# Date 2008-01-16 Time 05:12:26 PST -0800 (1200489146.25 s)
#phil __OFF__

Command line arguments: "../633.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28544
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 633

-------------------------------------------------------------------------------
  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, 46.2261, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 1.97266
Completeness in resolution range: 0.955747
Completeness with d_max=infinity: 0.952819

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0142
                             d_min =   1.9727

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, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0142 1.97266
Completeness in resolution range: 0.955747
Completeness with d_max=infinity: 0.952819

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0146 -  4.2214 [2155/2179]  1937   218  10.1%
  bin  2:  4.2214 -  3.3631 [2058/2078]  1854   204   9.9%
  bin  3:  3.3631 -  2.9416 [2049/2068]  1843   206  10.1%
  bin  4:  2.9416 -  2.6743 [2024/2054]  1824   200   9.9%
  bin  5:  2.6743 -  2.4835 [2006/2025]  1808   198   9.9%
  bin  6:  2.4835 -  2.3377 [1994/2019]  1791   203  10.2%
  bin  7:  2.3377 -  2.2210 [1997/2025]  1793   204  10.2%
  bin  8:  2.2210 -  2.1246 [1986/2022]  1791   195   9.8%
  bin  9:  2.1246 -  2.0430 [1969/2011]  1775   194   9.9%
  bin 10:  2.0430 -  1.9727 [1351/2015]  1214   137  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_633/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: 26
        2.42 -     3.04: 2198
        3.04 -     3.66: 4732
        3.66 -     4.28: 9082
        4.28 -     4.90: 12379
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.030 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.140 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28412 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_633/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_633/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 46.22605 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3400   r_free= 0.3344   ksol= 0.00   Bsol= 0.00   scale= 0.964    |
|                                                                             |
| 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: 6.107286                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7086 0.99   1400  155 0.2969 0.2843      6.3918       6.331|
|  2:  4.7086 -  3.7566 0.99   1345  151 0.2702 0.2501       6.515      6.4169|
|  3:  3.7566 -  3.2874 0.99   1317  143 0.2893 0.2762      6.4124      6.4681|
|  4:  3.2874 -  2.9894 0.99   1318  151 0.3115 0.3455      6.3029      6.3719|
|  5:  2.9894 -  2.7766 0.99   1299  145 0.3568 0.2819      6.1862      6.0547|
|  6:  2.7766 -  2.6138 0.99   1301  140 0.3468 0.3773      6.0818      6.0314|
|  7:  2.6138 -  2.4835 0.99   1286  141 0.3598 0.3287      6.0619      6.0224|
|  8:  2.4835 -  2.3758 0.98   1276  146 0.3685 0.4046      6.0255      6.0852|
|  9:  2.3758 -  2.2847 0.98   1277  142 0.3767 0.3852      5.9869      5.9845|
| 10:  2.2847 -  2.2061 1.00   1295  147 0.3879 0.3595      5.9717      5.8789|
| 11:  2.2061 -  2.1373 0.97   1267  136 0.3840 0.3997      5.9066      5.9751|
| 12:  2.1373 -  2.0764 0.98   1262  145 0.3966 0.3966      5.8803       5.888|
| 13:  2.0764 -  2.0219 0.99   1289  135 0.3985 0.3927      5.7562       5.737|
| 14:  2.0219 -  1.9727 0.54    698   82 0.4419 0.4456      5.8344      5.7427|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7086  1400   155  0.80  25.36   0.86     0.83      41489.83|
|  2:  4.7086 -  3.7566  1345   151  0.83  22.79   0.96     0.92      49406.68|
|  3:  3.7566 -  3.2874  1317   143  0.79  27.25   1.00     0.96      50619.02|
|  4:  3.2874 -  2.9894  1318   151  0.76  30.55   0.99     0.93      45449.02|
|  5:  2.9894 -  2.7766  1299   145  0.70  35.42   0.98     0.90      36713.67|
|  6:  2.7766 -  2.6138  1301   140  0.70  35.98   0.97     0.87      32501.84|
|  7:  2.6138 -  2.4835  1286   141  0.67  38.44   1.00     0.86      32023.04|
|  8:  2.4835 -  2.3758  1276   146  0.65  40.06   1.00     0.85      31254.09|
|  9:  2.3758 -  2.2847  1277   142  0.65  40.20   1.02     0.86      28926.23|
| 10:  2.2847 -  2.2061  1295   147  0.65  40.33   1.02     0.87      25875.30|
| 11:  2.2061 -  2.1373  1267   136  0.64  41.06   1.03     0.90      25537.88|
| 12:  2.1373 -  2.0764  1262   145  0.62  43.05   1.04     0.87      24545.78|
| 13:  2.0764 -  2.0219  1289   135  0.56  47.61   1.02     0.82      23190.61|
| 14:  2.0219 -  1.9727   698    82  0.56  47.81   1.04     0.75      20894.68|
|alpha:            min =        0.75 max =            0.96 mean =         0.88|
|beta:             min =    20894.68 max =        50619.02 mean =     34055.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.69|
|phase err.(work): min =        0.00 max =           90.00 mean =        36.32|
|phase err.(test): min =        0.00 max =           89.79 mean =        36.34|
|-----------------------------------------------------------------------------|

============================== 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 = 5.301885              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.318   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.862770              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.158   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      204 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1994 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1874 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2858 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4659 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4423 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5662 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6717 |
|-----------------------------------------------------------------------------|
|-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 |   4.111    4.900  1.806 |       0.214 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    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: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3400   r_free= 0.3344   ksol= 0.00   Bsol= 0.00   scale= 0.964    |
|                                                                             |
| 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: 6.107286                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3235   r_free= 0.3223   ksol= 0.35   Bsol= 50.00   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,2.51,-1.02,0.00,-0.00,-0.00); trace/3= -0.54                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.087132                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.606431              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.355   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.440010              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.056   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3235      final r-factor (work) = 0.2015          |
| start r-factor (free) = 0.3223      final r-factor (free) = 0.2286          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1834 = 4.61 * 0.50 * 6.0867 + 1.00 * 0.1643                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4707 = 4.61 * 0.50 * 5.8129 + 1.00 * 0.0824                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2015      final r-factor (work) = 0.1836          |
| start r-factor (free) = 0.2286      final r-factor (free) = 0.2380          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5637 = 0.44 * 1.00 * 5.8129 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4586 = 0.44 * 1.00 * 5.5645 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.36   17.23    None  None   None       |
|    all(noH): 2823   0      0.00    85.36   17.23    None  None   None       |
|    Sol.    : 438    0      5.14    85.36   40.01    None  None   None       |
|    Mac.    : 2385   0      0.00    76.09   13.04    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.536:  693   |   5:    42.680 -  51.216:   98        |
|      1:     8.536 -  17.072: 1275   |   6:    51.216 -  59.752:   79        |
|      2:    17.072 -  25.608:  341   |   7:    59.752 -  68.288:   33        |
|      3:    25.608 -  34.144:  152   |   8:    68.288 -  76.824:   12        |
|      4:    34.144 -  42.680:  139   |   9:    76.824 -  85.360:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1836 r_free = 0.2380             target_work(ml) = 5.577         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1834 r_free = 0.2376             target_work(ml) = 5.575         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1834   r_free= 0.2376   ksol= 0.35   Bsol= 50.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,2.51,-1.02,0.00,-0.00,-0.00); trace/3= -0.54                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.575453                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1805   r_free= 0.2324   ksol= 0.32   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-1.20,-1.19,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.559167                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.136935              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.495   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.125792              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.355  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1805      final r-factor (work) = 0.1338          |
| start r-factor (free) = 0.2324      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8128 = 3.14 * 0.50 * 5.5662 + 1.00 * 0.0824                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5760 = 3.14 * 0.50 * 5.4316 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1338      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1821      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6934 = 0.13 * 1.00 * 5.4316 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6706 = 0.13 * 1.00 * 5.2770 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.90    80.80   16.73    None  None   None       |
|    all(noH): 2823   0      1.90    80.80   16.73    None  None   None       |
|    Sol.    : 438    0      6.56    80.80   38.04    None  None   None       |
|    Mac.    : 2385   0      1.90    74.40   12.82    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:     1.903 -   9.793:  933   |   5:    41.353 -  49.243:   96        |
|      1:     9.793 -  17.683: 1143   |   6:    49.243 -  57.133:   71        |
|      2:    17.683 -  25.573:  270   |   7:    57.133 -  65.023:   31        |
|      3:    25.573 -  33.463:  130   |   8:    65.023 -  72.913:   15        |
|      4:    33.463 -  41.353:  132   |   9:    72.913 -  80.803:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1274 r_free = 0.1705             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1272 r_free = 0.1705             target_work(ml) = 5.245         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1705   ksol= 0.32   Bsol= 50.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-1.20,-1.19,-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: 5.245035                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1695   ksol= 0.32   Bsol= 50.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.25,-1.16,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.240134                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.176358              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.678  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.796721              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.232  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1695      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7972 = 2.18 * 0.50 * 5.2754 + 1.00 * 0.0567                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7127 = 2.18 * 0.50 * 5.1996 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.5486 = 2.80 * 1.00 * 5.1996 + 1.00 * 0.0068                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.4091 = 2.80 * 1.00 * 5.1487 + 1.00 * 0.0098                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.47   17.38    None  None   None       |
|    all(noH): 2823   0      0.00    90.47   17.38    None  None   None       |
|    Sol.    : 438    0      3.24    86.97   41.47    None  None   None       |
|    Mac.    : 2385   0      0.00    90.47   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.047:  820   |   5:    45.235 -  54.282:   96        |
|      1:     9.047 -  18.094: 1272   |   6:    54.282 -  63.329:   73        |
|      2:    18.094 -  27.141:  256   |   7:    63.329 -  72.376:   38        |
|      3:    27.141 -  36.188:  138   |   8:    72.376 -  81.423:   18        |
|      4:    36.188 -  45.235:  108   |   9:    81.423 -  90.470:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1582             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1582             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1582   ksol= 0.32   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.25,-1.16,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148069                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1580   ksol= 0.32   Bsol= 52.40   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.34,-1.00,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147225                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.986693              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.033  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.098426              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.553  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7429 = 2.99 * 0.50 * 5.1483 + 1.00 * 0.0546                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7203 = 2.99 * 0.50 * 5.1256 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1072      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6398 = 1.10 * 1.00 * 5.1256 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6267 = 1.10 * 1.00 * 5.1135 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.25   17.15    None  None   None       |
|    all(noH): 2823   0      0.00    95.25   17.15    None  None   None       |
|    Sol.    : 438    0      4.09    87.53   40.88    None  None   None       |
|    Mac.    : 2385   0      0.00    95.25   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.525:  986   |   5:    47.624 -  57.149:   92        |
|      1:     9.525 -  19.050: 1160   |   6:    57.149 -  66.673:   54        |
|      2:    19.050 -  28.574:  229   |   7:    66.673 -  76.198:   27        |
|      3:    28.574 -  38.099:  135   |   8:    76.198 -  85.723:   15        |
|      4:    38.099 -  47.624:  123   |   9:    85.723 -  95.248:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1541             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1542             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1542   ksol= 0.32   Bsol= 52.40   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.34,-1.00,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112898                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1541   ksol= 0.32   Bsol= 52.40   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.24,-0.77,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112865                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.989306              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.576  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.228992              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.585  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1059          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7102 = 2.99 * 0.50 * 5.1143 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7029 = 2.99 * 0.50 * 5.1108 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1059      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1802 = 0.23 * 1.00 * 5.1108 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1793 = 0.23 * 1.00 * 5.1159 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.13    91.43   16.40    None  None   None       |
|    all(noH): 2823   0      1.13    91.43   16.40    None  None   None       |
|    Sol.    : 438    0      5.91    83.52   37.99    None  None   None       |
|    Mac.    : 2385   0      1.13    91.43   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.134 -  10.164: 1169   |   5:    46.283 -  55.313:   99        |
|      1:    10.164 -  19.194: 1006   |   6:    55.313 -  64.342:   35        |
|      2:    19.194 -  28.224:  220   |   7:    64.342 -  73.372:   17        |
|      3:    28.224 -  37.253:  140   |   8:    73.372 -  82.402:    7        |
|      4:    37.253 -  46.283:  127   |   9:    82.402 -  91.432:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1066 r_free = 0.1537             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1066 r_free = 0.1537             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1537   ksol= 0.32   Bsol= 52.40   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.24,-0.77,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111298                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7086 0.99   1400  155 0.0968 0.1258      5.3683      5.5414|
|  2:  4.7086 -  3.7566 0.99   1345  151 0.0829 0.1140      5.4215       5.616|
|  3:  3.7566 -  3.2874 0.99   1317  143 0.1015 0.1497      5.4464      5.8459|
|  4:  3.2874 -  2.9894 0.99   1318  151 0.1154 0.1578      5.4122      5.5594|
|  5:  2.9894 -  2.7766 0.99   1299  145 0.1269 0.1709      5.2983      5.5679|
|  6:  2.7766 -  2.6138 0.99   1301  140 0.1129 0.1914      5.1728      5.4445|
|  7:  2.6138 -  2.4835 0.99   1286  141 0.1225 0.1485      5.1463      5.2986|
|  8:  2.4835 -  2.3758 0.98   1276  146 0.1086 0.1604      5.0104      5.2862|
|  9:  2.3758 -  2.2847 0.98   1277  142 0.1119 0.1623       4.994      5.2293|
| 10:  2.2847 -  2.2061 1.00   1295  147 0.1044 0.1732      4.8935      5.2169|
| 11:  2.2061 -  2.1373 0.97   1267  136 0.1059 0.1695      4.8946      5.2475|
| 12:  2.1373 -  2.0764 0.98   1262  145 0.1048 0.1645      4.8266      5.1417|
| 13:  2.0764 -  2.0219 0.99   1289  135 0.1081 0.1735      4.7463      5.0286|
| 14:  2.0219 -  1.9727 0.54    698   82 0.0988 0.1512      4.6557      4.8221|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7086  1400   155  0.94   9.06   0.98     0.95       7019.81|
|  2:  4.7086 -  3.7566  1345   151  0.95   7.72   1.02     1.01       8994.22|
|  3:  3.7566 -  3.2874  1317   143  0.94  10.91   1.03     1.02       9918.17|
|  4:  3.2874 -  2.9894  1318   151  0.92  13.25   1.01     0.99       9700.05|
|  5:  2.9894 -  2.7766  1299   145  0.90  15.62   1.00     0.97       8054.62|
|  6:  2.7766 -  2.6138  1301   140  0.90  15.68   0.98     0.96       6749.72|
|  7:  2.6138 -  2.4835  1286   141  0.91  15.35   0.99     0.96       6051.16|
|  8:  2.4835 -  2.3758  1276   146  0.91  14.42   0.99     0.97       4760.27|
|  9:  2.3758 -  2.2847  1277   142  0.92  14.43   1.00     0.97       4592.53|
| 10:  2.2847 -  2.2061  1295   147  0.91  14.71   1.00     0.98       3958.96|
| 11:  2.2061 -  2.1373  1267   136  0.90  15.52   0.99     0.94       3998.57|
| 12:  2.1373 -  2.0764  1262   145  0.92  14.33   1.01     1.01       3620.04|
| 13:  2.0764 -  2.0219  1289   135  0.91  15.72   1.00     0.98       3118.91|
| 14:  2.0219 -  1.9727   698    82  0.92  13.65   0.98     0.96       2539.83|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2539.83 max =         9918.17 mean =      6085.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.54|
|phase err.(test): min =        0.00 max =           88.50 mean =        13.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1538   ksol= 0.32   Bsol= 52.36   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.15,-0.60,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111352                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1538   ksol= 0.32   Bsol= 52.36   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.15,-0.60,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111352                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0146 -  4.7086 0.99   1400  155 0.0969 0.1260      5.3695      5.5427|
|  2:  4.7086 -  3.7566 0.99   1345  151 0.0829 0.1140      5.4216      5.6157|
|  3:  3.7566 -  3.2874 0.99   1317  143 0.1014 0.1497      5.4463       5.846|
|  4:  3.2874 -  2.9894 0.99   1318  151 0.1154 0.1578      5.4122      5.5594|
|  5:  2.9894 -  2.7766 0.99   1299  145 0.1269 0.1709      5.2983      5.5678|
|  6:  2.7766 -  2.6138 0.99   1301  140 0.1129 0.1913      5.1727       5.444|
|  7:  2.6138 -  2.4835 0.99   1286  141 0.1225 0.1488      5.1464       5.299|
|  8:  2.4835 -  2.3758 0.98   1276  146 0.1086 0.1603      5.0104       5.286|
|  9:  2.3758 -  2.2847 0.98   1277  142 0.1120 0.1621       4.994      5.2289|
| 10:  2.2847 -  2.2061 1.00   1295  147 0.1044 0.1734      4.8936       5.218|
| 11:  2.2061 -  2.1373 0.97   1267  136 0.1059 0.1695      4.8948      5.2477|
| 12:  2.1373 -  2.0764 0.98   1262  145 0.1047 0.1646      4.8267      5.1419|
| 13:  2.0764 -  2.0219 0.99   1289  135 0.1081 0.1732      4.7459      5.0275|
| 14:  2.0219 -  1.9727 0.54    698   82 0.0987 0.1510      4.6548       4.821|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0146 -  4.7086  1400   155  0.94   9.07   0.98     0.95       7041.16|
|  2:  4.7086 -  3.7566  1345   151  0.95   7.73   1.02     1.01       9004.59|
|  3:  3.7566 -  3.2874  1317   143  0.94  10.91   1.03     1.02       9916.60|
|  4:  3.2874 -  2.9894  1318   151  0.92  13.25   1.01     0.99       9699.80|
|  5:  2.9894 -  2.7766  1299   145  0.90  15.62   1.00     0.97       8051.16|
|  6:  2.7766 -  2.6138  1301   140  0.90  15.68   0.99     0.96       6749.39|
|  7:  2.6138 -  2.4835  1286   141  0.91  15.35   0.99     0.96       6051.72|
|  8:  2.4835 -  2.3758  1276   146  0.91  14.42   1.00     0.97       4758.36|
|  9:  2.3758 -  2.2847  1277   142  0.92  14.43   1.00     0.97       4591.23|
| 10:  2.2847 -  2.2061  1295   147  0.91  14.72   1.01     0.98       3961.76|
| 11:  2.2061 -  2.1373  1267   136  0.90  15.53   0.99     0.95       4003.35|
| 12:  2.1373 -  2.0764  1262   145  0.92  14.33   1.02     1.01       3622.43|
| 13:  2.0764 -  2.0219  1289   135  0.91  15.70   1.00     0.98       3115.50|
| 14:  2.0219 -  1.9727   698    82  0.92  13.63   0.99     0.96       2532.66|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2532.66 max =         9916.60 mean =      6087.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.54|
|phase err.(test): min =        0.00 max =           88.49 mean =        13.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.776)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    91.39   16.36    None  None   None       |
|    all(noH): 2823   0      1.09    91.39   16.36    None  None   None       |
|    Sol.    : 438    0      5.87    83.48   37.95    None  None   None       |
|    Mac.    : 2385   0      1.09    91.39   12.39    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:     1.095 -  10.125: 1169   |   5:    46.243 -  55.273:   99        |
|      1:    10.125 -  19.154: 1006   |   6:    55.273 -  64.303:   35        |
|      2:    19.154 -  28.184:  220   |   7:    64.303 -  73.333:   17        |
|      3:    28.184 -  37.214:  140   |   8:    73.333 -  82.362:    7        |
|      4:    37.214 -  46.243:  127   |   9:    82.362 -  91.392:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 290         
Filter by distance & map next to the model:
   mapped sites are within: 0.521 - 4.670
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 284 from: 290
   mapped sites are within: 0.739 - 4.670

peak=    6.047 closest distance to " NE2 GLN A  11 " =    1.259
peak=    5.751 closest distance to " NH2 ARG A  56 " =    2.171
peak=    5.353 closest distance to " O   HOH Z 126 " =    1.915
peak=    5.305 closest distance to " O   HOH Z 144 " =    1.766
peak=    5.286 closest distance to " CG  PRO A  54 " =    1.252
peak=    4.870 closest distance to " O   HOH Z 232 " =    2.358
peak=    4.755 closest distance to " CB  PRO A  54 " =    0.961
peak=    4.734 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.710 closest distance to " CB  ARG A  79 " =    1.418
peak=    4.707 closest distance to " CG  PRO A 213 " =    1.229
peak=    4.647 closest distance to " CB  GLN A 223 " =    1.453
peak=    4.639 closest distance to " O   HOH Z 427 " =    2.742
peak=    4.621 closest distance to " ND2 ASN A 187 " =    1.542
peak=    4.613 closest distance to " CB  SER A  63 " =    1.176
peak=    4.608 closest distance to " O   HOH Z 236 " =    2.216
peak=    4.570 closest distance to " C   PRO A 198 " =    1.475
peak=    4.500 closest distance to " O   HOH Z  78 " =    1.771
peak=    4.464 closest distance to " CB  GLU A 152 " =    1.260
peak=    4.458 closest distance to " CB  GLN A 183 " =    1.162
peak=    4.442 closest distance to " O   HOH Z 369 " =    2.113
peak=    4.369 closest distance to " O   HOH Z  63 " =    1.426
peak=    4.366 closest distance to " CG  TRP A 179 " =    2.211
peak=    4.350 closest distance to " O   HOH Z 371 " =    1.933
peak=    4.257 closest distance to " O   HOH Z 158 " =    3.071
peak=    4.228 closest distance to " CB  ASN A 148 " =    1.382
peak=    4.220 closest distance to " O   HOH Z 193 " =    1.835
peak=    4.216 closest distance to " O   HOH Z 298 " =    1.953
peak=    4.207 closest distance to " CB  ARG A 190 " =    1.651
peak=    4.199 closest distance to " O   HOH Z   9 " =    2.117
peak=    4.167 closest distance to " O   HOH Z 250 " =    1.508
peak=    4.159 closest distance to " O   HOH Z 209 " =    2.230
peak=    4.150 closest distance to " CB  ASN A 187 " =    1.215
peak=    4.149 closest distance to " O   HOH Z   1 " =    1.930
peak=    4.149 closest distance to " CG  PRO A 198 " =    1.252
peak=    4.149 closest distance to " CB  VAL A 265 " =    1.293
peak=    4.130 closest distance to " CD  ARG A  66 " =    2.286
peak=    4.120 closest distance to " CA  TYR A  30 " =    0.930
peak=    4.119 closest distance to " O   HOH Z 419 " =    2.230
peak=    4.108 closest distance to " CD  ARG A 159 " =    0.739
peak=    4.071 closest distance to " CB  TRP A 266 " =    1.025
peak=    4.042 closest distance to " NZ  LYS A 117 " =    3.265
peak=    4.042 closest distance to " O   HOH Z  61 " =    1.512
peak=    4.033 closest distance to " CB  LEU A 228 " =    1.092
peak=    4.023 closest distance to " CD2 TRP A 179 " =    1.317
peak=    4.010 closest distance to " OD1 ASN A  69 " =    2.652
peak=    4.009 closest distance to " CG2 VAL A 257 " =    0.896
peak=    4.002 closest distance to " O   HOH Z 272 " =    1.755
peak=    3.989 closest distance to " O   HOH Z 214 " =    2.110
peak=    3.987 closest distance to " O   HOH Z  61 " =    1.587
peak=    3.985 closest distance to " O   HOH Z 386 " =    3.077
peak=    3.977 closest distance to " O   HOH Z  40 " =    2.000
peak=    3.964 closest distance to " O   HOH Z 189 " =    2.442
peak=    3.961 closest distance to " O   HOH Z 234 " =    3.625
peak=    3.957 closest distance to " O   HOH Z 346 " =    1.669
peak=    3.956 closest distance to " CG  PRO A 243 " =    1.063
peak=    3.950 closest distance to " O   HOH Z 316 " =    3.095
peak=    3.946 closest distance to " O   HOH Z 261 " =    2.229
peak=    3.943 closest distance to " O   HOH Z 133 " =    2.467
peak=    3.917 closest distance to " O   HOH Z 389 " =    1.882
peak=    3.905 closest distance to " CG  PRO A 280 " =    0.739
peak=    3.901 closest distance to " O   HOH Z 265 " =    2.285
peak=    3.900 closest distance to " CB  SER A 212 " =    1.145
peak=    3.893 closest distance to " O   SER A  87 " =    2.118
peak=    3.885 closest distance to " O   HOH Z  10 " =    1.827
peak=    3.884 closest distance to " O   HOH Z 362 " =    2.557
peak=    3.872 closest distance to " CA  ASN A 215 " =    1.166
peak=    3.871 closest distance to " ND1 HIS A  86 " =    1.752
peak=    3.859 closest distance to " O   HOH Z 423 " =    1.476
peak=    3.851 closest distance to " O   HOH Z 132 " =    2.421
peak=    3.848 closest distance to " CE  LYS A  76 " =    0.874
peak=    3.817 closest distance to " O   HOH Z 180 " =    2.103
peak=    3.787 closest distance to " CB  SER A   3 " =    1.344
peak=    3.778 closest distance to " O   HOH Z 327 " =    1.579
peak=    3.764 closest distance to " O   HOH Z 423 " =    2.424
peak=    3.758 closest distance to " O   HOH Z   1 " =    1.732
peak=    3.757 closest distance to " O   HOH Z 128 " =    2.155
peak=    3.755 closest distance to " CZ  PHE A 218 " =    1.017
peak=    3.753 closest distance to " OG BSER A 164 " =    2.307
peak=    3.737 closest distance to " NH1AARG A 145 " =    1.210
peak=    3.734 closest distance to " CB  ARG A 139 " =    1.017
peak=    3.723 closest distance to " O   HOH Z 426 " =    1.975
peak=    3.722 closest distance to " CB  ASN A 142 " =    0.964
peak=    3.712 closest distance to " CG1 ILE A  33 " =    1.259
peak=    3.710 closest distance to " CB  GLU A 128 " =    0.971
peak=    3.709 closest distance to " O   HOH Z 175 " =    2.108
peak=    3.697 closest distance to " O   HOH Z 352 " =    1.812
peak=    3.695 closest distance to " O   HOH Z 403 " =    1.634
peak=    3.694 closest distance to " O   HOH Z 406 " =    1.613
peak=    3.681 closest distance to " CA  ALA A 233 " =    1.063
peak=    3.676 closest distance to " NH2BARG A 145 " =    2.156
peak=    3.673 closest distance to " O   HOH Z 368 " =    3.579
peak=    3.672 closest distance to " O   HOH Z 193 " =    2.028
peak=    3.656 closest distance to " CB  ASN A  39 " =    0.886
peak=    3.655 closest distance to " O   HOH Z 405 " =    1.267
peak=    3.650 closest distance to " CB  ASP A 140 " =    0.925
peak=    3.641 closest distance to " O   HOH Z 286 " =    2.240
peak=    3.639 closest distance to " O   HOH Z  21 " =    1.712
peak=    3.635 closest distance to " O   HOH Z 344 " =    3.141
peak=    3.631 closest distance to " CD1 ILE A 263 " =    1.382
peak=    3.631 closest distance to " O   HOH Z 425 " =    2.015
peak=    3.629 closest distance to " NH2AARG A 190 " =    1.930
peak=    3.622 closest distance to " CB  ALA A  34 " =    1.014
peak=    3.613 closest distance to " O   HOH Z 368 " =    2.010
peak=    3.609 closest distance to " OD1BASN A 224 " =    2.265
peak=    3.606 closest distance to " CB  VAL A 202 " =    1.607
peak=    3.598 closest distance to " N   PHE A 130 " =    1.246
peak=    3.597 closest distance to " O   HOH Z 437 " =    1.674
peak=    3.594 closest distance to " O   HOH Z 371 " =    2.906
peak=    3.594 closest distance to " CA  ALA A  84 " =    1.386
peak=    3.590 closest distance to " O   HOH Z 380 " =    1.694
peak=    3.586 closest distance to " CB  GLU A 277 " =    3.539
peak=    3.580 closest distance to " CA  SER A  87 " =    0.978
peak=    3.567 closest distance to " O   HOH Z  66 " =    2.179
peak=    3.562 closest distance to " O   HOH Z 193 " =    1.647
peak=    3.559 closest distance to " CG  LEU A 167 " =    1.237
peak=    3.556 closest distance to " CB  SER A  26 " =    1.666
peak=    3.555 closest distance to " ND2 ASN A 249 " =    0.871
peak=    3.547 closest distance to " CG  PRO A  90 " =    1.170
peak=    3.540 closest distance to " O   HOH Z 261 " =    2.352
peak=    3.525 closest distance to " O   HOH Z 147 " =    1.818
peak=    3.525 closest distance to " O   HOH Z  44 " =    1.648
peak=    3.523 closest distance to " O   HOH Z 325 " =    3.941
peak=    3.515 closest distance to " O   HOH Z 291 " =    1.552
peak=    3.510 closest distance to " OG  SER A  22 " =    2.724
peak=    3.507 closest distance to " CG2 THR A 221 " =    1.032
peak=    3.507 closest distance to " O   HOH Z 126 " =    1.499
peak=    3.506 closest distance to " O   HOH Z 329 " =    3.840
peak=    3.505 closest distance to " O   HOH Z 213 " =    2.011
peak=    3.503 closest distance to " O   HOH Z 245 " =    1.308
peak=    3.496 closest distance to " CB  SER A 216 " =    0.813
peak=    3.490 closest distance to " O   HOH Z 345 " =    1.789
peak=    3.489 closest distance to " CG2AVAL A  72 " =    1.536
peak=    3.489 closest distance to " N   ALA A   1 " =    2.164
peak=    3.483 closest distance to " CD BLYS A 290 " =    1.174
peak=    3.480 closest distance to " CB  TYR A 116 " =    0.826
peak=    3.471 closest distance to " CB  LYS A 117 " =    1.218
peak=    3.471 closest distance to " N   ASN A 127 " =    1.334
peak=    3.470 closest distance to " CD  PRO A 243 " =    1.566
peak=    3.462 closest distance to " CA  THR A 264 " =    0.864
peak=    3.455 closest distance to " OD2 ASP A 286 " =    2.782
peak=    3.454 closest distance to " O   HOH Z 359 " =    1.510
peak=    3.453 closest distance to " O   HOH Z 128 " =    2.060
peak=    3.452 closest distance to " CD2 LEU A 297 " =    0.890
peak=    3.449 closest distance to " O   HOH Z 219 " =    2.102
peak=    3.447 closest distance to " O   HOH Z 391 " =    2.889
peak=    3.443 closest distance to " O   ASN A 209 " =    1.284
peak=    3.443 closest distance to " O   HOH Z 172 " =    2.871
peak=    3.438 closest distance to " CB  ALA A   1 " =    4.670
peak=    3.438 closest distance to " N   SER A 146 " =    1.720
peak=    3.436 closest distance to " CD1 LEU A 300 " =    1.202
peak=    3.434 closest distance to " O   HOH Z 287 " =    2.280
peak=    3.429 closest distance to " O   HOH Z 257 " =    2.179
peak=    3.428 closest distance to " CB  ASP A 124 " =    0.828
peak=    3.427 closest distance to " CB  ASN A 110 " =    1.053
peak=    3.427 closest distance to " O   HOH Z 417 " =    1.178
peak=    3.425 closest distance to " NH2AARG A 275 " =    3.633
peak=    3.423 closest distance to " NE2 GLN A  73 " =    3.761
peak=    3.418 closest distance to " O   HOH Z  89 " =    2.075
peak=    3.413 closest distance to " O   HOH Z  93 " =    2.485
peak=    3.412 closest distance to " CB  TRP A 179 " =    1.395
peak=    3.410 closest distance to " CB  GLN A  89 " =    1.352
peak=    3.409 closest distance to " O   HOH Z 116 " =    1.732
peak=    3.406 closest distance to " CA  ALA A  21 " =    1.148
peak=    3.404 closest distance to " CD1 ILE A 106 " =    0.833
peak=    3.403 closest distance to " O   HOH Z 365 " =    2.839
peak=    3.403 closest distance to " O   HOH Z 188 " =    1.964
peak=    3.401 closest distance to " O   HOH Z 248 " =    1.562
peak=    3.396 closest distance to " O   HOH Z 411 " =    3.817
peak=    3.392 closest distance to " O   HOH Z   3 " =    1.936
peak=    3.390 closest distance to " O   HOH Z  88 " =    2.681
peak=    3.390 closest distance to " CB  GLU A  46 " =    0.927
peak=    3.390 closest distance to " O   HOH Z  88 " =    3.820
peak=    3.390 closest distance to " CB  MET A  47 " =    1.127
peak=    3.388 closest distance to " O   HOH Z 407 " =    2.244
peak=    3.378 closest distance to " O  BHOH Z 338 " =    2.378
peak=    3.373 closest distance to " O   HOH Z 422 " =    2.643
peak=    3.372 closest distance to " CB  THR A 157 " =    1.135
peak=    3.370 closest distance to " CB  ILE A 120 " =    1.240
peak=    3.367 closest distance to " O   HOH Z 305 " =    3.547
peak=    3.365 closest distance to " O   HOH Z 116 " =    3.001
peak=    3.365 closest distance to " O   HOH Z 336 " =    1.953
peak=    3.364 closest distance to " CD  LYS A 166 " =    1.268
peak=    3.361 closest distance to " CE1 TYR A 186 " =    1.364
peak=    3.360 closest distance to " O   HOH Z 234 " =    1.834
peak=    3.351 closest distance to " N   CYS A 260 " =    0.814
peak=    3.347 closest distance to " N   ARG A 156 " =    1.320
peak=    3.346 closest distance to " CA  THR A 221 " =    1.034
peak=    3.340 closest distance to " NH1BARG A 145 " =    1.244
peak=    3.340 closest distance to " O   HOH Z 402 " =    1.395
peak=    3.337 closest distance to " O   HOH Z  88 " =    2.568
peak=    3.337 closest distance to " CG  GLN A  89 " =    1.487
peak=    3.335 closest distance to " O   HOH Z 146 " =    1.688
peak=    3.333 closest distance to " O   HOH Z 415 " =    3.656
peak=    3.333 closest distance to " O   HOH Z 280 " =    2.978
peak=    3.332 closest distance to " CA  TYR A 116 " =    1.285
peak=    3.324 closest distance to " O   HOH Z 302 " =    1.989
peak=    3.322 closest distance to " CB  ASN A 215 " =    1.110
peak=    3.319 closest distance to " O   ALA A   1 " =    1.671
peak=    3.317 closest distance to " CG2 ILE A 120 " =    1.103
peak=    3.310 closest distance to " CB  SER A  62 " =    1.193
peak=    3.308 closest distance to " O   HOH Z 153 " =    1.725
peak=    3.308 closest distance to " CB  THR A  31 " =    1.672
peak=    3.307 closest distance to " N   GLN A 278 " =    1.221
peak=    3.304 closest distance to " O   HOH Z 285 " =    2.601
peak=    3.304 closest distance to " CA  ARG A 195 " =    1.223
peak=    3.302 closest distance to " O   HOH Z 409 " =    2.395
peak=    3.302 closest distance to " N   ASN A  39 " =    1.256
peak=    3.298 closest distance to " O   HOH Z  64 " =    2.233
peak=    3.289 closest distance to " O   HOH Z 213 " =    1.873
peak=    3.289 closest distance to " ND2 ASN A 110 " =    1.793
peak=    3.287 closest distance to " CA  ASP A 162 " =    1.037
peak=    3.286 closest distance to " NE2 HIS A 207 " =    1.338
peak=    3.285 closest distance to " CA  ALA A 299 " =    0.863
peak=    3.282 closest distance to " O   HOH Z 421 " =    2.179
peak=    3.278 closest distance to " OG  SER A  62 " =    2.909
peak=    3.277 closest distance to " CB  ALA A 248 " =    0.947
peak=    3.268 closest distance to " CD  ARG A 269 " =    0.932
peak=    3.268 closest distance to " O   HOH Z  43 " =    2.140
peak=    3.268 closest distance to " CA  ALA A  51 " =    0.902
peak=    3.264 closest distance to " CA  MET A  40 " =    1.149
peak=    3.261 closest distance to " CB  ALA A 114 " =    1.422
peak=    3.259 closest distance to " CB  GLN A  88 " =    1.208
peak=    3.259 closest distance to " CG  MET A 113 " =    1.149
peak=    3.258 closest distance to " CA  ALA A 291 " =    0.873
peak=    3.253 closest distance to " O   HOH Z 139 " =    2.967
peak=    3.243 closest distance to " CB  MET A  40 " =    0.817
peak=    3.241 closest distance to " CG1 VAL A 189 " =    1.787
peak=    3.239 closest distance to " O   HOH Z 332 " =    1.508
peak=    3.237 closest distance to " CA  PRO A 280 " =    1.252
peak=    3.235 closest distance to " O   ASN A  74 " =    1.518
peak=    3.232 closest distance to " O   HOH Z 425 " =    1.274
peak=    3.232 closest distance to " CG2 VAL A 197 " =    1.053
peak=    3.227 closest distance to " O   HOH Z 390 " =    2.507
peak=    3.223 closest distance to " O   HOH Z 345 " =    3.377
peak=    3.221 closest distance to " NH1 ARG A 138 " =    1.128
peak=    3.221 closest distance to " CG1 ILE A 151 " =    1.082
peak=    3.221 closest distance to " O   HOH Z 148 " =    3.395
peak=    3.218 closest distance to " CD  ARG A  79 " =    2.301
peak=    3.218 closest distance to " O   HOH Z 294 " =    1.488
peak=    3.218 closest distance to " CG  GLN A 278 " =    1.299
peak=    3.215 closest distance to " O   HOH Z 128 " =    1.931
peak=    3.213 closest distance to " CB  TYR A 169 " =    0.891
peak=    3.209 closest distance to " CD  ARG A 138 " =    0.758
peak=    3.204 closest distance to " O   HOH Z  59 " =    1.994
peak=    3.203 closest distance to " O   HOH Z 435 " =    1.926
peak=    3.203 closest distance to " N   SER A 134 " =    1.277
peak=    3.195 closest distance to " CA  ALA A 158 " =    1.133
peak=    3.193 closest distance to " CG BARG A 102 " =    1.814
peak=    3.193 closest distance to " CD1 LEU A 255 " =    1.702
peak=    3.190 closest distance to " O   HOH Z 319 " =    2.228
peak=    3.189 closest distance to " O   MET A 105 " =    1.741
peak=    3.187 closest distance to " CZ3 TRP A 266 " =    1.105
peak=    3.174 closest distance to " CB  ALA A 291 " =    1.346
peak=    3.170 closest distance to " O   HOH Z 271 " =    2.531
peak=    3.168 closest distance to " O   HOH Z 298 " =    2.442
peak=    3.163 closest distance to " O   HOH Z 188 " =    2.440
peak=    3.148 closest distance to " CB  ARG A 138 " =    0.986
peak=    3.146 closest distance to " OG  SER A 206 " =    1.314
peak=    3.145 closest distance to " O   HOH Z  44 " =    2.925
peak=    3.143 closest distance to " CA  SER A  32 " =    1.669
peak=    3.141 closest distance to " CA  ARG A 102 " =    1.073
peak=    3.132 closest distance to " O   HOH Z 359 " =    4.212
peak=    3.130 closest distance to " O   HOH Z 272 " =    2.170
peak=    3.129 closest distance to " CE BLYS A 290 " =    1.253
peak=    3.128 closest distance to " CB  GLN A 278 " =    0.808
peak=    3.116 closest distance to " CA  LYS A 290 " =    1.329
peak=    3.115 closest distance to " O   HOH Z 238 " =    3.754
peak=    3.109 closest distance to " CG  LYS A  76 " =    0.953
peak=    3.109 closest distance to " CB  ASN A 224 " =    0.974
peak=    3.102 closest distance to " O   HOH Z 326 " =    2.487
peak=    3.097 closest distance to " O   HOH Z  99 " =    1.825
peak=    3.092 closest distance to " CA  ARG A  36 " =    1.021
peak=    3.092 closest distance to " O   HOH Z 266 " =    3.481
peak=    3.091 closest distance to " O   PRO A  90 " =    1.531
peak=    3.090 closest distance to " O   HOH Z  17 " =    1.737
peak=    3.088 closest distance to " ND1 HIS A  81 " =    1.682
peak=    3.085 closest distance to " O   HOH Z  87 " =    2.037
peak=    3.069 closest distance to " CA  SER A  95 " =    1.010
peak=    3.067 closest distance to " O   HOH Z 124 " =    2.396
peak=    3.062 closest distance to " CG  MET A 185 " =    1.195
peak=    3.054 closest distance to " OE2 GLU A  53 " =    2.112
peak=    3.048 closest distance to " O   HOH Z  50 " =    1.623
peak=    3.023 closest distance to " OG BSER A  99 " =    2.243
peak=    3.009 closest distance to " O   HOH Z 124 " =    2.193

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.591 - 5.639
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.708 - 5.639

peak=   -5.012 closest distance to " CB  PRO A 243 " =    2.614
peak=   -4.878 closest distance to " O   HOH Z 377 " =    2.125
peak=   -4.650 closest distance to " O   HOH Z 266 " =    4.929
peak=   -4.378 closest distance to " O   HOH Z 290 " =    1.196
peak=   -4.358 closest distance to " CD  ARG A 156 " =    2.089
peak=   -4.248 closest distance to " CG  GLN A 223 " =    1.922
peak=   -4.224 closest distance to " C   HIS A 108 " =    1.195
peak=   -4.209 closest distance to " O   HOH Z 435 " =    2.843
peak=   -4.159 closest distance to " O   VAL A  67 " =    2.671
peak=   -4.144 closest distance to " O   HOH Z 389 " =    1.949
peak=   -4.106 closest distance to " O   PRO A 198 " =    1.263
peak=   -4.094 closest distance to " O   HOH Z 351 " =    1.529
peak=   -4.084 closest distance to " SG  CYS A 254 " =    3.450
peak=   -4.060 closest distance to " CG1 VAL A 112 " =    2.889
peak=   -4.032 closest distance to " OG BSER A 134 " =    1.289
peak=   -3.970 closest distance to " ND2 ASN A  45 " =    1.902
peak=   -3.958 closest distance to " O   HOH Z 231 " =    2.296
peak=   -3.921 closest distance to " CZ3 TRP A 179 " =    1.220
peak=   -3.900 closest distance to " O   HOH Z 185 " =    2.225
peak=   -3.867 closest distance to " CZ  TYR A 169 " =    1.645
peak=   -3.851 closest distance to " CB  ALA A  43 " =    2.509
peak=   -3.827 closest distance to " CD  GLN A  58 " =    1.015
peak=   -3.827 closest distance to " O   HOH Z 372 " =    2.468
peak=   -3.810 closest distance to " O   HOH Z 407 " =    3.128
peak=   -3.808 closest distance to " CA  VAL A  67 " =    2.924
peak=   -3.801 closest distance to " N   ALA A  43 " =    2.592
peak=   -3.799 closest distance to " OD1 ASP A 171 " =    1.619
peak=   -3.787 closest distance to " O   HOH Z  38 " =    1.616
peak=   -3.775 closest distance to " CB  TRP A  85 " =    2.441
peak=   -3.755 closest distance to " O   HOH Z 313 " =    1.895
peak=   -3.755 closest distance to " O   PRO A 198 " =    1.255
peak=   -3.735 closest distance to " CB  ALA A 291 " =    2.178
peak=   -3.712 closest distance to " O   ARG A 145 " =    1.593
peak=   -3.695 closest distance to " CB  PRO A 163 " =    2.474
peak=   -3.686 closest distance to " O   HOH Z  73 " =    2.327
peak=   -3.679 closest distance to " CD2 LEU A 237 " =    2.850
peak=   -3.675 closest distance to " CD2 PHE A 192 " =    2.032
peak=   -3.664 closest distance to " CE  MET A 105 " =    2.368
peak=   -3.649 closest distance to " CA  GLY A  98 " =    1.803
peak=   -3.648 closest distance to " CB  ALA A 248 " =    2.404
peak=   -3.640 closest distance to " CG  PHE A 283 " =    2.605
peak=   -3.639 closest distance to " ND2 ASN A 249 " =    2.347
peak=   -3.637 closest distance to " ND2 ASN A 187 " =    1.450
peak=   -3.634 closest distance to " N   THR A 157 " =    1.540
peak=   -3.625 closest distance to " ND2 ASN A  45 " =    1.246
peak=   -3.618 closest distance to " OD1 ASN A 148 " =    1.594
peak=   -3.611 closest distance to " O   HOH Z 131 " =    4.101
peak=   -3.606 closest distance to " OD2 ASP A 171 " =    2.129
peak=   -3.604 closest distance to " O   HOH Z 359 " =    3.308
peak=   -3.593 closest distance to " OD1 ASP A 191 " =    1.823
peak=   -3.593 closest distance to " CA  GLY A 241 " =    2.270
peak=   -3.591 closest distance to " CD  ARG A 139 " =    1.572
peak=   -3.590 closest distance to " CE2 TYR A  30 " =    2.727
peak=   -3.589 closest distance to " CD1 PHE A  59 " =    1.956
peak=   -3.566 closest distance to " O   HOH Z 395 " =    5.158
peak=   -3.561 closest distance to " O   PRO A 243 " =    2.522
peak=   -3.559 closest distance to " CZ  PHE A  59 " =    1.517
peak=   -3.551 closest distance to " O   HOH Z 394 " =    1.371
peak=   -3.549 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.545 closest distance to " NH2BARG A 275 " =    1.747
peak=   -3.538 closest distance to " O   PRO A 163 " =    2.026
peak=   -3.537 closest distance to " O   HOH Z 198 " =    1.483
peak=   -3.523 closest distance to " O   HOH Z 385 " =    2.050
peak=   -3.519 closest distance to " O   HOH Z 198 " =    2.028
peak=   -3.514 closest distance to " OXT GLY A 302 " =    2.998
peak=   -3.508 closest distance to " O   HOH Z 377 " =    0.775
peak=   -3.507 closest distance to " CB  ALA A 248 " =    2.051
peak=   -3.499 closest distance to " O   HOH Z  52 " =    1.289
peak=   -3.497 closest distance to " O   HOH Z 140 " =    1.536
peak=   -3.485 closest distance to " O   HOH Z 298 " =    1.203
peak=   -3.485 closest distance to " O   HOH Z 211 " =    1.606
peak=   -3.484 closest distance to " OG  SER A  97 " =    2.220
peak=   -3.481 closest distance to " O   VAL A 189 " =    2.511
peak=   -3.480 closest distance to " CG2 ILE A 263 " =    2.242
peak=   -3.478 closest distance to " O   HOH Z  11 " =    1.785
peak=   -3.472 closest distance to " N   GLN A  58 " =    1.657
peak=   -3.470 closest distance to " N   SER A 212 " =    1.961
peak=   -3.467 closest distance to " NH2AARG A 275 " =    5.262
peak=   -3.463 closest distance to " CE3 TRP A 274 " =    2.338
peak=   -3.460 closest distance to " CB  ASN A  39 " =    2.301
peak=   -3.459 closest distance to " O   ALA A 161 " =    1.633
peak=   -3.457 closest distance to " O   SER A  95 " =    1.482
peak=   -3.452 closest distance to " O   HOH Z  43 " =    1.718
peak=   -3.445 closest distance to " CD1 LEU A 101 " =    2.210
peak=   -3.441 closest distance to " CG1 VAL A 197 " =    2.128
peak=   -3.437 closest distance to " NE2 GLN A 278 " =    1.614
peak=   -3.430 closest distance to " NE  ARG A  36 " =    1.933
peak=   -3.430 closest distance to " O   TRP A  70 " =    1.474
peak=   -3.428 closest distance to " O   HOH Z 266 " =    4.770
peak=   -3.426 closest distance to " O   HOH Z 348 " =    1.795
peak=   -3.424 closest distance to " O   HOH Z 317 " =    1.506
peak=   -3.420 closest distance to " CB  TYR A  15 " =    2.167
peak=   -3.418 closest distance to " O   SER A 135 " =    1.421
peak=   -3.418 closest distance to " CA  GLY A 133 " =    2.050
peak=   -3.415 closest distance to " C   ALA A 158 " =    1.499
peak=   -3.414 closest distance to " CB  ASP A 132 " =    2.381
peak=   -3.413 closest distance to " O   HOH Z  63 " =    1.952
peak=   -3.410 closest distance to " CD  GLU A 277 " =    1.186
peak=   -3.410 closest distance to " N   ASP A 286 " =    2.350
peak=   -3.403 closest distance to " O   HOH Z  51 " =    1.179
peak=   -3.400 closest distance to " OG BSER A 134 " =    1.692
peak=   -3.394 closest distance to " O   ALA A  34 " =    2.488
peak=   -3.388 closest distance to " N   MET A 188 " =    1.886
peak=   -3.388 closest distance to " CA  GLY A 203 " =    2.307
peak=   -3.386 closest distance to " O   PHE A 218 " =    1.570
peak=   -3.384 closest distance to " O   HOH Z  13 " =    1.582
peak=   -3.383 closest distance to " CB  CYS A 254 " =    2.254
peak=   -3.378 closest distance to " CG1 VAL A 230 " =    2.021
peak=   -3.375 closest distance to " OG  SER A  87 " =    1.309
peak=   -3.361 closest distance to " CB  ALA A 161 " =    2.550
peak=   -3.360 closest distance to " CD2 PHE A  61 " =    2.142
peak=   -3.360 closest distance to " O   HOH Z  60 " =    2.323
peak=   -3.354 closest distance to " O   ALA A  51 " =    1.385
peak=   -3.346 closest distance to " O   HOH Z 102 " =    1.577
peak=   -3.343 closest distance to " O   HOH Z 282 " =    0.977
peak=   -3.340 closest distance to " CD1 LEU A 228 " =    2.235
peak=   -3.336 closest distance to " O   SER A  22 " =    2.457
peak=   -3.329 closest distance to " CB  PHE A 208 " =    2.245
peak=   -3.324 closest distance to " O   HOH Z 298 " =    2.471
peak=   -3.321 closest distance to " NH2 ARG A  79 " =    2.001
peak=   -3.320 closest distance to " CG  ASP A 231 " =    0.740
peak=   -3.320 closest distance to " O   HOH Z 281 " =    2.664
peak=   -3.313 closest distance to " CE3 TRP A 274 " =    1.114
peak=   -3.307 closest distance to " CA  GLY A 241 " =    3.118
peak=   -3.306 closest distance to " CG  GLN A  88 " =    0.773
peak=   -3.306 closest distance to " O   HOH Z 111 " =    1.837
peak=   -3.306 closest distance to " OD2 ASP A 191 " =    1.377
peak=   -3.306 closest distance to " O   HOH Z 176 " =    0.803
peak=   -3.298 closest distance to " CG  GLU A 152 " =    0.810
peak=   -3.293 closest distance to " CB  ASP A 286 " =    2.095
peak=   -3.289 closest distance to " O   VAL A 189 " =    1.696
peak=   -3.286 closest distance to " CG2 THR A 178 " =    2.230
peak=   -3.284 closest distance to " CG  PRO A 163 " =    2.670
peak=   -3.280 closest distance to " CD1 LEU A 297 " =    2.432
peak=   -3.280 closest distance to " CE  LYS A  76 " =    2.714
peak=   -3.276 closest distance to " NH1AARG A 275 " =    1.840
peak=   -3.275 closest distance to " O   HOH Z 114 " =    2.987
peak=   -3.266 closest distance to " CD2 PHE A 225 " =    1.126
peak=   -3.264 closest distance to " OE1 GLN A 223 " =    1.839
peak=   -3.252 closest distance to " O   HOH Z  10 " =    1.432
peak=   -3.246 closest distance to " O   HOH Z 371 " =    1.398
peak=   -3.245 closest distance to " O   HOH Z 253 " =    3.884
peak=   -3.243 closest distance to " OH  TYR A 172 " =    1.739
peak=   -3.241 closest distance to " CG  ARG A 269 " =    2.361
peak=   -3.239 closest distance to " C   LEU A 143 " =    1.169
peak=   -3.236 closest distance to " OE1 GLN A  88 " =    1.181
peak=   -3.235 closest distance to " O   ALA A 292 " =    2.049
peak=   -3.234 closest distance to " C   MET A 188 " =    1.476
peak=   -3.234 closest distance to " O   VAL A 174 " =    2.176
peak=   -3.234 closest distance to " CA  GLY A  57 " =    2.152
peak=   -3.232 closest distance to " O   HOH Z  90 " =    2.426
peak=   -3.227 closest distance to " N   THR A 235 " =    1.320
peak=   -3.226 closest distance to " O   HOH Z 353 " =    2.237
peak=   -3.225 closest distance to " O   HOH Z  15 " =    1.591
peak=   -3.224 closest distance to " O   HOH Z 191 " =    5.639
peak=   -3.224 closest distance to " O   ALA A  10 " =    1.654
peak=   -3.223 closest distance to " O   HOH Z 244 " =    1.955
peak=   -3.220 closest distance to " C   LEU A 222 " =    0.708
peak=   -3.211 closest distance to " O   HOH Z 166 " =    1.403
peak=   -3.210 closest distance to " ND2BASN A 224 " =    1.830
peak=   -3.208 closest distance to " CG  TRP A 266 " =    1.849
peak=   -3.207 closest distance to " CE2 PHE A 218 " =    2.360
peak=   -3.207 closest distance to " CE BMET A  47 " =    1.608
peak=   -3.201 closest distance to " O   GLN A 240 " =    2.004
peak=   -3.199 closest distance to " O   HOH Z 189 " =    1.742
peak=   -3.193 closest distance to " O   HOH Z 426 " =    1.569
peak=   -3.190 closest distance to " O   HOH Z 357 " =    2.037
peak=   -3.190 closest distance to " CB  PRO A  54 " =    2.408
peak=   -3.186 closest distance to " SD  MET A 188 " =    2.284
peak=   -3.180 closest distance to " CB  LEU A  83 " =    2.380
peak=   -3.172 closest distance to " OD1 ASN A 187 " =    1.570
peak=   -3.171 closest distance to " N   ALA A 248 " =    1.583
peak=   -3.169 closest distance to " CE1 TYR A 247 " =    2.920
peak=   -3.165 closest distance to " N   PHE A  59 " =    1.912
peak=   -3.160 closest distance to " CE3 TRP A 150 " =    2.129
peak=   -3.147 closest distance to " CA  ASP A 298 " =    1.081
peak=   -3.147 closest distance to " SG BCYS A 201 " =    1.962
peak=   -3.143 closest distance to " O   HOH Z 256 " =    1.490
peak=   -3.142 closest distance to " O   GLY A 211 " =    1.300
peak=   -3.142 closest distance to " CB  ASP A  27 " =    2.446
peak=   -3.141 closest distance to " CG2 THR A  18 " =    2.808
peak=   -3.138 closest distance to " O   HOH Z 243 " =    1.931
peak=   -3.137 closest distance to " O   HOH Z 275 " =    1.708
peak=   -3.133 closest distance to " O   HOH Z 133 " =    1.512
peak=   -3.133 closest distance to " CE  MET A 105 " =    2.290
peak=   -3.129 closest distance to " O   HOH Z 390 " =    2.405
peak=   -3.125 closest distance to " O   HOH Z 174 " =    2.580
peak=   -3.125 closest distance to " O   HOH Z 263 " =    3.062
peak=   -3.119 closest distance to " NH2 ARG A  79 " =    1.690
peak=   -3.115 closest distance to " O   HOH Z 323 " =    1.362
peak=   -3.112 closest distance to " CG2 VAL A 189 " =    1.913
peak=   -3.111 closest distance to " ND2 ASN A  60 " =    1.426
peak=   -3.106 closest distance to " OE2 GLU A 152 " =    1.146
peak=   -3.100 closest distance to " O   HOH Z 134 " =    3.182
peak=   -3.099 closest distance to " N   ASP A 171 " =    2.287
peak=   -3.097 closest distance to " O   HOH Z 174 " =    4.290
peak=   -3.095 closest distance to " OG  SER A 245 " =    1.260
peak=   -3.090 closest distance to " O   HOH Z 412 " =    4.316
peak=   -3.090 closest distance to " CH2 TRP A 179 " =    2.136
peak=   -3.088 closest distance to " CD2 TYR A 293 " =    1.925
peak=   -3.079 closest distance to " O   VAL A 153 " =    2.343
peak=   -3.079 closest distance to " O   HOH Z 184 " =    1.730
peak=   -3.073 closest distance to " N   ASP A 270 " =    1.396
peak=   -3.057 closest distance to " O   GLU A 152 " =    1.435
peak=   -3.053 closest distance to " C   LYS A  76 " =    1.748
peak=   -3.050 closest distance to " O   HOH Z 166 " =    1.821
peak=   -3.044 closest distance to " CD2 PHE A 192 " =    2.282
peak=   -3.035 closest distance to " CA  GLY A 241 " =    2.836
peak=   -3.031 closest distance to " NH2 ARG A  24 " =    1.712
peak=   -3.031 closest distance to " CD1 ILE A 199 " =    2.518
peak=   -3.017 closest distance to " O   HOH Z 350 " =    1.839

================= 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    :  0.3400 0.3344   6.107286e+00   6.086298e+00
   1_bss:  0.3235 0.3223   6.087132e+00   6.062412e+00
   1_xyz:  0.2015 0.2286   5.629687e+00   5.724934e+00
   1_adp:  0.1836 0.2380   5.576780e+00   5.757034e+00
   1_occ:  0.1834 0.2376   5.575453e+00   5.755384e+00
   2_bss:  0.1805 0.2324   5.559167e+00   5.735419e+00
   2_xyz:  0.1338 0.1821   5.295996e+00   5.514507e+00
   2_adp:  0.1274 0.1705   5.245560e+00   5.456622e+00
   2_occ:  0.1272 0.1705   5.245035e+00   5.456607e+00
   3_bss:  0.1270 0.1695   5.240134e+00   5.450867e+00
   3_xyz:  0.1162 0.1584   5.164692e+00   5.388522e+00
   3_adp:  0.1127 0.1582   5.148008e+00   5.385098e+00
   3_occ:  0.1127 0.1582   5.148069e+00   5.385304e+00
   4_bss:  0.1126 0.1580   5.147225e+00   5.384570e+00
   4_xyz:  0.1072 0.1548   5.117012e+00   5.371844e+00
   4_adp:  0.1065 0.1541   5.112671e+00   5.369443e+00
   4_occ:  0.1065 0.1542   5.112898e+00   5.369879e+00
   5_bss:  0.1064 0.1541   5.112865e+00   5.369814e+00
   5_xyz:  0.1059 0.1550   5.112758e+00   5.373971e+00
   5_adp:  0.1066 0.1537   5.111272e+00   5.366781e+00
   5_occ:  0.1066 0.1537   5.111298e+00   5.366892e+00
   5_bss:  0.1065 0.1538   5.111352e+00   5.366920e+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:  0.346  50.000  -3.108   2.513  -1.020   0.000  -0.000  -0.000
   1_xyz:  0.346  50.000  -3.108   2.513  -1.020   0.000  -0.000  -0.000
   1_adp:  0.346  50.000  -3.108   2.513  -1.020   0.000  -0.000  -0.000
   1_occ:  0.346  50.000  -3.108   2.513  -1.020   0.000  -0.000  -0.000
   2_bss:  0.325  50.000  -2.885  -1.202  -1.193  -0.000  -0.000  -0.000
   2_xyz:  0.325  50.000  -2.885  -1.202  -1.193  -0.000  -0.000  -0.000
   2_adp:  0.325  50.000  -2.885  -1.202  -1.193  -0.000  -0.000  -0.000
   2_occ:  0.325  50.000  -2.885  -1.202  -1.193  -0.000  -0.000  -0.000
   3_bss:  0.325  50.000  -2.760  -2.246  -1.157  -0.000  -0.000  -0.000
   3_xyz:  0.325  50.000  -2.760  -2.246  -1.157  -0.000  -0.000  -0.000
   3_adp:  0.325  50.000  -2.760  -2.246  -1.157  -0.000  -0.000  -0.000
   3_occ:  0.325  50.000  -2.760  -2.246  -1.157  -0.000  -0.000  -0.000
   4_bss:  0.321  52.398  -2.533  -2.343  -1.003  -0.000  -0.000  -0.000
   4_xyz:  0.321  52.398  -2.533  -2.343  -1.003  -0.000  -0.000  -0.000
   4_adp:  0.321  52.398  -2.533  -2.343  -1.003  -0.000  -0.000  -0.000
   4_occ:  0.321  52.398  -2.533  -2.343  -1.003  -0.000  -0.000  -0.000
   5_bss:  0.322  52.398  -2.277  -2.240  -0.768  -0.000  -0.000  -0.000
   5_xyz:  0.322  52.398  -2.277  -2.240  -0.768  -0.000  -0.000  -0.000
   5_adp:  0.322  52.398  -2.277  -2.240  -0.768  -0.000  -0.000  -0.000
   5_occ:  0.322  52.398  -2.277  -2.240  -0.768  -0.000  -0.000  -0.000
   5_bss:  0.324  52.359  -2.128  -2.155  -0.603  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.324 0.6887  0.8752    34056.494
   1_bss:  35.365 0.6977  0.8697    31258.366
   1_xyz:  21.982 0.8436  0.9965    13307.227
   1_adp:  22.944 0.8331  0.9876    14095.479
   1_occ:  22.922 0.8332  0.9874    14031.233
   2_bss:  22.192 0.8405  0.9542    13326.672
   2_xyz:  17.016 0.8885  0.9845     8212.449
   2_adp:  15.570 0.9020  0.9868     7419.295
   2_occ:  15.571 0.9019  0.9867     7414.800
   3_bss:  15.434 0.9030  0.9771     7303.759
   3_xyz:  14.104 0.9139  0.9814     6381.117
   3_adp:  13.973 0.9152  0.9758     6288.600
   3_occ:  13.978 0.9151  0.9756     6291.632
   4_bss:  13.959 0.9153  0.9793     6283.287
   4_xyz:  13.637 0.9179  0.9803     6103.184
   4_adp:  13.577 0.9184  0.9738     6054.276
   4_occ:  13.585 0.9184  0.9737     6059.598
   5_bss:  13.587 0.9184  0.9808     6061.167
   5_xyz:  13.644 0.9180  0.9805     6153.099
   5_adp:  13.497 0.9191  0.9755     6085.531
   5_occ:  13.500 0.9191  0.9755     6085.751
   5_bss:  13.501 0.9191  0.9788     6087.819
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6434e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6434e-01
   1_xyz:   1.180  0.010  0.081 15.252  0.006  4.109   8.2385e-02
   1_adp:   1.180  0.010  0.081 15.252  0.006  4.109   8.2385e-02
   1_occ:   1.180  0.010  0.081 15.252  0.006  4.109   8.2385e-02
   2_bss:   1.180  0.010  0.081 15.252  0.006  4.109   8.2385e-02
   2_xyz:   0.990  0.006  0.074 14.533  0.004  4.116   5.6687e-02
   2_adp:   0.990  0.006  0.074 14.533  0.004  4.116   5.6687e-02
   2_occ:   0.990  0.006  0.074 14.533  0.004  4.116   5.6687e-02
   3_bss:   0.990  0.006  0.074 14.533  0.004  4.116   5.6687e-02
   3_xyz:   0.949  0.006  0.072 14.518  0.004  4.110   5.4639e-02
   3_adp:   0.949  0.006  0.072 14.518  0.004  4.110   5.4639e-02
   3_occ:   0.949  0.006  0.072 14.518  0.004  4.110   5.4639e-02
   4_bss:   0.949  0.006  0.072 14.518  0.004  4.110   5.4639e-02
   4_xyz:   1.055  0.008  0.080 14.807  0.004  4.111   6.6090e-02
   4_adp:   1.055  0.008  0.080 14.807  0.004  4.111   6.6090e-02
   4_occ:   1.055  0.008  0.080 14.807  0.004  4.111   6.6090e-02
   5_bss:   1.055  0.008  0.080 14.807  0.004  4.111   6.6090e-02
   5_xyz:   1.033  0.008  0.079 14.623  0.004  4.112   6.4015e-02
   5_adp:   1.033  0.008  0.079 14.623  0.004  4.112   6.4015e-02
   5_occ:   1.033  0.008  0.079 14.623  0.004  4.112   6.4015e-02
   5_bss:   1.033  0.008  0.079 14.623  0.004  4.112   6.4015e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_xyz:   9.974  0.078  0.284 84.462  0.053  2.177   1.3111e-01
   1_adp:   9.974  0.078  0.284 84.462  0.053  2.177   1.3111e-01
   1_occ:   9.974  0.078  0.284 84.462  0.053  2.177   1.3111e-01
   2_bss:   9.974  0.078  0.284 84.462  0.053  2.177   1.3111e-01
   2_xyz:   7.029  0.048  0.199 81.524  0.044  2.326   4.8599e-02
   2_adp:   7.029  0.048  0.199 81.524  0.044  2.326   4.8599e-02
   2_occ:   7.029  0.048  0.199 81.524  0.044  2.326   4.8599e-02
   3_bss:   7.029  0.048  0.199 81.524  0.044  2.326   4.8599e-02
   3_xyz:   6.995  0.042  0.230 84.117  0.036  2.335   4.1619e-02
   3_adp:   6.995  0.042  0.230 84.117  0.036  2.335   4.1619e-02
   3_occ:   6.995  0.042  0.230 84.117  0.036  2.335   4.1619e-02
   4_bss:   6.995  0.042  0.230 84.117  0.036  2.335   4.1619e-02
   4_xyz:   6.693  0.038  0.269 84.557  0.035  2.288   5.4417e-02
   4_adp:   6.693  0.038  0.269 84.557  0.035  2.288   5.4417e-02
   4_occ:   6.693  0.038  0.269 84.557  0.035  2.288   5.4417e-02
   5_bss:   6.693  0.038  0.269 84.557  0.035  2.288   5.4417e-02
   5_xyz:   6.694  0.038  0.261 84.702  0.034  2.291   5.6203e-02
   5_adp:   6.694  0.038  0.261 84.702  0.034  2.291   5.6203e-02
   5_occ:   6.694  0.038  0.261 84.702  0.034  2.291   5.6203e-02
   5_bss:   6.694  0.038  0.261 84.702  0.034  2.291   5.6203e-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:  85.36   0.00  17.23  76.09   0.00  13.04  85.36   5.14  40.01
   1_occ:  85.36   0.00  17.23  76.09   0.00  13.04  85.36   5.14  40.01
   2_bss:  85.36   0.00  17.23  76.09   0.00  13.04  85.36   5.14  40.01
   2_xyz:  85.36   0.00  17.23  76.09   0.00  13.04  85.36   5.14  40.01
   2_adp:  80.80   1.90  16.73  74.40   1.90  12.82  80.80   6.56  38.04
   2_occ:  80.80   1.90  16.73  74.40   1.90  12.82  80.80   6.56  38.04
   3_bss:  80.80   1.90  16.73  74.40   1.90  12.82  80.80   6.56  38.04
   3_xyz:  80.80   1.90  16.73  74.40   1.90  12.82  80.80   6.56  38.04
   3_adp:  90.47   0.00  17.38  90.47   0.00  12.95  86.97   3.24  41.47
   3_occ:  90.47   0.00  17.38  90.47   0.00  12.95  86.97   3.24  41.47
   4_bss:  90.47   0.00  17.38  90.47   0.00  12.95  86.97   3.24  41.47
   4_xyz:  90.47   0.00  17.38  90.47   0.00  12.95  86.97   3.24  41.47
   4_adp:  95.25   0.00  17.15  95.25   0.00  12.79  87.53   4.09  40.88
   4_occ:  95.25   0.00  17.15  95.25   0.00  12.79  87.53   4.09  40.88
   5_bss:  95.25   0.00  17.15  95.25   0.00  12.79  87.53   4.09  40.88
   5_xyz:  95.25   0.00  17.15  95.25   0.00  12.79  87.53   4.09  40.88
   5_adp:  91.43   1.13  16.40  91.43   1.13  12.43  83.52   5.91  37.99
   5_occ:  91.43   1.13  16.40  91.43   1.13  12.43  83.52   5.91  37.99
   5_bss:  91.39   1.09  16.36  91.39   1.09  12.39  83.48   5.87  37.95
------------------------------------------------------------------------
 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:    1.193    0.021    0.362
   1_adp:    1.193    0.021    0.362
   1_occ:    1.193    0.021    0.362
   2_bss:    1.193    0.021    0.362
   2_xyz:    0.972    0.014    0.420
   2_adp:    0.972    0.014    0.420
   2_occ:    0.972    0.014    0.420
   3_bss:    0.972    0.014    0.420
   3_xyz:    1.002    0.027    0.450
   3_adp:    1.002    0.027    0.450
   3_occ:    1.002    0.027    0.450
   4_bss:    1.002    0.027    0.450
   4_xyz:    1.151    0.058    0.472
   4_adp:    1.151    0.058    0.472
   4_occ:    1.151    0.058    0.472
   5_bss:    1.151    0.058    0.472
   5_xyz:    1.254    0.083    0.478
   5_adp:    1.254    0.083    0.478
   5_occ:    1.254    0.083    0.478
   5_bss:    1.254    0.083    0.478
------------------------------------------------------------------------

CPU time actual refinement: 318.95


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_633/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_633/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_633/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_633/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_633/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 318.80 
  Macro-tasks:
    bulk solvent and scale       = 37.71  
    individual site refinement   = 130.49 
    weights calculation          = 29.26  
    collect and process          = 6.62   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 204.20 
  Micro-tasks:
    mask                            = 1.21   
    f_calc                          = 100.24 
    alpha_beta                      = 8.13   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 109.29 
    fmodel                         = 6.55   
    r_factors                      = 0.29   
    phase_errors                   = 11.12  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 238.21 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.538 micro seconds
Total CPU time: 5.54 minutes
from_scatterers_fft:    640 calls, 99.79 s
gradients_fft:          585 calls, 95.98 s

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

# Date 2008-01-16 Time 05:17:57 PST -0800 (1200489477.60 s)
Start R-work = 0.3400, R-free = 0.3344 (no bulk solvent and anisotropic scale)
Final R-work = 0.1300, R-free = 0.1728 (no bulk solvent and anisotropic scale)

Start R-work = 0.3235, R-free = 0.3223
Final R-work = 0.1065, R-free = 0.1538