|      3:    26.151 -  34.756:  127   |   8:    69.175 -  77.780:   22        |
|      4:    34.756 -  43.360:  111   |   9:    77.780 -  86.385:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1099 r_free = 0.1574             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1099 r_free = 0.1574             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1099   r_free= 0.1574   ksol= 0.33   Bsol= 59.27   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.35,-0.59,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1573   ksol= 0.33   Bsol= 59.27   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.17,-0.41,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139151                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.454166              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.749  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.211003              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.846  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3671 = 2.45 * 0.50 * 5.1392 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3625 = 2.45 * 0.50 * 5.1350 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2284 = 1.21 * 1.00 * 5.1350 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2296 = 1.21 * 1.00 * 5.1359 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.27    87.49   16.88    None  None   None       |
|    all(noH): 2823   0      0.27    87.49   16.88    None  None   None       |
|    Sol.    : 438    0      5.70    82.86   40.41    None  None   None       |
|    Mac.    : 2385   0      0.27    87.49   12.56    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:     0.271 -   8.992:  906   |   5:    43.879 -  52.601:   90        |
|      1:     8.992 -  17.714: 1189   |   6:    52.601 -  61.323:   75        |
|      2:    17.714 -  26.436:  261   |   7:    61.323 -  70.045:   36        |
|      3:    26.436 -  35.158:  124   |   8:    70.045 -  78.766:   21        |
|      4:    35.158 -  43.879:  115   |   9:    78.766 -  87.488:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1581             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1581             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1581   ksol= 0.33   Bsol= 59.27   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.17,-0.41,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136013                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7317 0.99   1396  154 0.0980 0.1309      5.3893      5.5515|
|  2:  4.7317 -  3.7752 0.99   1348  153 0.0831 0.1122      5.4258      5.6236|
|  3:  3.7752 -  3.3037 0.99   1316  141 0.1024 0.1518        5.46      5.8589|
|  4:  3.3037 -  3.0043 0.99   1312  151 0.1175 0.1673      5.4335      5.5963|
|  5:  3.0043 -  2.7904 0.99   1306  145 0.1272 0.1683      5.3077      5.5645|
|  6:  2.7904 -  2.6268 0.99   1301  142 0.1162 0.1979      5.1928      5.4939|
|  7:  2.6268 -  2.4958 0.99   1285  144 0.1250 0.1601      5.1624      5.3343|
|  8:  2.4958 -  2.3876 0.98   1279  142 0.1097 0.1598      5.0453      5.2979|
|  9:  2.3876 -  2.2961 0.98   1284  144 0.1131 0.1771      5.0174      5.3026|
| 10:  2.2961 -  2.2171 1.00   1290  141 0.1106 0.1686      4.9466      5.1906|
| 11:  2.2171 -  2.1480 0.98   1281  139 0.1106 0.1811      4.9367      5.2896|
| 12:  2.1480 -  2.0867 0.98   1254  144 0.1121 0.1679       4.882      5.1994|
| 13:  2.0867 -  2.0319 0.99   1287  141 0.1077 0.1793       4.769      5.0516|
| 14:  2.0319 -  1.9825 0.53    691   78 0.0954 0.1613      4.6524      4.8744|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7317  1396   154  0.94   9.33   0.97     0.94       7368.85|
|  2:  4.7317 -  3.7752  1348   153  0.95   7.93   1.01     1.00       9211.83|
|  3:  3.7752 -  3.3037  1316   141  0.94  11.13   1.02     1.02      10252.83|
|  4:  3.3037 -  3.0043  1312   151  0.92  13.50   1.01     0.98      10073.03|
|  5:  3.0043 -  2.7904  1306   145  0.90  15.66   1.00     0.98       8291.69|
|  6:  2.7904 -  2.6268  1301   142  0.90  16.06   0.98     0.96       7072.02|
|  7:  2.6268 -  2.4958  1285   144  0.90  15.81   0.99     0.95       6299.88|
|  8:  2.4958 -  2.3876  1279   142  0.91  14.96   0.99     0.96       5177.81|
|  9:  2.3876 -  2.2961  1284   144  0.91  14.96   1.00     0.96       4942.51|
| 10:  2.2961 -  2.2171  1290   141  0.90  16.06   0.99     0.96       4435.48|
| 11:  2.2171 -  2.1480  1281   139  0.90  16.20   0.98     0.94       4373.80|
| 12:  2.1480 -  2.0867  1254   144  0.91  15.84   1.00     0.99       4074.93|
| 13:  2.0867 -  2.0319  1287   141  0.90  16.22   0.98     0.96       3344.54|
| 14:  2.0319 -  1.9825   691    78  0.92  13.71   0.96     0.94       2569.27|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2569.27 max =        10252.83 mean =      6410.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.05|
|phase err.(test): min =        0.00 max =           89.01 mean =        13.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1580   ksol= 0.32   Bsol= 59.26   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.99,-0.23,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135985                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1580   ksol= 0.32   Bsol= 59.26   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.99,-0.23,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135985                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7317 0.99   1396  154 0.0979 0.1309      5.3888      5.5521|
|  2:  4.7317 -  3.7752 0.99   1348  153 0.0832 0.1122      5.4264      5.6238|
|  3:  3.7752 -  3.3037 0.99   1316  141 0.1024 0.1518      5.4602      5.8594|
|  4:  3.3037 -  3.0043 0.99   1312  151 0.1175 0.1672      5.4334      5.5962|
|  5:  3.0043 -  2.7904 0.99   1306  145 0.1271 0.1682      5.3074      5.5638|
|  6:  2.7904 -  2.6268 0.99   1301  142 0.1162 0.1979      5.1926      5.4938|
|  7:  2.6268 -  2.4958 0.99   1285  144 0.1250 0.1601      5.1624      5.3346|
|  8:  2.4958 -  2.3876 0.98   1279  142 0.1097 0.1598      5.0455      5.2975|
|  9:  2.3876 -  2.2961 0.98   1284  144 0.1131 0.1770      5.0175      5.3026|
| 10:  2.2961 -  2.2171 1.00   1290  141 0.1106 0.1686      4.9466      5.1908|
| 11:  2.2171 -  2.1480 0.98   1281  139 0.1105 0.1810      4.9368      5.2894|
| 12:  2.1480 -  2.0867 0.98   1254  144 0.1121 0.1678      4.8819       5.199|
| 13:  2.0867 -  2.0319 0.99   1287  141 0.1077 0.1793      4.7688      5.0514|
| 14:  2.0319 -  1.9825 0.53    691   78 0.0954 0.1612      4.6523       4.874|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7317  1396   154  0.94   9.33   0.98     0.94       7364.87|
|  2:  4.7317 -  3.7752  1348   153  0.95   7.93   1.01     1.00       9216.02|
|  3:  3.7752 -  3.3037  1316   141  0.94  11.14   1.03     1.02      10256.79|
|  4:  3.3037 -  3.0043  1312   151  0.92  13.50   1.01     0.99      10069.98|
|  5:  3.0043 -  2.7904  1306   145  0.90  15.66   1.01     0.98       8286.90|
|  6:  2.7904 -  2.6268  1301   142  0.90  16.06   0.99     0.96       7068.53|
|  7:  2.6268 -  2.4958  1285   144  0.90  15.81   0.99     0.96       6299.48|
|  8:  2.4958 -  2.3876  1279   142  0.91  14.96   1.00     0.97       5177.57|
|  9:  2.3876 -  2.2961  1284   144  0.91  14.97   1.00     0.97       4943.52|
| 10:  2.2961 -  2.2171  1290   141  0.90  16.06   1.00     0.97       4435.20|
| 11:  2.2171 -  2.1480  1281   139  0.90  16.20   0.99     0.95       4372.82|
| 12:  2.1480 -  2.0867  1254   144  0.91  15.84   1.01     1.00       4074.23|
| 13:  2.0867 -  2.0319  1287   141  0.90  16.22   0.99     0.97       3342.86|
| 14:  2.0319 -  1.9825   691    78  0.92  13.69   0.98     0.95       2567.29|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2567.29 max =        10256.79 mean =      6409.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.05|
|phase err.(test): min =        0.00 max =           89.03 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.26    87.48   16.87    None  None   None       |
|    all(noH): 2823   0      0.26    87.48   16.87    None  None   None       |
|    Sol.    : 438    0      5.70    82.85   40.40    None  None   None       |
|    Mac.    : 2385   0      0.26    87.48   12.55    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:     0.263 -   8.985:  906   |   5:    43.872 -  52.594:   90        |
|      1:     8.985 -  17.707: 1189   |   6:    52.594 -  61.316:   75        |
|      2:    17.707 -  26.429:  261   |   7:    61.316 -  70.037:   36        |
|      3:    26.429 -  35.150:  124   |   8:    70.037 -  78.759:   21        |
|      4:    35.150 -  43.872:  115   |   9:    78.759 -  87.481:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 296         
Filter by distance & map next to the model:
   mapped sites are within: 0.470 - 4.751
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 296
   mapped sites are within: 0.717 - 4.751

peak=    5.553 closest distance to " NE2 GLN A  11 " =    1.175
peak=    5.491 closest distance to " NH2 ARG A  56 " =    2.218
peak=    5.398 closest distance to " CG  PRO A  54 " =    1.320
peak=    5.201 closest distance to " O   HOH Z 144 " =    1.832
peak=    5.045 closest distance to " O   HOH Z 232 " =    2.345
peak=    4.977 closest distance to " O   HOH Z 126 " =    1.967
peak=    4.876 closest distance to " CB  GLN A 223 " =    1.471
peak=    4.805 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.730 closest distance to " CB  PRO A  54 " =    0.984
peak=    4.721 closest distance to " O   HOH Z  78 " =    1.836
peak=    4.611 closest distance to " CB  ARG A 190 " =    1.654
peak=    4.603 closest distance to " CG  PRO A 213 " =    1.201
peak=    4.600 closest distance to " CB  ARG A  79 " =    1.420
peak=    4.591 closest distance to " CB  GLN A 183 " =    1.256
peak=    4.503 closest distance to " O   HOH Z 427 " =    2.895
peak=    4.497 closest distance to " O   HOH Z 287 " =    2.122
peak=    4.469 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.451 closest distance to " ND2 ASN A 187 " =    1.525
peak=    4.427 closest distance to " CZ  PHE A 218 " =    1.070
peak=    4.389 closest distance to " O   HOH Z 303 " =    2.202
peak=    4.385 closest distance to " O   HOH Z 298 " =    1.916
peak=    4.311 closest distance to " O   HOH Z 369 " =    2.130
peak=    4.270 closest distance to " CG2 VAL A 257 " =    0.892
peak=    4.270 closest distance to " CB  ASN A 148 " =    1.441
peak=    4.259 closest distance to " CB  VAL A 265 " =    1.285
peak=    4.249 closest distance to " O   HOH Z 189 " =    2.827
peak=    4.236 closest distance to " CA  TYR A  30 " =    0.931
peak=    4.201 closest distance to " O   HOH Z   9 " =    2.182
peak=    4.145 closest distance to " O   HOH Z 158 " =    3.062
peak=    4.124 closest distance to " CB  SER A  63 " =    1.212
peak=    4.122 closest distance to " C   PRO A 198 " =    1.527
peak=    4.116 closest distance to " CD  ARG A 159 " =    0.748
peak=    4.106 closest distance to " O   HOH Z 250 " =    1.437
peak=    4.104 closest distance to " O   HOH Z  61 " =    1.625
peak=    4.098 closest distance to " O   HOH Z 406 " =    1.650
peak=    4.095 closest distance to " OD1 ASN A  69 " =    2.566
peak=    4.085 closest distance to " CD2 TRP A 179 " =    1.304
peak=    4.066 closest distance to " CB  ASN A 142 " =    1.038
peak=    4.043 closest distance to " CB  LEU A 228 " =    1.088
peak=    4.012 closest distance to " CD  ARG A  66 " =    2.442
peak=    4.010 closest distance to " CE  LYS A  76 " =    0.864
peak=    4.003 closest distance to " CB  TRP A 266 " =    1.061
peak=    3.993 closest distance to " O   HOH Z 346 " =    1.630
peak=    3.968 closest distance to " O   HOH Z 371 " =    1.901
peak=    3.965 closest distance to " O   HOH Z 272 " =    1.799
peak=    3.963 closest distance to " NZ  LYS A 117 " =    3.165
peak=    3.951 closest distance to " O   HOH Z 180 " =    2.177
peak=    3.944 closest distance to " O   HOH Z 133 " =    2.653
peak=    3.939 closest distance to " CB  GLU A 152 " =    1.270
peak=    3.924 closest distance to " O   HOH Z 214 " =    2.165
peak=    3.872 closest distance to " O   HOH Z 392 " =    3.102
peak=    3.847 closest distance to " CA  ASN A 215 " =    1.119
peak=    3.847 closest distance to " CB  SER A 212 " =    1.152
peak=    3.823 closest distance to " CG  PRO A 243 " =    1.074
peak=    3.818 closest distance to " CB  GLU A 277 " =    3.660
peak=    3.812 closest distance to " O   HOH Z  63 " =    1.935
peak=    3.811 closest distance to " O   HOH Z 313 " =    2.003
peak=    3.809 closest distance to " O   HOH Z 234 " =    3.631
peak=    3.808 closest distance to " OG ASER A 258 " =    3.102
peak=    3.797 closest distance to " ND1 HIS A  86 " =    1.759
peak=    3.797 closest distance to " O   HOH Z 209 " =    2.277
peak=    3.797 closest distance to " O   HOH Z 419 " =    2.199
peak=    3.794 closest distance to " ND2 ASN A 249 " =    0.829
peak=    3.774 closest distance to " O   HOH Z 126 " =    1.528
peak=    3.766 closest distance to " O   HOH Z 359 " =    1.515
peak=    3.763 closest distance to " CB  TYR A 169 " =    0.753
peak=    3.762 closest distance to " O   SER A  87 " =    2.243
peak=    3.749 closest distance to " O   HOH Z 353 " =    2.651
peak=    3.747 closest distance to " CG  LEU A 167 " =    1.276
peak=    3.746 closest distance to " O   HOH Z 172 " =    2.987
peak=    3.742 closest distance to " O   HOH Z 327 " =    1.554
peak=    3.737 closest distance to " O   HOH Z 261 " =    1.964
peak=    3.732 closest distance to " CB  GLU A  46 " =    0.998
peak=    3.731 closest distance to " O   HOH Z  10 " =    1.823
peak=    3.728 closest distance to " O   HOH Z   1 " =    1.839
peak=    3.723 closest distance to " CB  VAL A 202 " =    1.643
peak=    3.720 closest distance to " O   HOH Z  40 " =    1.763
peak=    3.720 closest distance to " NH1AARG A 145 " =    1.257
peak=    3.713 closest distance to " O   HOH Z  53 " =    2.549
peak=    3.709 closest distance to " CB  ASN A  39 " =    0.925
peak=    3.689 closest distance to " CZ3 TRP A 266 " =    1.141
peak=    3.688 closest distance to " O   HOH Z 368 " =    3.596
peak=    3.684 closest distance to " CB  ASP A 140 " =    1.014
peak=    3.682 closest distance to " OG BSER A 164 " =    2.290
peak=    3.672 closest distance to " O   HOH Z 193 " =    1.751
peak=    3.671 closest distance to " CA  ALA A  51 " =    0.930
peak=    3.665 closest distance to " O   HOH Z 265 " =    2.275
peak=    3.660 closest distance to " CB  ASN A 110 " =    1.107
peak=    3.656 closest distance to " O   HOH Z 285 " =    2.374
peak=    3.650 closest distance to " CB  ASN A 187 " =    1.400
peak=    3.642 closest distance to " O   HOH Z 203 " =    1.807
peak=    3.640 closest distance to " O   HOH Z   1 " =    1.693
peak=    3.627 closest distance to " O   HOH Z 394 " =    4.000
peak=    3.618 closest distance to " CB  SER A   3 " =    1.345
peak=    3.617 closest distance to " CA  ALA A 158 " =    1.241
peak=    3.616 closest distance to " CA  THR A 264 " =    0.882
peak=    3.600 closest distance to " O   HOH Z 368 " =    2.066
peak=    3.599 closest distance to " CB  PRO A  90 " =    1.183
peak=    3.596 closest distance to " O   HOH Z 411 " =    3.826
peak=    3.594 closest distance to " O  BHOH Z 338 " =    2.341
peak=    3.592 closest distance to " CG2 ILE A 120 " =    1.264
peak=    3.592 closest distance to " CB  TYR A 116 " =    0.839
peak=    3.589 closest distance to " O   HOH Z 132 " =    2.490
peak=    3.588 closest distance to " CE1 PHE A 218 " =    1.061
peak=    3.581 closest distance to " CB  MET A  40 " =    0.818
peak=    3.567 closest distance to " CA  ARG A 195 " =    1.210
peak=    3.567 closest distance to " O   HOH Z 425 " =    2.035
peak=    3.562 closest distance to " CB  MET A  47 " =    1.170
peak=    3.562 closest distance to " O   HOH Z  61 " =    1.499
peak=    3.561 closest distance to " O   HOH Z 422 " =    2.685
peak=    3.553 closest distance to " O   HOH Z 290 " =    0.975
peak=    3.551 closest distance to " CB  LYS A 117 " =    1.249
peak=    3.546 closest distance to " CG1 ILE A  33 " =    1.218
peak=    3.544 closest distance to " O   HOH Z  21 " =    1.742
peak=    3.543 closest distance to " CB  GLU A 128 " =    0.969
peak=    3.542 closest distance to " CA  ALA A 233 " =    1.082
peak=    3.541 closest distance to " O   HOH Z 389 " =    1.795
peak=    3.536 closest distance to " N   ASN A 127 " =    1.314
peak=    3.535 closest distance to " O   ASN A  74 " =    1.541
peak=    3.535 closest distance to " CB  ARG A 139 " =    0.999
peak=    3.528 closest distance to " O   HOH Z 405 " =    1.146
peak=    3.521 closest distance to " O   HOH Z 371 " =    2.868
peak=    3.506 closest distance to " O   HOH Z  40 " =    1.987
peak=    3.488 closest distance to " CB  TRP A 179 " =    1.390
peak=    3.484 closest distance to " NE2 HIS A 207 " =    1.262
peak=    3.473 closest distance to " O   HOH Z 280 " =    3.014
peak=    3.472 closest distance to " NH2BARG A 145 " =    2.132
peak=    3.467 closest distance to " CD  ARG A 269 " =    0.944
peak=    3.463 closest distance to " O   HOH Z 294 " =    1.521
peak=    3.462 closest distance to " CD BLYS A 290 " =    1.059
peak=    3.458 closest distance to " OD1BASN A 224 " =    2.286
peak=    3.456 closest distance to " CD1 LEU A  96 " =    0.787
peak=    3.456 closest distance to " O   HOH Z 329 " =    3.997
peak=    3.454 closest distance to " CA  THR A 221 " =    1.093
peak=    3.453 closest distance to " O   HOH Z 426 " =    1.995
peak=    3.451 closest distance to " O   HOH Z 291 " =    1.521
peak=    3.448 closest distance to " CG2 THR A 221 " =    1.045
peak=    3.447 closest distance to " CA  ALA A  21 " =    1.169
peak=    3.440 closest distance to " CA  SER A  87 " =    1.047
peak=    3.438 closest distance to " O   HOH Z 250 " =    1.819
peak=    3.426 closest distance to " CB  SER A 210 " =    0.717
peak=    3.425 closest distance to " O   HOH Z   3 " =    1.923
peak=    3.423 closest distance to " CB  GLN A  88 " =    1.200
peak=    3.423 closest distance to " O   HOH Z  59 " =    1.631
peak=    3.421 closest distance to " CB  THR A  31 " =    1.728
peak=    3.421 closest distance to " O   HOH Z 245 " =    1.280
peak=    3.416 closest distance to " O   HOH Z 234 " =    1.872
peak=    3.415 closest distance to " O   HOH Z 298 " =    2.437
peak=    3.411 closest distance to " O   HOH Z 403 " =    1.455
peak=    3.406 closest distance to " CE1 TYR A 186 " =    1.311
peak=    3.401 closest distance to " CA  GLU A  46 " =    0.826
peak=    3.401 closest distance to " O   HOH Z 116 " =    3.072
peak=    3.392 closest distance to " CA  ARG A  36 " =    1.063
peak=    3.390 closest distance to " CB  GLN A  89 " =    1.363
peak=    3.389 closest distance to " CB  ALA A   1 " =    4.751
peak=    3.388 closest distance to " O   HOH Z  66 " =    2.182
peak=    3.388 closest distance to " O   HOH Z 286 " =    2.313
peak=    3.384 closest distance to " CD1 LEU A 300 " =    1.152
peak=    3.383 closest distance to " O   HOH Z 128 " =    2.242
peak=    3.381 closest distance to " CG2AVAL A  72 " =    1.555
peak=    3.378 closest distance to " O   PHE A 192 " =    1.395
peak=    3.377 closest distance to " O   HOH Z 248 " =    1.585
peak=    3.374 closest distance to " CA  TYR A 116 " =    1.334
peak=    3.371 closest distance to " N   PHE A 130 " =    1.220
peak=    3.370 closest distance to " O   HOH Z 325 " =    2.508
peak=    3.364 closest distance to " O   HOH Z 345 " =    1.674
peak=    3.355 closest distance to " O   HOH Z 213 " =    2.065
peak=    3.352 closest distance to " O   HOH Z 135 " =    1.629
peak=    3.349 closest distance to " O   HOH Z 193 " =    1.668
peak=    3.349 closest distance to " N   ASN A  39 " =    1.312
peak=    3.348 closest distance to " CG2 ILE A  20 " =    1.485
peak=    3.348 closest distance to " O   HOH Z 365 " =    2.834
peak=    3.347 closest distance to " O   HOH Z 421 " =    2.075
peak=    3.347 closest distance to " NE2 GLN A  73 " =    3.835
peak=    3.346 closest distance to " O   HOH Z 423 " =    1.309
peak=    3.346 closest distance to " CB  ILE A 120 " =    1.355
peak=    3.345 closest distance to " CG2 VAL A 197 " =    1.075
peak=    3.344 closest distance to " CB  SER A  62 " =    1.110
peak=    3.342 closest distance to " CD2 LEU A 255 " =    1.475
peak=    3.336 closest distance to " CD2 LEU A 297 " =    0.897
peak=    3.335 closest distance to " NH1 ARG A 138 " =    1.086
peak=    3.334 closest distance to " O   HOH Z 193 " =    2.081
peak=    3.332 closest distance to " CB  SER A 216 " =    0.834
peak=    3.330 closest distance to " CB  ASN A 215 " =    1.132
peak=    3.324 closest distance to " O   HOH Z  88 " =    3.191
peak=    3.324 closest distance to " O   HOH Z 185 " =    1.871
peak=    3.323 closest distance to " O   HOH Z 258 " =    2.203
peak=    3.321 closest distance to " O   HOH Z 305 " =    3.558
peak=    3.314 closest distance to " OG BSER A  99 " =    2.241
peak=    3.307 closest distance to " O   HOH Z 403 " =    1.562
peak=    3.307 closest distance to " CE1 PHE A  38 " =    1.217
peak=    3.307 closest distance to " CD  LYS A 166 " =    1.270
peak=    3.304 closest distance to " CA  ALA A 291 " =    0.818
peak=    3.304 closest distance to " NH2AARG A 275 " =    3.697
peak=    3.304 closest distance to " N   GLN A 278 " =    1.425
peak=    3.304 closest distance to " CB  TYR A 169 " =    0.729
peak=    3.299 closest distance to " OG  SER A  62 " =    2.900
peak=    3.299 closest distance to " CB  SER A  26 " =    1.718
peak=    3.297 closest distance to " O   HOH Z 147 " =    1.798
peak=    3.295 closest distance to " O   TYR A 116 " =    1.332
peak=    3.293 closest distance to " O   HOH Z 437 " =    1.324
peak=    3.293 closest distance to " O   HOH Z 336 " =    1.835
peak=    3.290 closest distance to " O   HOH Z 380 " =    1.648
peak=    3.289 closest distance to " CG  MET A 185 " =    1.180
peak=    3.286 closest distance to " CA  ALA A 160 " =    0.943
peak=    3.281 closest distance to " N   SER A 146 " =    1.731
peak=    3.281 closest distance to " O   HOH Z 345 " =    3.396
peak=    3.275 closest distance to " O   HOH Z 423 " =    2.665
peak=    3.266 closest distance to " CA  PRO A 280 " =    1.281
peak=    3.266 closest distance to " O   ALA A 165 " =    1.541
peak=    3.264 closest distance to " O   HOH Z  43 " =    1.991
peak=    3.259 closest distance to " OG  SER A  22 " =    2.748
peak=    3.257 closest distance to " CB  ALA A  34 " =    1.079
peak=    3.252 closest distance to " CB  SER A 273 " =    0.848
peak=    3.251 closest distance to " CG1 ILE A  49 " =    1.483
peak=    3.249 closest distance to " O   HOH Z 128 " =    2.161
peak=    3.249 closest distance to " CB  THR A 157 " =    1.115
peak=    3.248 closest distance to " CE  LYS A  48 " =    1.150
peak=    3.248 closest distance to " O   HOH Z 261 " =    2.442
peak=    3.244 closest distance to " O   HOH Z 391 " =    2.892
peak=    3.241 closest distance to " CG1 VAL A 153 " =    1.000
peak=    3.241 closest distance to " O   THR A 220 " =    1.271
peak=    3.237 closest distance to " CA  ARG A 102 " =    1.112
peak=    3.235 closest distance to " CB  ALA A 248 " =    0.932
peak=    3.234 closest distance to " O   HOH Z 148 " =    3.415
peak=    3.233 closest distance to " CB  THR A 235 " =    1.193
peak=    3.231 closest distance to " O   HOH Z  88 " =    3.772
peak=    3.231 closest distance to " CB  ALA A 291 " =    1.309
peak=    3.229 closest distance to " O   MET A 105 " =    1.868
peak=    3.227 closest distance to " O   HOH Z 175 " =    2.133
peak=    3.226 closest distance to " CA  VAL A 125 " =    1.173
peak=    3.225 closest distance to " O   HOH Z 417 " =    3.359
peak=    3.225 closest distance to " CD1 ILE A 263 " =    1.315
peak=    3.224 closest distance to " O   HOH Z  44 " =    2.915
peak=    3.222 closest distance to " O   HOH Z 171 " =    4.166
peak=    3.222 closest distance to " O   HOH Z 273 " =    2.844
peak=    3.222 closest distance to " CG1 VAL A 189 " =    1.954
peak=    3.222 closest distance to " CD  LYS A  76 " =    1.887
peak=    3.221 closest distance to " CA  LYS A 117 " =    1.192
peak=    3.215 closest distance to " CG1 ILE A 151 " =    1.028
peak=    3.210 closest distance to " CG AARG A 275 " =    1.109
peak=    3.209 closest distance to " CA  ILE A 234 " =    1.020
peak=    3.206 closest distance to " CB  LEU A  96 " =    1.292
peak=    3.205 closest distance to " O   HOH Z 407 " =    2.305
peak=    3.204 closest distance to " O   THR A 251 " =    1.129
peak=    3.202 closest distance to " CG  GLU A  37 " =    0.912
peak=    3.197 closest distance to " O   HOH Z  97 " =    2.705
peak=    3.193 closest distance to " N   ARG A 156 " =    1.334
peak=    3.188 closest distance to " CA  ASN A 217 " =    1.198
peak=    3.187 closest distance to " ND2 ASN A 110 " =    1.671
peak=    3.185 closest distance to " CG  MET A 113 " =    1.207
peak=    3.181 closest distance to " O   HOH Z 116 " =    1.766
peak=    3.179 closest distance to " O   HOH Z 285 " =    1.930
peak=    3.179 closest distance to " CA  ARG A 159 " =    1.256
peak=    3.178 closest distance to " O   HOH Z 233 " =    1.776
peak=    3.175 closest distance to " O   HOH Z   9 " =    3.484
peak=    3.174 closest distance to " CD  ARG A 195 " =    3.471
peak=    3.172 closest distance to " CA  MET A 105 " =    0.986
peak=    3.169 closest distance to " CB  GLN A 103 " =    0.858
peak=    3.167 closest distance to " CD  PRO A 243 " =    1.570
peak=    3.164 closest distance to " CB  LEU A  83 " =    0.785
peak=    3.161 closest distance to " CG  LYS A  76 " =    0.929
peak=    3.160 closest distance to " CA  ALA A  84 " =    1.328
peak=    3.159 closest distance to " CB  ARG A 138 " =    0.973
peak=    3.157 closest distance to " OG  SER A  62 " =    2.908
peak=    3.157 closest distance to " CB  HIS A 108 " =    0.764
peak=    3.155 closest distance to " O   HOH Z  64 " =    2.019
peak=    3.153 closest distance to " O   HOH Z 368 " =    4.195
peak=    3.147 closest distance to " O   HOH Z 373 " =    1.488
peak=    3.142 closest distance to " CD1 ILE A 106 " =    0.773
peak=    3.132 closest distance to " OE2 GLU A  53 " =    1.942
peak=    3.130 closest distance to " O   HOH Z 409 " =    2.557
peak=    3.129 closest distance to " CA  ALA A 299 " =    0.862
peak=    3.113 closest distance to " O   PRO A  90 " =    1.508
peak=    3.108 closest distance to " CB  TRP A 179 " =    1.443
peak=    3.099 closest distance to " NZ  LYS A  48 " =    1.237
peak=    3.096 closest distance to " NH1BARG A 145 " =    1.058
peak=    3.091 closest distance to " O   ALA A   1 " =    1.628
peak=    3.088 closest distance to " CB  ALA A 114 " =    0.731
peak=    3.087 closest distance to " CA  ALA A 100 " =    1.018
peak=    3.083 closest distance to " CD1AILE A 234 " =    0.948
peak=    3.082 closest distance to " OG BSER A 134 " =    3.035
peak=    3.080 closest distance to " CG BARG A 102 " =    1.787
peak=    3.073 closest distance to " O   HOH Z 287 " =    2.310
peak=    3.069 closest distance to " CB  ALA A 114 " =    1.323
peak=    3.068 closest distance to " CA  LYS A 290 " =    1.273
peak=    3.050 closest distance to " CB  PHE A 204 " =    0.778
peak=    3.049 closest distance to " N   ASP A 162 " =    1.172
peak=    3.023 closest distance to " O   HOH Z 175 " =    2.179
peak=    3.005 closest distance to " O   HOH Z  88 " =    3.605

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.765 - 5.511
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 201
   mapped sites are within: 0.765 - 5.511

peak=   -4.695 closest distance to " O   HOH Z 377 " =    2.135
peak=   -4.612 closest distance to " CD  ARG A 156 " =    2.093
peak=   -4.591 closest distance to " OG BSER A 134 " =    1.299
peak=   -4.461 closest distance to " CB  PRO A 243 " =    2.675
peak=   -4.444 closest distance to " CD  ARG A  14 " =    3.446
peak=   -4.409 closest distance to " O   HOH Z 266 " =    5.337
peak=   -4.326 closest distance to " CG  GLN A 223 " =    2.020
peak=   -4.253 closest distance to " N   ALA A  43 " =    2.684
peak=   -4.212 closest distance to " O   HOH Z 231 " =    2.305
peak=   -4.187 closest distance to " CD  GLN A  58 " =    1.002
peak=   -4.132 closest distance to " C   HIS A 108 " =    1.148
peak=   -4.067 closest distance to " CG1 VAL A 112 " =    2.920
peak=   -4.059 closest distance to " CE BMET A  47 " =    1.302
peak=   -4.058 closest distance to " ND2 ASN A  45 " =    1.859
peak=   -4.056 closest distance to " CB  PHE A 192 " =    2.017
peak=   -4.047 closest distance to " O   VAL A  67 " =    2.645
peak=   -3.958 closest distance to " CG1 VAL A 112 " =    2.625
peak=   -3.953 closest distance to " O   HOH Z 198 " =    1.916
peak=   -3.943 closest distance to " CZ3 TRP A 179 " =    1.191
peak=   -3.935 closest distance to " ND2 ASN A 249 " =    2.354
peak=   -3.906 closest distance to " CE  MET A 105 " =    2.429
peak=   -3.897 closest distance to " O   HOH Z 313 " =    1.824
peak=   -3.882 closest distance to " O   HOH Z 372 " =    2.456
peak=   -3.864 closest distance to " O   HOH Z 389 " =    2.044
peak=   -3.860 closest distance to " ND2 ASN A  45 " =    1.219
peak=   -3.854 closest distance to " O   HOH Z  73 " =    2.208
peak=   -3.847 closest distance to " O   HOH Z 185 " =    2.281
peak=   -3.833 closest distance to " CB  ALA A 291 " =    2.239
peak=   -3.805 closest distance to " O   HOH Z 351 " =    1.474
peak=   -3.776 closest distance to " CB  ALA A  43 " =    2.581
peak=   -3.772 closest distance to " O   PRO A 198 " =    1.249
peak=   -3.754 closest distance to " O   HOH Z 290 " =    1.219
peak=   -3.752 closest distance to " CD1 LEU A 255 " =    2.872
peak=   -3.751 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.735 closest distance to " CG2 ILE A  49 " =    2.750
peak=   -3.703 closest distance to " CG1 VAL A  67 " =    2.954
peak=   -3.700 closest distance to " O   HOH Z 407 " =    3.070
peak=   -3.697 closest distance to " CA  GLY A 241 " =    2.275
peak=   -3.693 closest distance to " N   THR A 157 " =    1.512
peak=   -3.669 closest distance to " CD2 TYR A 293 " =    1.934
peak=   -3.663 closest distance to " O   HOH Z  38 " =    1.600
peak=   -3.628 closest distance to " CA  ASP A 298 " =    1.056
peak=   -3.627 closest distance to " CG2 ILE A 263 " =    2.273
peak=   -3.618 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.608 closest distance to " O   HOH Z  52 " =    1.349
peak=   -3.596 closest distance to " CD1 PHE A  59 " =    2.001
peak=   -3.594 closest distance to " CB  ALA A 248 " =    2.367
peak=   -3.587 closest distance to " CG2 THR A 178 " =    2.295
peak=   -3.575 closest distance to " O   HOH Z 394 " =    1.471
peak=   -3.569 closest distance to " O   HOH Z 253 " =    3.909
peak=   -3.569 closest distance to " O   HOH Z 357 " =    2.039
peak=   -3.564 closest distance to " CE2 PHE A 218 " =    2.436
peak=   -3.562 closest distance to " O   HOH Z  13 " =    1.892
peak=   -3.557 closest distance to " CD  ARG A 139 " =    1.607
peak=   -3.550 closest distance to " CB  TYR A  15 " =    2.219
peak=   -3.545 closest distance to " O   HOH Z 102 " =    1.590
peak=   -3.541 closest distance to " CB  ASN A  39 " =    2.340
peak=   -3.531 closest distance to " OD2 ASP A 191 " =    1.362
peak=   -3.529 closest distance to " NH2AARG A 275 " =    5.361
peak=   -3.528 closest distance to " OG  SER A  97 " =    2.231
peak=   -3.522 closest distance to " ND2 ASN A 187 " =    1.503
peak=   -3.520 closest distance to " OXT GLY A 302 " =    2.954
peak=   -3.515 closest distance to " CD2 PHE A  61 " =    2.107
peak=   -3.513 closest distance to " O   SER A 210 " =    2.013
peak=   -3.513 closest distance to " CZ  TYR A 169 " =    1.797
peak=   -3.511 closest distance to " CB  ALA A 291 " =    2.155
peak=   -3.508 closest distance to " CB  ALA A 161 " =    2.557
peak=   -3.505 closest distance to " O   HOH Z 348 " =    2.229
peak=   -3.501 closest distance to " O   HOH Z 166 " =    2.011
peak=   -3.495 closest distance to " CD2 TYR A 247 " =    2.522
peak=   -3.495 closest distance to " CB  TRP A  85 " =    2.450
peak=   -3.481 closest distance to " CD2 LEU A 237 " =    2.863
peak=   -3.480 closest distance to " O   PRO A 163 " =    2.052
peak=   -3.478 closest distance to " CA  GLY A 203 " =    2.376
peak=   -3.464 closest distance to " O   PHE A 218 " =    1.519
peak=   -3.460 closest distance to " OD1 ASP A 191 " =    1.816
peak=   -3.456 closest distance to " O   HOH Z 114 " =    2.922
peak=   -3.455 closest distance to " CE3 TRP A 274 " =    2.344
peak=   -3.441 closest distance to " OH  TYR A 172 " =    1.822
peak=   -3.439 closest distance to " NH2BARG A 275 " =    1.859
peak=   -3.438 closest distance to " O   SER A 135 " =    1.422
peak=   -3.422 closest distance to " CG  ARG A 269 " =    2.453
peak=   -3.419 closest distance to " CB  ASP A 286 " =    2.125
peak=   -3.419 closest distance to " OD1 ASN A 148 " =    1.553
peak=   -3.411 closest distance to " CG1 VAL A 250 " =    2.635
peak=   -3.406 closest distance to " O   ALA A  10 " =    1.639
peak=   -3.405 closest distance to " CD  ARG A 195 " =    5.201
peak=   -3.405 closest distance to " O   HOH Z 429 " =    1.996
peak=   -3.401 closest distance to " O   VAL A 189 " =    2.533
peak=   -3.399 closest distance to " CD1 LEU A   5 " =    2.477
peak=   -3.398 closest distance to " O   HOH Z 174 " =    2.629
peak=   -3.392 closest distance to " NE2 GLN A 278 " =    1.555
peak=   -3.385 closest distance to " O   HOH Z 211 " =    1.555
peak=   -3.383 closest distance to " O   VAL A 189 " =    1.690
peak=   -3.382 closest distance to " CZ  PHE A  59 " =    1.592
peak=   -3.380 closest distance to " O   HOH Z 292 " =    4.648
peak=   -3.376 closest distance to " CB  ALA A   7 " =    2.313
peak=   -3.367 closest distance to " O   PRO A 198 " =    1.340
peak=   -3.363 closest distance to " ND2 ASN A  60 " =    1.366
peak=   -3.363 closest distance to " CA  GLY A 133 " =    2.062
peak=   -3.363 closest distance to " O   HOH Z 196 " =    2.128
peak=   -3.362 closest distance to " ND2 ASN A  60 " =    4.141
peak=   -3.361 closest distance to " O   HOH Z  10 " =    1.515
peak=   -3.354 closest distance to " N   ASP A 286 " =    2.348
peak=   -3.352 closest distance to " O   HOH Z 131 " =    4.110
peak=   -3.349 closest distance to " O   HOH Z 295 " =    1.614
peak=   -3.341 closest distance to " CD1 LEU A 101 " =    2.262
peak=   -3.340 closest distance to " CG  PHE A 283 " =    2.688
peak=   -3.340 closest distance to " O   HOH Z 318 " =    2.037
peak=   -3.338 closest distance to " O   HOH Z  22 " =    2.493
peak=   -3.333 closest distance to " OG BSER A 134 " =    1.727
peak=   -3.328 closest distance to " CG  GLU A 277 " =    1.294
peak=   -3.328 closest distance to " OD1 ASN A 187 " =    1.564
peak=   -3.320 closest distance to " CE3 TRP A 150 " =    2.233
peak=   -3.315 closest distance to " O   HOH Z 123 " =    2.588
peak=   -3.311 closest distance to " NE  ARG A  36 " =    1.983
peak=   -3.310 closest distance to " OE1 GLN A  88 " =    1.143
peak=   -3.308 closest distance to " N   ALA A 248 " =    1.563
peak=   -3.304 closest distance to " CD  GLU A 236 " =    1.086
peak=   -3.304 closest distance to " O   TRP A  70 " =    1.408
peak=   -3.302 closest distance to " CE2 PHE A  61 " =    2.635
peak=   -3.301 closest distance to " O   ARG A 145 " =    1.595
peak=   -3.298 closest distance to " CG1 VAL A 125 " =    1.909
peak=   -3.294 closest distance to " O   HOH Z 298 " =    1.245
peak=   -3.293 closest distance to " CA  GLY A 241 " =    3.169
peak=   -3.293 closest distance to " O   HOH Z  63 " =    1.821
peak=   -3.290 closest distance to " CD2 PHE A 225 " =    1.165
peak=   -3.289 closest distance to " O   HOH Z 353 " =    2.227
peak=   -3.287 closest distance to " O   HOH Z 191 " =    5.511
peak=   -3.281 closest distance to " O   HOH Z  51 " =    1.651
peak=   -3.279 closest distance to " N   SER A 276 " =    1.301
peak=   -3.279 closest distance to " CA  GLY A  57 " =    2.174
peak=   -3.279 closest distance to " O   HOH Z  71 " =    2.110
peak=   -3.275 closest distance to " C   LEU A 143 " =    1.129
peak=   -3.274 closest distance to " O   HOH Z 359 " =    3.194
peak=   -3.271 closest distance to " O   GLN A 240 " =    2.474
peak=   -3.262 closest distance to " O   HOH Z   6 " =    1.461
peak=   -3.254 closest distance to " O   HOH Z 189 " =    1.963
peak=   -3.253 closest distance to " CG  LEU A  83 " =    1.946
peak=   -3.245 closest distance to " CD1 LEU A 297 " =    2.615
peak=   -3.245 closest distance to " O   HOH Z 292 " =    1.823
peak=   -3.243 closest distance to " O   HOH Z  11 " =    1.753
peak=   -3.242 closest distance to " CB  ASP A 132 " =    2.249
peak=   -3.241 closest distance to " CB  ALA A 100 " =    2.216
peak=   -3.238 closest distance to " O   HOH Z 281 " =    2.702
peak=   -3.238 closest distance to " O   HOH Z 298 " =    2.497
peak=   -3.235 closest distance to " O   HOH Z  43 " =    1.687
peak=   -3.233 closest distance to " CD2 PHE A 192 " =    2.282
peak=   -3.232 closest distance to " CG2 THR A  18 " =    2.850
peak=   -3.225 closest distance to " CG2 VAL A 189 " =    1.987
peak=   -3.224 closest distance to " O   HOH Z 165 " =    2.194
peak=   -3.223 closest distance to " OD2 ASP A 171 " =    1.770
peak=   -3.218 closest distance to " O   HOH Z 243 " =    1.961
peak=   -3.216 closest distance to " O   HOH Z 350 " =    1.844
peak=   -3.209 closest distance to " CD2 HIS A 207 " =    2.257
peak=   -3.208 closest distance to " O   HOH Z  60 " =    1.965
peak=   -3.204 closest distance to " O   ALA A  51 " =    1.327
peak=   -3.203 closest distance to " O   HOH Z 103 " =    1.810
peak=   -3.197 closest distance to " O   HOH Z 252 " =    4.339
peak=   -3.190 closest distance to " NE2 GLN A 194 " =    1.801
peak=   -3.189 closest distance to " N   MET A 188 " =    1.906
peak=   -3.189 closest distance to " O   ALA A 292 " =    2.158
peak=   -3.189 closest distance to " CB  PRO A  54 " =    2.460
peak=   -3.179 closest distance to " CB  ASP A 132 " =    2.389
peak=   -3.179 closest distance to " O   ILE A 106 " =    1.978
peak=   -3.175 closest distance to " O   HOH Z 140 " =    1.638
peak=   -3.170 closest distance to " O   HOH Z 244 " =    2.034
peak=   -3.164 closest distance to " N   THR A  52 " =    1.702
peak=   -3.152 closest distance to " O   HOH Z 390 " =    2.409
peak=   -3.151 closest distance to " CG  ASP A 231 " =    0.765
peak=   -3.150 closest distance to " OE2 GLU A 152 " =    1.209
peak=   -3.150 closest distance to " C   ASP A 272 " =    2.334
peak=   -3.149 closest distance to " O   HOH Z 412 " =    4.252
peak=   -3.147 closest distance to " O   HOH Z 134 " =    3.343
peak=   -3.144 closest distance to " CA  SER A  62 " =    2.668
peak=   -3.138 closest distance to " CG  MET A 105 " =    0.968
peak=   -3.134 closest distance to " O   GLU A 152 " =    1.343
peak=   -3.129 closest distance to " CD1 LEU A 228 " =    2.268
peak=   -3.129 closest distance to " CB  PRO A 163 " =    2.483
peak=   -3.126 closest distance to " O   ALA A 161 " =    1.705
peak=   -3.126 closest distance to " CG2 THR A 221 " =    2.693
peak=   -3.122 closest distance to " O   HOH Z 426 " =    1.580
peak=   -3.120 closest distance to " NH2 ARG A 219 " =    1.581
peak=   -3.115 closest distance to " O   HOH Z 278 " =    1.648
peak=   -3.113 closest distance to " O   HOH Z 198 " =    1.782
peak=   -3.112 closest distance to " O   HOH Z 371 " =    1.498
peak=   -3.111 closest distance to " O   ARG A  24 " =    1.713
peak=   -3.101 closest distance to " O   VAL A 174 " =    2.179
peak=   -3.093 closest distance to " CB  GLN A  11 " =    1.764
peak=   -3.086 closest distance to " NH2 ARG A  79 " =    1.560
peak=   -3.080 closest distance to " CA  SER A 135 " =    1.271
peak=   -3.079 closest distance to " CG  PRO A 163 " =    2.659
peak=   -3.075 closest distance to " OE1 GLN A  58 " =    3.158
peak=   -3.073 closest distance to " CA  GLY A 241 " =    2.871
peak=   -3.066 closest distance to " C   ALA A 114 " =    2.273
peak=   -3.055 closest distance to " O   SER A  62 " =    2.255
peak=   -3.050 closest distance to " O   HOH Z  60 " =    1.990
peak=   -3.038 closest distance to " CD1 ILE A 199 " =    2.503
peak=   -3.025 closest distance to " OG  SER A 245 " =    1.373
peak=   -3.023 closest distance to " O   HOH Z 111 " =    2.177
peak=   -3.021 closest distance to " O   HOH Z 166 " =    1.509

================= 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    :  0.3487 0.3431   6.104030e+00   6.076691e+00
   1_bss:  0.3344 0.3314   6.085762e+00   6.051284e+00
   1_xyz:  0.1884 0.2172   5.556214e+00   5.655922e+00
   1_adp:  0.1705 0.2238   5.502926e+00   5.694114e+00
   1_occ:  0.1703 0.2235   5.501600e+00   5.692742e+00
   2_bss:  0.1680 0.2205   5.495150e+00   5.685499e+00
   2_xyz:  0.1302 0.1761   5.268837e+00   5.485492e+00
   2_adp:  0.1249 0.1673   5.225141e+00   5.437867e+00
   2_occ:  0.1247 0.1672   5.224373e+00   5.437449e+00
   3_bss:  0.1246 0.1669   5.222354e+00   5.435215e+00
   3_xyz:  0.1178 0.1590   5.176415e+00   5.397767e+00
   3_adp:  0.1155 0.1594   5.167121e+00   5.397768e+00
   3_occ:  0.1155 0.1595   5.167379e+00   5.398349e+00
   4_bss:  0.1154 0.1593   5.166836e+00   5.398085e+00
   4_xyz:  0.1105 0.1575   5.141600e+00   5.388450e+00
   4_adp:  0.1099 0.1574   5.138833e+00   5.388153e+00
   4_occ:  0.1099 0.1574   5.139084e+00   5.388735e+00
   5_bss:  0.1098 0.1573   5.139151e+00   5.388808e+00
   5_xyz:  0.1087 0.1582   5.137442e+00   5.393954e+00
   5_adp:  0.1086 0.1581   5.135868e+00   5.393137e+00
   5_occ:  0.1085 0.1581   5.136013e+00   5.393459e+00
   5_bss:  0.1084 0.1580   5.135985e+00   5.393430e+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:  0.328  50.568  -3.261  -0.195   2.282  -0.000   0.000   0.000
   1_xyz:  0.328  50.568  -3.261  -0.195   2.282  -0.000   0.000   0.000
   1_adp:  0.328  50.568  -3.261  -0.195   2.282  -0.000   0.000   0.000
   1_occ:  0.328  50.568  -3.261  -0.195   2.282  -0.000   0.000   0.000
   2_bss:  0.336  59.265  -3.095  -2.018  -0.170  -0.000  -0.000  -0.000
   2_xyz:  0.336  59.265  -3.095  -2.018  -0.170  -0.000  -0.000  -0.000
   2_adp:  0.336  59.265  -3.095  -2.018  -0.170  -0.000  -0.000  -0.000
   2_occ:  0.336  59.265  -3.095  -2.018  -0.170  -0.000  -0.000  -0.000
   3_bss:  0.336  59.265  -2.830  -2.379  -0.559  -0.000  -0.000  -0.000
   3_xyz:  0.336  59.265  -2.830  -2.379  -0.559  -0.000  -0.000  -0.000
   3_adp:  0.336  59.265  -2.830  -2.379  -0.559  -0.000  -0.000  -0.000
   3_occ:  0.336  59.265  -2.830  -2.379  -0.559  -0.000  -0.000  -0.000
   4_bss:  0.328  59.265  -2.597  -2.352  -0.593  -0.000  -0.000  -0.000
   4_xyz:  0.328  59.265  -2.597  -2.352  -0.593  -0.000  -0.000  -0.000
   4_adp:  0.328  59.265  -2.597  -2.352  -0.593  -0.000  -0.000  -0.000
   4_occ:  0.328  59.265  -2.597  -2.352  -0.593  -0.000  -0.000  -0.000
   5_bss:  0.328  59.265  -2.324  -2.168  -0.411  -0.000  -0.000  -0.000
   5_xyz:  0.328  59.265  -2.324  -2.168  -0.411  -0.000  -0.000  -0.000
   5_adp:  0.328  59.265  -2.324  -2.168  -0.411  -0.000  -0.000  -0.000
   5_occ:  0.328  59.265  -2.324  -2.168  -0.411  -0.000  -0.000  -0.000
   5_bss:  0.324  59.258  -2.106  -1.994  -0.231  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.019 0.6922  0.8665    33022.123
   1_bss:  34.809 0.7041  0.8708    30094.458
   1_xyz:  20.228 0.8603  1.0055    11450.446
   1_adp:  21.185 0.8503  0.9978    12239.706
   1_occ:  21.160 0.8505  0.9975    12186.468
   2_bss:  20.835 0.8541  0.9554    12023.353
   2_xyz:  16.230 0.8958  0.9797     7736.069
   2_adp:  15.155 0.9054  0.9792     7130.181
   2_occ:  15.152 0.9055  0.9791     7116.441
   3_bss:  15.101 0.9059  0.9739     7084.998
   3_xyz:  14.197 0.9135  0.9769     6500.376
   3_adp:  14.168 0.9138  0.9711     6467.750
   3_occ:  14.180 0.9137  0.9709     6473.436
   4_bss:  14.171 0.9138  0.9737     6467.911
   4_xyz:  13.976 0.9154  0.9748     6355.130
   4_adp:  13.959 0.9156  0.9682     6327.143
   4_occ:  13.970 0.9155  0.9681     6333.420
   5_bss:  13.972 0.9155  0.9755     6335.596
   5_xyz:  14.028 0.9151  0.9754     6431.704
   5_adp:  14.000 0.9154  0.9682     6408.191
   5_occ:  14.006 0.9153  0.9681     6410.978
   5_bss:  14.006 0.9153  0.9745     6410.123
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6431e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6431e-01
   1_xyz:   1.142  0.009  0.078 15.599  0.005  4.111   7.4217e-02
   1_adp:   1.142  0.009  0.078 15.599  0.005  4.111   7.4217e-02
   1_occ:   1.142  0.009  0.078 15.599  0.005  4.111   7.4217e-02
   2_bss:   1.142  0.009  0.078 15.599  0.005  4.111   7.4217e-02
   2_xyz:   0.986  0.007  0.073 15.021  0.003  4.120   5.8163e-02
   2_adp:   0.986  0.007  0.073 15.021  0.003  4.120   5.8163e-02
   2_occ:   0.986  0.007  0.073 15.021  0.003  4.120   5.8163e-02
   3_bss:   0.986  0.007  0.073 15.021  0.003  4.120   5.8163e-02
   3_xyz:   0.906  0.006  0.070 14.832  0.003  4.113   5.2042e-02
   3_adp:   0.906  0.006  0.070 14.832  0.003  4.113   5.2042e-02
   3_occ:   0.906  0.006  0.070 14.832  0.003  4.113   5.2042e-02
   4_bss:   0.906  0.006  0.070 14.832  0.003  4.113   5.2042e-02
   4_xyz:   1.002  0.008  0.077 14.890  0.004  4.115   6.0874e-02
   4_adp:   1.002  0.008  0.077 14.890  0.004  4.115   6.0874e-02
   4_occ:   1.002  0.008  0.077 14.890  0.004  4.115   6.0874e-02
   5_bss:   1.002  0.008  0.077 14.890  0.004  4.115   6.0874e-02
   5_xyz:   0.995  0.008  0.077 14.835  0.004  4.116   6.1357e-02
   5_adp:   0.995  0.008  0.077 14.835  0.004  4.116   6.1357e-02
   5_occ:   0.995  0.008  0.077 14.835  0.004  4.116   6.1357e-02
   5_bss:   0.995  0.008  0.077 14.835  0.004  4.116   6.1357e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4132e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4132e-01
   1_xyz:   8.970  0.050  0.288 83.943  0.046  2.149   6.0473e-02
   1_adp:   8.970  0.050  0.288 83.943  0.046  2.149   6.0473e-02
   1_occ:   8.970  0.050  0.288 83.943  0.046  2.149   6.0473e-02
   2_bss:   8.970  0.050  0.288 83.943  0.046  2.149   6.0473e-02
   2_xyz:   6.896  0.041  0.223 82.215  0.029  2.359   7.3382e-02
   2_adp:   6.896  0.041  0.223 82.215  0.029  2.359   7.3382e-02
   2_occ:   6.896  0.041  0.223 82.215  0.029  2.359   7.3382e-02
   3_bss:   6.896  0.041  0.223 82.215  0.029  2.359   7.3382e-02
   3_xyz:   6.951  0.040  0.221 84.092  0.035  2.388   4.0196e-02
   3_adp:   6.951  0.040  0.221 84.092  0.035  2.388   4.0196e-02
   3_occ:   6.951  0.040  0.221 84.092  0.035  2.388   4.0196e-02
   4_bss:   6.951  0.040  0.221 84.092  0.035  2.388   4.0196e-02
   4_xyz:   6.553  0.045  0.247 83.193  0.036  2.333   4.2614e-02
   4_adp:   6.553  0.045  0.247 83.193  0.036  2.333   4.2614e-02
   4_occ:   6.553  0.045  0.247 83.193  0.036  2.333   4.2614e-02
   5_bss:   6.553  0.045  0.247 83.193  0.036  2.333   4.2614e-02
   5_xyz:   6.472  0.049  0.261 83.801  0.036  2.354   4.5320e-02
   5_adp:   6.472  0.049  0.261 83.801  0.036  2.354   4.5320e-02
   5_occ:   6.472  0.049  0.261 83.801  0.036  2.354   4.5320e-02
   5_bss:   6.472  0.049  0.261 83.801  0.036  2.354   4.5320e-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:  79.64   0.74  17.22  68.28   0.74  13.03  79.64   3.74  40.08
   1_occ:  79.64   0.74  17.22  68.28   0.74  13.03  79.64   3.74  40.08
   2_bss:  79.64   0.74  17.22  68.28   0.74  13.03  79.64   3.74  40.08
   2_xyz:  79.64   0.74  17.22  68.28   0.74  13.03  79.64   3.74  40.08
   2_adp:  76.18   1.21  16.89  67.97   1.21  12.83  76.18   6.29  39.00
   2_occ:  76.18   1.21  16.89  67.97   1.21  12.83  76.18   6.29  39.00
   3_bss:  76.18   1.21  16.89  67.97   1.21  12.83  76.18   6.29  39.00
   3_xyz:  76.18   1.21  16.89  67.97   1.21  12.83  76.18   6.29  39.00
   3_adp:  78.49   0.69  17.14  78.49   0.69  12.85  77.62   4.02  40.47
   3_occ:  78.49   0.69  17.14  78.49   0.69  12.85  77.62   4.02  40.47
   4_bss:  78.49   0.69  17.14  78.49   0.69  12.85  77.62   4.02  40.47
   4_xyz:  78.49   0.69  17.14  78.49   0.69  12.85  77.62   4.02  40.47
   4_adp:  86.38   0.34  17.07  86.38   0.34  12.76  82.35   4.33  40.55
   4_occ:  86.38   0.34  17.07  86.38   0.34  12.76  82.35   4.33  40.55
   5_bss:  86.38   0.34  17.07  86.38   0.34  12.76  82.35   4.33  40.55
   5_xyz:  86.38   0.34  17.07  86.38   0.34  12.76  82.35   4.33  40.55
   5_adp:  87.49   0.27  16.88  87.49   0.27  12.56  82.86   5.70  40.41
   5_occ:  87.49   0.27  16.88  87.49   0.27  12.56  82.86   5.70  40.41
   5_bss:  87.48   0.26  16.87  87.48   0.26  12.55  82.85   5.70  40.40
------------------------------------------------------------------------
 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:    1.145    0.004    0.347
   1_adp:    1.145    0.004    0.347
   1_occ:    1.145    0.004    0.347
   2_bss:    1.145    0.004    0.347
   2_xyz:    0.993    0.037    0.401
   2_adp:    0.993    0.037    0.401
   2_occ:    0.993    0.037    0.401
   3_bss:    0.993    0.037    0.401
   3_xyz:    1.084    0.048    0.429
   3_adp:    1.084    0.048    0.429
   3_occ:    1.084    0.048    0.429
   4_bss:    1.084    0.048    0.429
   4_xyz:    1.310    0.073    0.444
   4_adp:    1.310    0.073    0.444
   4_occ:    1.310    0.073    0.444
   5_bss:    1.310    0.073    0.444
   5_xyz:    1.410    0.071    0.452
   5_adp:    1.410    0.071    0.452
   5_occ:    1.410    0.071    0.452
   5_bss:    1.410    0.071    0.452
------------------------------------------------------------------------

CPU time actual refinement: 325.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_646/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_646/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_646/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_646/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_646/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.07 
  Macro-tasks:
    bulk solvent and scale       = 36.02  
    individual site refinement   = 134.24 
    weights calculation          = 29.24  
    collect and process          = 6.60   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 206.21 
  Micro-tasks:
    mask                            = 1.23   
    f_calc                          = 103.84 
    alpha_beta                      = 8.14   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 113.16 
    fmodel                         = 6.79   
    r_factors                      = 0.18   
    phase_errors                   = 10.87  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 245.68 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.592 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    658 calls, 103.53 s
gradients_fft:          603 calls,  99.39 s

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

# Date 2008-01-16 Time 05:19:18 PST -0800 (1200489558.22 s)
Start R-work = 0.3487, R-free = 0.3431 (no bulk solvent and anisotropic scale)
Final R-work = 0.1307, R-free = 0.1754 (no bulk solvent and anisotropic scale)

Start R-work = 0.3344, R-free = 0.3314
Final R-work = 0.1084, R-free = 0.1580