# Date 2008-01-16 Time 04:43:38 PST -0800 (1200487418.32 s)
#phil __OFF__

Command line arguments: "../433.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10041
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 433

-------------------------------------------------------------------------------
  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: (69.5475, 47.1647, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.37, per 1000 atoms: 1.19


================================== 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: (69.5475, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8642 1.98056
Completeness in resolution range: 0.967262
Completeness with d_max=infinity: 0.964215

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8642
                             d_min =   1.9806

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: (69.5475, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8642 1.98056
Completeness in resolution range: 0.967262
Completeness with d_max=infinity: 0.964215

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8647 -  4.2371 [2125/2152]  1912   213  10.0%
  bin  2:  4.2371 -  3.3761 [2037/2053]  1834   203  10.0%
  bin  3:  3.3761 -  2.9531 [2028/2047]  1826   202  10.0%
  bin  4:  2.9531 -  2.6849 [1991/2021]  1793   198   9.9%
  bin  5:  2.6849 -  2.4934 [1989/2008]  1789   200  10.1%
  bin  6:  2.4934 -  2.3470 [1968/2004]  1772   196  10.0%
  bin  7:  2.3470 -  2.2298 [1964/1997]  1766   198  10.1%
  bin  8:  2.2298 -  2.1331 [1953/1988]  1756   197  10.1%
  bin  9:  2.1331 -  2.0512 [1941/1968]  1747   194  10.0%
  bin 10:  2.0512 -  1.9806 [1593/2014]  1435   158   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_433/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: 0.15 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: 22
        2.42 -     3.04: 2213
        3.04 -     3.66: 4700
        3.66 -     4.28: 9077
        4.28 -     4.90: 12403
  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  18 " - " O   HOH Z 102 "  1.969 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.979 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.127 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  2.161 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28410 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_433/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_433/model_refine_001.geo

CPU time processing inputs: 9.30


============================ 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 = 69.5475 47.16465 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2579   r_free= 0.2533   ksol= 0.00   Bsol= 0.00   scale= 1.002    |
|                                                                             |
| 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:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.832896                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8647 -  4.7255 0.99   1381  153 0.2587 0.2625      6.2799      6.2713|
|  2:  4.7255 -  3.7709 0.99   1323  150 0.1978 0.1808      6.1901       6.154|
|  3:  3.7709 -  3.3002 0.99   1309  145 0.2112 0.1999      6.0768      6.0999|
|  4:  3.3002 -  3.0012 0.99   1295  136 0.2251 0.2355      5.9698      5.9413|
|  5:  3.0012 -  2.7876 0.99   1281  146 0.2550 0.2131      5.8623      5.7864|
|  6:  2.7876 -  2.6242 0.99   1282  145 0.2649 0.2659      5.8147      5.7202|
|  7:  2.6242 -  2.4934 0.99   1283  141 0.2708 0.2263      5.8101      5.6141|
|  8:  2.4934 -  2.3853 0.98   1262  141 0.2726 0.2749      5.7479      5.7827|
|  9:  2.3853 -  2.2938 0.98   1275  143 0.2849 0.2874      5.7085      5.7095|
| 10:  2.2938 -  2.2149 0.98   1248  135 0.2839 0.3023      5.7021      5.6898|
| 11:  2.2149 -  2.1459 1.00   1262  146 0.2828 0.3079      5.6418      5.7318|
| 12:  2.1459 -  2.0847 0.97   1262  134 0.3048 0.2711      5.6287      5.5965|
| 13:  2.0847 -  2.0300 0.98   1260  141 0.2985 0.3099      5.5547      5.5166|
| 14:  2.0300 -  1.9806 0.72    907  103 0.3014 0.2834      5.5095      5.3631|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8647 -  4.7255  1381   153  0.80  25.22   0.88     0.80      39520.02|
|  2:  4.7255 -  3.7709  1323   150  0.88  17.71   1.00     0.94      30244.48|
|  3:  3.7709 -  3.3002  1309   145  0.88  18.01   1.02     1.01      23504.51|
|  4:  3.3002 -  3.0012  1295   136  0.88  19.01   1.02     1.01      19521.47|
|  5:  3.0012 -  2.7876  1281   146  0.84  22.49   1.03     1.00      16172.85|
|  6:  2.7876 -  2.6242  1282   145  0.84  23.13   1.04     1.01      13798.78|
|  7:  2.6242 -  2.4934  1283   141  0.85  22.18   1.03     1.03      12387.63|
|  8:  2.4934 -  2.3853  1262   141  0.83  23.49   1.06     1.03      12360.81|
|  9:  2.3853 -  2.2938  1275   143  0.81  25.67   1.07     1.02      12477.29|
| 10:  2.2938 -  2.2149  1248   135  0.80  27.02   1.10     1.01      12538.50|
| 11:  2.2149 -  2.1459  1262   146  0.80  26.98   1.09     1.04      11960.39|
| 12:  2.1459 -  2.0847  1262   134  0.80  27.05   1.10     1.06      10810.89|
| 13:  2.0847 -  2.0300  1260   141  0.80  26.91   1.09     1.06       9455.20|
| 14:  2.0300 -  1.9806   907   103  0.80  27.07   1.08     1.03       8083.13|
|alpha:            min =        0.80 max =            1.06 mean =         1.00|
|beta:             min =     8083.13 max =        39520.02 mean =     17020.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.92 mean =        23.60|
|phase err.(test): min =        0.00 max =           89.31 mean =        23.25|
|-----------------------------------------------------------------------------|

============================== 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 = 2.685610              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.440   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.407590              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.027   (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:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      197 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2016 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1856 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2844 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4677 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4400 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5634 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6769 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.187 |              |
|-----------------------------------------------------------------------------|

|-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: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2579   r_free= 0.2533   ksol= 0.00   Bsol= 0.00   scale= 1.002    |
|                                                                             |
| 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:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.832896                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2424   r_free= 0.2340   ksol= 0.31   Bsol= 38.86   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.71,-1.37,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.800660                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.445244              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.401   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.219142              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.858   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2424      final r-factor (work) = 0.1433          |
| start r-factor (free) = 0.2340      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3127 = 2.45 * 0.50 * 5.8482 + 1.00 * 0.1626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7467 = 2.45 * 0.50 * 5.4715 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1433      final r-factor (work) = 0.1317          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2051 = 0.22 * 1.00 * 5.4715 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1662 = 0.22 * 1.00 * 5.2291 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-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    62.46   16.57    None  None   None       |
|    all(noH): 2823   0      0.00    62.46   16.57    None  None   None       |
|    Sol.    : 438    0      6.88    62.46   37.28    None  None   None       |
|    Mac.    : 2385   0      0.00    53.79   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.246:  159   |   5:    31.232 -  37.478:   96        |
|      1:     6.246 -  12.493: 1308   |   6:    37.478 -  43.724:  102        |
|      2:    12.493 -  18.739:  668   |   7:    43.724 -  49.971:   82        |
|      3:    18.739 -  24.985:  207   |   8:    49.971 -  56.217:   62        |
|      4:    24.985 -  31.232:  117   |   9:    56.217 -  62.463:   22        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1317 r_free = 0.1621             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1312 r_free = 0.1622             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1312   r_free= 0.1622   ksol= 0.31   Bsol= 38.86   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.71,-1.37,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.236093                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1612   ksol= 0.32   Bsol= 43.72   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-2.35,-1.75,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.236673                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.076057              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.217  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.147913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.570   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1612      final r-factor (free) = 0.1504          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4931 = 2.08 * 0.50 * 5.2373 + 1.00 * 0.0566                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4199 = 2.08 * 0.50 * 5.1651 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1135      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1504      final r-factor (free) = 0.1495          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9650 = 0.15 * 1.00 * 5.1651 + 1.00 * 0.2010                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7638 = 0.15 * 1.00 * 5.1194 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-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      2.19    63.34   16.46    None  None   None       |
|    all(noH): 2823   0      2.19    63.34   16.46    None  None   None       |
|    Sol.    : 438    0      6.00    63.28   36.60    None  None   None       |
|    Mac.    : 2385   0      2.19    63.34   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.192 -   8.308:  532   |   5:    32.768 -  38.884:  105        |
|      1:     8.308 -  14.423: 1287   |   6:    38.884 -  44.999:   94        |
|      2:    14.423 -  20.538:  406   |   7:    44.999 -  51.114:   90        |
|      3:    20.538 -  26.653:  148   |   8:    51.114 -  57.229:   51        |
|      4:    26.653 -  32.768:   98   |   9:    57.229 -  63.344:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1495             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1494             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1494   ksol= 0.32   Bsol= 43.72   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.05,-2.35,-1.75,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117236                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1495   ksol= 0.33   Bsol= 43.70   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.18,-1.48,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117476                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.985389              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.724  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.806417              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.361  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1495      final r-factor (free) = 0.1499          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1412 = 1.99 * 0.50 * 5.1202 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1286 = 1.99 * 0.50 * 5.1075 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1069          |
| start r-factor (free) = 0.1499      final r-factor (free) = 0.1519          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2327 = 1.81 * 1.00 * 5.1075 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2195 = 1.81 * 1.00 * 5.0988 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| 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      0.79    81.55   16.93    None  None   None       |
|    all(noH): 2823   0      0.79    81.55   16.93    None  None   None       |
|    Sol.    : 438    0      5.85    74.41   39.15    None  None   None       |
|    Mac.    : 2385   0      0.79    81.55   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.787 -   8.864:  746   |   5:    41.170 -  49.247:  117        |
|      1:     8.864 -  16.941: 1285   |   6:    49.247 -  57.323:   79        |
|      2:    16.941 -  25.017:  299   |   7:    57.323 -  65.400:   50        |
|      3:    25.017 -  33.094:  127   |   8:    65.400 -  73.477:   14        |
|      4:    33.094 -  41.170:  100   |   9:    73.477 -  81.553:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1069 r_free = 0.1519             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1519             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1519   ksol= 0.33   Bsol= 43.70   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.18,-1.48,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106199                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1518   ksol= 0.32   Bsol= 45.79   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-1.96,-1.23,-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: 5.105972                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.949985              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.094  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.116087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.770  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1067      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0308 = 1.95 * 0.50 * 5.0999 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0335 = 1.95 * 0.50 * 5.1044 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1514          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6014 = 0.12 * 1.00 * 5.1044 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6007 = 0.12 * 1.00 * 5.1167 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-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      2.19    78.44   16.24    None  None   None       |
|    all(noH): 2823   0      2.19    78.44   16.24    None  None   None       |
|    Sol.    : 438    0      5.50    67.88   36.29    None  None   None       |
|    Mac.    : 2385   0      2.19    78.44   12.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.190 -   9.816: 1001   |   5:    40.317 -  47.943:   97        |
|      1:     9.816 -  17.441: 1092   |   6:    47.943 -  55.568:   79        |
|      2:    17.441 -  25.067:  260   |   7:    55.568 -  63.194:   27        |
|      3:    25.067 -  32.692:  124   |   8:    63.194 -  70.819:    8        |
|      4:    32.692 -  40.317:  131   |   9:    70.819 -  78.444:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1082 r_free = 0.1514             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1515             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1515   ksol= 0.32   Bsol= 45.79   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-1.96,-1.23,-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: 5.111494                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1509   ksol= 0.32   Bsol= 45.79   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-1.86,-1.11,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112546                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.149452              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.681  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.220130              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.061  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1069          |
| start r-factor (free) = 0.1509      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5579 = 2.15 * 0.50 * 5.1186 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5477 = 2.15 * 0.50 * 5.1059 + 1.00 * 0.0603                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1069      final r-factor (work) = 0.1056          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2366 = 1.22 * 1.00 * 5.1059 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2306 = 1.22 * 1.00 * 5.0994 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| 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      0.48    86.03   16.54    None  None   None       |
|    all(noH): 2823   0      0.48    86.03   16.54    None  None   None       |
|    Sol.    : 438    0      5.42    74.42   38.42    None  None   None       |
|    Mac.    : 2385   0      0.48    86.03   12.52    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:     0.480 -   9.036:  873   |   5:    43.257 -  51.812:  109        |
|      1:     9.036 -  17.591: 1223   |   6:    51.812 -  60.368:   68        |
|      2:    17.591 -  26.146:  265   |   7:    60.368 -  68.923:   26        |
|      3:    26.146 -  34.702:  127   |   8:    68.923 -  77.478:    8        |
|      4:    34.702 -  43.257:  119   |   9:    77.478 -  86.034:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1056 r_free = 0.1534             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1056 r_free = 0.1534             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1534   ksol= 0.32   Bsol= 45.79   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-1.86,-1.11,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106198                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8647 -  4.7255 0.99   1381  153 0.0978 0.1247      5.3681      5.4908|
|  2:  4.7255 -  3.7709 0.99   1323  150 0.0833 0.1107      5.4182      5.6242|
|  3:  3.7709 -  3.3002 0.99   1309  145 0.1010 0.1467      5.4403      5.8293|
|  4:  3.3002 -  3.0012 0.99   1295  136 0.1129 0.1488      5.4056      5.5581|
|  5:  3.0012 -  2.7876 0.99   1281  146 0.1216 0.1649      5.2724      5.5167|
|  6:  2.7876 -  2.6242 0.99   1282  145 0.1165 0.1835      5.1843      5.4183|
|  7:  2.6242 -  2.4934 0.99   1283  141 0.1148 0.1595      5.1109      5.3248|
|  8:  2.4934 -  2.3853 0.98   1262  141 0.1102 0.1711      5.0466      5.3362|
|  9:  2.3853 -  2.2938 0.98   1275  143 0.1100 0.1758      4.9811      5.2563|
| 10:  2.2938 -  2.2149 0.98   1248  135 0.1054 0.1645      4.9445      5.1716|
| 11:  2.2149 -  2.1459 1.00   1262  146 0.1065 0.1741      4.8965      5.2625|
| 12:  2.1459 -  2.0847 0.97   1262  134 0.1031 0.1577      4.8269      5.1439|
| 13:  2.0847 -  2.0300 0.98   1260  141 0.1035 0.1640      4.7513      5.0066|
| 14:  2.0300 -  1.9806 0.72    907  103 0.0971 0.1828      4.6454      4.9647|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8647 -  4.7255  1381   153  0.94   8.87   0.98     0.95       6800.62|
|  2:  4.7255 -  3.7709  1323   150  0.95   7.66   1.02     1.00       8636.80|
|  3:  3.7709 -  3.3002  1309   145  0.94  10.73   1.03     1.02       9777.60|
|  4:  3.3002 -  3.0012  1295   136  0.93  12.63   1.01     1.00       9521.72|
|  5:  3.0012 -  2.7876  1281   146  0.91  14.94   0.99     0.97       7603.24|
|  6:  2.7876 -  2.6242  1282   145  0.90  15.60   0.98     0.94       6718.46|
|  7:  2.6242 -  2.4934  1283   141  0.91  14.82   0.98     0.96       5726.41|
|  8:  2.4934 -  2.3853  1262   141  0.91  14.54   0.99     0.96       5159.01|
|  9:  2.3853 -  2.2938  1275   143  0.91  15.02   1.00     0.96       4611.71|
| 10:  2.2938 -  2.2149  1248   135  0.91  15.12   1.00     0.96       4338.13|
| 11:  2.2149 -  2.1459  1262   146  0.91  15.25   0.99     0.96       4092.15|
| 12:  2.1459 -  2.0847  1262   134  0.92  14.60   1.00     0.99       3662.46|
| 13:  2.0847 -  2.0300  1260   141  0.91  14.99   0.99     0.98       3150.67|
| 14:  2.0300 -  1.9806   907   103  0.91  14.54   0.97     0.93       2542.62|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2542.62 max =         9777.60 mean =      5984.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.78 mean =        13.45|
|phase err.(test): min =        0.00 max =           89.99 mean =        13.11|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1534   ksol= 0.32   Bsol= 45.77   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.65,-0.90,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106063                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1534   ksol= 0.32   Bsol= 45.77   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-1.65,-0.90,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.106063                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8647 -  4.7255 0.99   1381  153 0.0977 0.1248      5.3666      5.4891|
|  2:  4.7255 -  3.7709 0.99   1323  150 0.0834 0.1108      5.4186      5.6248|
|  3:  3.7709 -  3.3002 0.99   1309  145 0.1010 0.1467      5.4406      5.8296|
|  4:  3.3002 -  3.0012 0.99   1295  136 0.1128 0.1488      5.4055       5.558|
|  5:  3.0012 -  2.7876 0.99   1281  146 0.1216 0.1648      5.2722      5.5163|
|  6:  2.7876 -  2.6242 0.99   1282  145 0.1164 0.1834      5.1842      5.4181|
|  7:  2.6242 -  2.4934 0.99   1283  141 0.1148 0.1595      5.1108      5.3247|
|  8:  2.4934 -  2.3853 0.98   1262  141 0.1102 0.1711      5.0465       5.336|
|  9:  2.3853 -  2.2938 0.98   1275  143 0.1100 0.1758      4.9811      5.2563|
| 10:  2.2938 -  2.2149 0.98   1248  135 0.1054 0.1645      4.9445      5.1715|
| 11:  2.2149 -  2.1459 1.00   1262  146 0.1065 0.1740      4.8964      5.2624|
| 12:  2.1459 -  2.0847 0.97   1262  134 0.1031 0.1577      4.8268      5.1438|
| 13:  2.0847 -  2.0300 0.98   1260  141 0.1035 0.1640      4.7512      5.0064|
| 14:  2.0300 -  1.9806 0.72    907  103 0.0971 0.1828      4.6455      4.9647|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8647 -  4.7255  1381   153  0.94   8.84   0.98     0.95       6763.16|
|  2:  4.7255 -  3.7709  1323   150  0.95   7.65   1.02     1.00       8625.00|
|  3:  3.7709 -  3.3002  1309   145  0.94  10.74   1.03     1.02       9783.80|
|  4:  3.3002 -  3.0012  1295   136  0.93  12.63   1.01     1.00       9519.42|
|  5:  3.0012 -  2.7876  1281   146  0.91  14.94   1.00     0.97       7600.40|
|  6:  2.7876 -  2.6242  1282   145  0.90  15.60   0.99     0.95       6715.39|
|  7:  2.6242 -  2.4934  1283   141  0.91  14.82   0.99     0.97       5724.69|
|  8:  2.4934 -  2.3853  1262   141  0.91  14.54   1.00     0.97       5157.49|
|  9:  2.3853 -  2.2938  1275   143  0.91  15.03   1.00     0.97       4611.24|
| 10:  2.2938 -  2.2149  1248   135  0.91  15.12   1.01     0.97       4337.06|
| 11:  2.2149 -  2.1459  1262   146  0.91  15.25   1.00     0.97       4090.94|
| 12:  2.1459 -  2.0847  1262   134  0.92  14.60   1.01     1.00       3661.02|
| 13:  2.0847 -  2.0300  1260   141  0.91  14.98   1.01     0.99       3149.67|
| 14:  2.0300 -  1.9806   907   103  0.91  14.54   0.98     0.95       2542.27|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2542.27 max =         9783.80 mean =      5980.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.79 mean =        13.44|
|phase err.(test): min =        0.00 max =           89.95 mean =        13.11|
|-----------------------------------------------------------------------------|

|-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      0.47    86.02   16.52    None  None   None       |
|    all(noH): 2823   0      0.47    86.02   16.52    None  None   None       |
|    Sol.    : 438    0      5.40    74.40   38.40    None  None   None       |
|    Mac.    : 2385   0      0.47    86.02   12.50    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:     0.465 -   9.021:  873   |   5:    43.242 -  51.797:  109        |
|      1:     9.021 -  17.576: 1223   |   6:    51.797 -  60.353:   68        |
|      2:    17.576 -  26.131:  265   |   7:    60.353 -  68.908:   26        |
|      3:    26.131 -  34.687:  127   |   8:    68.908 -  77.463:    8        |
|      4:    34.687 -  43.242:  119   |   9:    77.463 -  86.018:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 276         
Filter by distance & map next to the model:
   mapped sites are within: 0.495 - 4.446
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 272 from: 276
   mapped sites are within: 0.732 - 4.446

peak=    5.720 closest distance to " CB  ARG A 275 " =    0.942
peak=    5.329 closest distance to " CB  GLN A 223 " =    1.413
peak=    5.304 closest distance to " NH2 ARG A  56 " =    2.236
peak=    5.136 closest distance to " O   HOH Z 126 " =    1.866
peak=    5.043 closest distance to " O   HOH Z 232 " =    2.416
peak=    4.948 closest distance to " O   HOH Z 142 " =    1.633
peak=    4.873 closest distance to " CB  SER A  63 " =    1.155
peak=    4.785 closest distance to " C   PRO A 198 " =    1.457
peak=    4.754 closest distance to " CA  TYR A  30 " =    0.909
peak=    4.753 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.698 closest distance to " CG  PRO A 213 " =    1.219
peak=    4.693 closest distance to " NE2 GLN A  11 " =    1.014
peak=    4.686 closest distance to " CB  GLU A 152 " =    1.189
peak=    4.471 closest distance to " O   HOH Z 298 " =    1.889
peak=    4.468 closest distance to " O   HOH Z  78 " =    1.672
peak=    4.456 closest distance to " CB  ASN A 148 " =    1.471
peak=    4.455 closest distance to " O   HOH Z 209 " =    2.230
peak=    4.452 closest distance to " O   HOH Z 427 " =    2.867
peak=    4.430 closest distance to " CB  ARG A  79 " =    1.338
peak=    4.411 closest distance to " O   HOH Z 236 " =    2.044
peak=    4.358 closest distance to " O   HOH Z 272 " =    1.866
peak=    4.332 closest distance to " O   HOH Z  43 " =    1.943
peak=    4.299 closest distance to " O   HOH Z 203 " =    1.662
peak=    4.297 closest distance to " O   HOH Z 234 " =    3.610
peak=    4.287 closest distance to " O   HOH Z 193 " =    1.773
peak=    4.278 closest distance to " CB  TYR A 169 " =    0.789
peak=    4.239 closest distance to " O   HOH Z  40 " =    1.788
peak=    4.239 closest distance to " O   HOH Z 303 " =    2.052
peak=    4.228 closest distance to " O   HOH Z 250 " =    1.453
peak=    4.203 closest distance to " O   HOH Z 403 " =    1.727
peak=    4.198 closest distance to " O   HOH Z  54 " =    1.760
peak=    4.197 closest distance to " CB  ARG A 190 " =    1.686
peak=    4.150 closest distance to " O   HOH Z 369 " =    2.146
peak=    4.126 closest distance to " CB  VAL A 265 " =    1.260
peak=    4.109 closest distance to " O   HOH Z  15 " =    2.195
peak=    4.095 closest distance to " CZ  PHE A 218 " =    1.079
peak=    4.091 closest distance to " O   HOH Z  61 " =    1.587
peak=    4.089 closest distance to " O   HOH Z 158 " =    3.012
peak=    4.083 closest distance to " O   SER A  87 " =    2.197
peak=    4.081 closest distance to " O   HOH Z 402 " =    1.427
peak=    4.072 closest distance to " OD1 ASN A  69 " =    2.594
peak=    4.063 closest distance to " CD2 TRP A 179 " =    1.385
peak=    4.059 closest distance to " O   HOH Z 197 " =    2.925
peak=    4.053 closest distance to " CG  PRO A  90 " =    1.141
peak=    4.041 closest distance to " NZ  LYS A 117 " =    3.230
peak=    4.039 closest distance to " O   HOH Z 368 " =    2.025
peak=    4.037 closest distance to " ND2 ASN A 187 " =    1.429
peak=    4.035 closest distance to " CB  LEU A 228 " =    1.081
peak=    4.024 closest distance to " O   HOH Z 316 " =    3.071
peak=    4.021 closest distance to " O   HOH Z 289 " =    1.714
peak=    4.018 closest distance to " CG  PRO A 198 " =    1.232
peak=    4.011 closest distance to " O   HOH Z 144 " =    2.212
peak=    3.991 closest distance to " O   HOH Z 189 " =    2.139
peak=    3.988 closest distance to " O   HOH Z  44 " =    1.908
peak=    3.986 closest distance to " O   HOH Z  97 " =    1.920
peak=    3.950 closest distance to " O   HOH Z  97 " =    2.495
peak=    3.934 closest distance to " O   HOH Z 344 " =    3.134
peak=    3.927 closest distance to " CG1 ILE A  33 " =    1.211
peak=    3.923 closest distance to " O   HOH Z 128 " =    1.984
peak=    3.922 closest distance to " O   HOH Z  66 " =    2.097
peak=    3.919 closest distance to " CA  ALA A  21 " =    1.144
peak=    3.911 closest distance to " CA  ASN A 215 " =    1.093
peak=    3.899 closest distance to " CB  SER A   3 " =    1.268
peak=    3.896 closest distance to " CB  TRP A 266 " =    0.978
peak=    3.873 closest distance to " CG  ARG A  66 " =    2.478
peak=    3.863 closest distance to " O   HOH Z 407 " =    2.608
peak=    3.847 closest distance to " CB  GLU A 277 " =    3.513
peak=    3.845 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.840 closest distance to " O   HOH Z 147 " =    1.774
peak=    3.839 closest distance to " CB  GLU A 128 " =    1.059
peak=    3.837 closest distance to " CG2 VAL A 257 " =    0.843
peak=    3.835 closest distance to " CA  ARG A  36 " =    1.023
peak=    3.826 closest distance to " CB  ARG A  79 " =    0.886
peak=    3.819 closest distance to " O   HOH Z 214 " =    2.054
peak=    3.788 closest distance to " O   HOH Z  59 " =    2.125
peak=    3.784 closest distance to " CG  PRO A 243 " =    1.049
peak=    3.778 closest distance to " O   MET A 105 " =    1.882
peak=    3.769 closest distance to " O   HOH Z 389 " =    1.897
peak=    3.746 closest distance to " O   HOH Z  63 " =    2.132
peak=    3.734 closest distance to " CG2 ILE A 120 " =    1.061
peak=    3.732 closest distance to " O   HOH Z   1 " =    2.104
peak=    3.729 closest distance to " CB  TRP A 179 " =    1.319
peak=    3.709 closest distance to " OE1 GLU A   2 " =    2.242
peak=    3.707 closest distance to " O   HOH Z 327 " =    1.603
peak=    3.707 closest distance to " CG1BVAL A  72 " =    1.626
peak=    3.703 closest distance to " O   HOH Z 245 " =    1.283
peak=    3.703 closest distance to " O   HOH Z 423 " =    1.990
peak=    3.700 closest distance to " OD2 ASP A 286 " =    2.828
peak=    3.696 closest distance to " CB  ASN A  39 " =    0.846
peak=    3.694 closest distance to " NH2BARG A 145 " =    2.018
peak=    3.691 closest distance to " O   HOH Z  19 " =    2.311
peak=    3.685 closest distance to " CB  ALA A 291 " =    1.324
peak=    3.679 closest distance to " O   HOH Z  10 " =    1.826
peak=    3.668 closest distance to " CB  ASP A 140 " =    0.931
peak=    3.662 closest distance to " O   HOH Z 417 " =    2.987
peak=    3.653 closest distance to " CA  ASN A 176 " =    1.147
peak=    3.651 closest distance to " CA  ARG A 195 " =    1.271
peak=    3.630 closest distance to " O   HOH Z 280 " =    2.941
peak=    3.629 closest distance to " CB  SER A  26 " =    1.629
peak=    3.622 closest distance to " OG BSER A 164 " =    2.231
peak=    3.611 closest distance to " O   HOH Z 172 " =    3.773
peak=    3.607 closest distance to " CB  VAL A 202 " =    1.490
peak=    3.607 closest distance to " O   HOH Z 337 " =    3.569
peak=    3.601 closest distance to " O   HOH Z 132 " =    2.559
peak=    3.593 closest distance to " O   HOH Z 291 " =    1.522
peak=    3.590 closest distance to " CB  ILE A 120 " =    1.288
peak=    3.588 closest distance to " CZ2 TRP A 179 " =    1.729
peak=    3.580 closest distance to " O   HOH Z 261 " =    1.621
peak=    3.578 closest distance to " O   HOH Z 371 " =    3.272
peak=    3.576 closest distance to " CB  THR A  31 " =    1.668
peak=    3.573 closest distance to " CG2 ILE A  20 " =    1.337
peak=    3.562 closest distance to " O   HOH Z 299 " =    4.446
peak=    3.561 closest distance to " CD  ARG A 159 " =    0.732
peak=    3.561 closest distance to " CB  ARG A 139 " =    0.935
peak=    3.556 closest distance to " OG1 THR A 294 " =    2.386
peak=    3.554 closest distance to " CB  TYR A 169 " =    0.886
peak=    3.552 closest distance to " O   HOH Z 128 " =    2.127
peak=    3.536 closest distance to " CE1 TYR A 186 " =    1.326
peak=    3.536 closest distance to " O   HOH Z 148 " =    3.254
peak=    3.533 closest distance to " N   ARG A 156 " =    1.352
peak=    3.524 closest distance to " O   HOH Z 180 " =    2.179
peak=    3.519 closest distance to " O   HOH Z  61 " =    1.496
peak=    3.514 closest distance to " ND2 ASN A 110 " =    1.690
peak=    3.513 closest distance to " CA  ALA A 291 " =    0.828
peak=    3.512 closest distance to " CA  ASP A 162 " =    1.061
peak=    3.509 closest distance to " O   HOH Z 421 " =    1.692
peak=    3.501 closest distance to " CD  ARG A 269 " =    1.002
peak=    3.493 closest distance to " NH1AARG A 145 " =    1.147
peak=    3.490 closest distance to " O   HOH Z 426 " =    1.550
peak=    3.478 closest distance to " O   HOH Z 173 " =    2.006
peak=    3.478 closest distance to " CA  ALA A  51 " =    0.895
peak=    3.474 closest distance to " CD2 LEU A 297 " =    0.835
peak=    3.474 closest distance to " O   HOH Z 411 " =    3.877
peak=    3.465 closest distance to " CA  LYS A 117 " =    1.233
peak=    3.465 closest distance to " NE2 GLN A  77 " =    3.253
peak=    3.463 closest distance to " O   HOH Z 227 " =    1.539
peak=    3.462 closest distance to " O   HOH Z 425 " =    2.007
peak=    3.460 closest distance to " CA  ASP A 140 " =    1.111
peak=    3.460 closest distance to " O   ALA A 165 " =    1.460
peak=    3.459 closest distance to " O   HOH Z 193 " =    2.085
peak=    3.450 closest distance to " CA  ARG A 275 " =    1.927
peak=    3.443 closest distance to " CD BLYS A 290 " =    1.140
peak=    3.438 closest distance to " N   ASN A  39 " =    1.247
peak=    3.436 closest distance to " CA  MET A  40 " =    1.068
peak=    3.429 closest distance to " CG  GLN A  77 " =    2.062
peak=    3.423 closest distance to " O   HOH Z 368 " =    3.609
peak=    3.420 closest distance to " O   HOH Z 133 " =    2.768
peak=    3.418 closest distance to " CG AARG A 275 " =    1.111
peak=    3.418 closest distance to " O   HOH Z 286 " =    2.217
peak=    3.410 closest distance to " O   HOH Z 248 " =    1.618
peak=    3.409 closest distance to " CB  GLU A  46 " =    1.005
peak=    3.403 closest distance to " O  BHOH Z 338 " =    2.297
peak=    3.394 closest distance to " CD1 LEU A 300 " =    1.265
peak=    3.391 closest distance to " CB  ALA A  34 " =    1.054
peak=    3.389 closest distance to " CD1 ILE A 106 " =    0.817
peak=    3.389 closest distance to " CA  THR A 221 " =    0.955
peak=    3.389 closest distance to " O   HOH Z   9 " =    2.200
peak=    3.389 closest distance to " CA  ALA A  84 " =    1.266
peak=    3.385 closest distance to " CG  GLN A  58 " =    2.698
peak=    3.383 closest distance to " CB  SER A 212 " =    1.011
peak=    3.380 closest distance to " N   TYR A 116 " =    1.580
peak=    3.380 closest distance to " O   HOH Z 163 " =    1.887
peak=    3.380 closest distance to " O   HOH Z 365 " =    2.898
peak=    3.378 closest distance to " CA  THR A 264 " =    0.903
peak=    3.378 closest distance to " O   HOH Z  88 " =    3.015
peak=    3.376 closest distance to " CB  ASN A 110 " =    1.134
peak=    3.371 closest distance to " O   HOH Z 305 " =    3.562
peak=    3.358 closest distance to " CB  GLN A  88 " =    1.175
peak=    3.358 closest distance to " O   HOH Z  66 " =    2.117
peak=    3.358 closest distance to " O   HOH Z 185 " =    1.749
peak=    3.352 closest distance to " CB  ALA A 248 " =    1.320
peak=    3.351 closest distance to " NH2 ARG A 156 " =    1.130
peak=    3.347 closest distance to " CB  GLN A  89 " =    1.327
peak=    3.343 closest distance to " O   HOH Z 166 " =    3.861
peak=    3.342 closest distance to " CB  SER A  62 " =    0.907
peak=    3.341 closest distance to " CB  SER A 141 " =    1.010
peak=    3.340 closest distance to " CD1 LEU A  96 " =    0.769
peak=    3.339 closest distance to " CD  LYS A 119 " =    1.299
peak=    3.337 closest distance to " O   HOH Z 359 " =    1.429
peak=    3.333 closest distance to " CD  LYS A 166 " =    1.256
peak=    3.333 closest distance to " O   HOH Z  21 " =    1.764
peak=    3.332 closest distance to " CA  TYR A 116 " =    1.383
peak=    3.328 closest distance to " O   HOH Z 433 " =    1.718
peak=    3.317 closest distance to " C   TYR A 214 " =    1.467
peak=    3.306 closest distance to " CG2 THR A 221 " =    1.182
peak=    3.305 closest distance to " CA  ASN A 217 " =    1.224
peak=    3.304 closest distance to " CG2 VAL A 197 " =    1.099
peak=    3.304 closest distance to " O   HOH Z 357 " =    1.875
peak=    3.299 closest distance to " CB  HIS A 108 " =    0.851
peak=    3.297 closest distance to " O   HOH Z 227 " =    2.144
peak=    3.294 closest distance to " O   HOH Z  85 " =    2.257
peak=    3.292 closest distance to " O   HOH Z 406 " =    1.517
peak=    3.291 closest distance to " O   HOH Z 417 " =    2.083
peak=    3.290 closest distance to " O   HOH Z 175 " =    2.137
peak=    3.280 closest distance to " O   HOH Z 265 " =    2.348
peak=    3.276 closest distance to " O   ALA A   1 " =    1.635
peak=    3.274 closest distance to " O   HOH Z 403 " =    1.351
peak=    3.274 closest distance to " O   HOH Z 199 " =    1.551
peak=    3.273 closest distance to " CB  GLN A 205 " =    1.124
peak=    3.271 closest distance to " CA  MET A 105 " =    1.007
peak=    3.270 closest distance to " CD1AILE A 234 " =    0.960
peak=    3.270 closest distance to " O   HOH Z 108 " =    2.544
peak=    3.264 closest distance to " O   HOH Z 273 " =    2.751
peak=    3.264 closest distance to " O   HOH Z 391 " =    2.949
peak=    3.263 closest distance to " O   HOH Z 353 " =    2.665
peak=    3.261 closest distance to " O   HOH Z 261 " =    2.172
peak=    3.259 closest distance to " CG  MET A 185 " =    1.096
peak=    3.256 closest distance to " CB  ASN A 215 " =    1.187
peak=    3.251 closest distance to " O   HOH Z 163 " =    1.668
peak=    3.240 closest distance to " N   ASN A 127 " =    1.238
peak=    3.237 closest distance to " CB  SER A 216 " =    0.816
peak=    3.237 closest distance to " O   HOH Z 435 " =    1.889
peak=    3.233 closest distance to " CA  GLY A  80 " =    0.885
peak=    3.233 closest distance to " CA  ILE A  33 " =    1.449
peak=    3.231 closest distance to " O   HOH Z 345 " =    3.157
peak=    3.231 closest distance to " CD2 TYR A 186 " =    1.045
peak=    3.229 closest distance to " CB  ALA A 114 " =    1.155
peak=    3.228 closest distance to " O   HOH Z 383 " =    1.828
peak=    3.227 closest distance to " OH  TYR A 116 " =    1.042
peak=    3.224 closest distance to " CG  LYS A  76 " =    1.018
peak=    3.224 closest distance to " CB  VAL A 126 " =    1.100
peak=    3.220 closest distance to " CG2 VAL A  78 " =    0.886
peak=    3.217 closest distance to " O   HOH Z  35 " =    2.509
peak=    3.210 closest distance to " CB  TYR A 116 " =    0.746
peak=    3.203 closest distance to " O   THR A 220 " =    1.256
peak=    3.183 closest distance to " O   HOH Z 279 " =    2.150
peak=    3.182 closest distance to " CD2 TYR A  30 " =    1.036
peak=    3.178 closest distance to " CD2 HIS A  81 " =    1.145
peak=    3.176 closest distance to " CG  GLU A 277 " =    2.194
peak=    3.174 closest distance to " CA  SER A 146 " =    1.708
peak=    3.172 closest distance to " CB  GLN A 103 " =    0.851
peak=    3.170 closest distance to " ND1 HIS A  81 " =    1.666
peak=    3.169 closest distance to " O   HOH Z 325 " =    2.529
peak=    3.168 closest distance to " O   HOH Z 193 " =    1.601
peak=    3.167 closest distance to " O   HOH Z  88 " =    2.420
peak=    3.163 closest distance to " CE  LYS A  48 " =    1.074
peak=    3.157 closest distance to " CE  LYS A 119 " =    1.158
peak=    3.155 closest distance to " CA  ILE A 234 " =    0.938
peak=    3.152 closest distance to " CG2BVAL A  41 " =    0.836
peak=    3.150 closest distance to " O   HOH Z 380 " =    1.964
peak=    3.144 closest distance to " O   HOH Z 250 " =    1.514
peak=    3.143 closest distance to " O   HOH Z 313 " =    1.935
peak=    3.139 closest distance to " O   HOH Z  49 " =    2.112
peak=    3.136 closest distance to " CD  ARG A  66 " =    2.543
peak=    3.135 closest distance to " O   HOH Z 329 " =    3.889
peak=    3.135 closest distance to " CB  ALA A   9 " =    1.539
peak=    3.134 closest distance to " CB  GLN A 278 " =    0.850
peak=    3.125 closest distance to " CA  ALA A 158 " =    1.314
peak=    3.125 closest distance to " CG  GLN A  11 " =    1.545
peak=    3.125 closest distance to " O   HOH Z 419 " =    1.888
peak=    3.123 closest distance to " OG  SER A  62 " =    2.799
peak=    3.123 closest distance to " CB  ALA A 248 " =    0.896
peak=    3.120 closest distance to " O   HOH Z 342 " =    0.878
peak=    3.119 closest distance to " O   HOH Z 126 " =    1.664
peak=    3.117 closest distance to " N   VAL A 126 " =    1.280
peak=    3.113 closest distance to " O   HOH Z 437 " =    1.426
peak=    3.108 closest distance to " O   HOH Z 409 " =    3.154
peak=    3.108 closest distance to " NE2 GLN A  58 " =    2.799
peak=    3.102 closest distance to " O   HOH Z 371 " =    1.569
peak=    3.094 closest distance to " O   HOH Z 256 " =    2.435
peak=    3.094 closest distance to " O   HOH Z 267 " =    2.025
peak=    3.089 closest distance to " CG1 ILE A 120 " =    1.140
peak=    3.089 closest distance to " O   HOH Z 374 " =    2.608
peak=    3.084 closest distance to " N   ASP A 162 " =    1.205
peak=    3.079 closest distance to " CA  ARG A 159 " =    1.267
peak=    3.069 closest distance to " O   HOH Z 336 " =    1.639
peak=    3.068 closest distance to " O   HOH Z 258 " =    1.923
peak=    3.067 closest distance to " CB  LYS A 290 " =    1.268
peak=    3.056 closest distance to " NZ  LYS A 166 " =    2.986
peak=    3.055 closest distance to " N   SER A 135 " =    1.280
peak=    3.047 closest distance to " O   HOH Z 392 " =    1.926
peak=    3.047 closest distance to " O   HOH Z 163 " =    1.478

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.836 - 5.969
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 203
   mapped sites are within: 0.836 - 5.969

peak=   -4.849 closest distance to " O   HOH Z 266 " =    4.860
peak=   -4.585 closest distance to " C   HIS A 108 " =    1.099
peak=   -4.432 closest distance to " CD  ARG A 156 " =    2.043
peak=   -4.429 closest distance to " SG  CYS A 254 " =    3.315
peak=   -4.388 closest distance to " O   VAL A  67 " =    2.790
peak=   -4.333 closest distance to " CB  PRO A 243 " =    2.583
peak=   -4.281 closest distance to " CD  GLN A  58 " =    1.080
peak=   -4.280 closest distance to " CG  GLN A 223 " =    2.002
peak=   -4.205 closest distance to " O   HOH Z 198 " =    1.982
peak=   -4.169 closest distance to " C   ILE A 239 " =    2.163
peak=   -4.155 closest distance to " CB  ALA A 161 " =    2.585
peak=   -4.147 closest distance to " CG1 VAL A 112 " =    2.767
peak=   -4.100 closest distance to " O   HOH Z 372 " =    2.266
peak=   -4.079 closest distance to " OG BSER A 134 " =    1.243
peak=   -4.063 closest distance to " O   HOH Z 231 " =    2.280
peak=   -3.990 closest distance to " ND2 ASN A  45 " =    1.494
peak=   -3.970 closest distance to " O   VAL A  67 " =    2.864
peak=   -3.959 closest distance to " CE2 TYR A  30 " =    2.723
peak=   -3.893 closest distance to " O   HOH Z 196 " =    2.004
peak=   -3.893 closest distance to " CZ3 TRP A 179 " =    1.235
peak=   -3.891 closest distance to " O   HOH Z 290 " =    1.213
peak=   -3.870 closest distance to " CB  ASN A  39 " =    2.301
peak=   -3.867 closest distance to " O   HOH Z 126 " =    1.894
peak=   -3.861 closest distance to " OXT GLY A 302 " =    2.765
peak=   -3.850 closest distance to " O   HOH Z 353 " =    2.111
peak=   -3.824 closest distance to " O   PRO A 198 " =    1.273
peak=   -3.819 closest distance to " O   HOH Z 407 " =    2.911
peak=   -3.816 closest distance to " ND2 ASN A  45 " =    1.028
peak=   -3.815 closest distance to " OG  SER A  97 " =    2.160
peak=   -3.805 closest distance to " N   ALA A  43 " =    2.539
peak=   -3.795 closest distance to " O   HOH Z  13 " =    1.595
peak=   -3.782 closest distance to " CG  ASP A 231 " =    0.836
peak=   -3.765 closest distance to " CG2 ILE A 263 " =    2.234
peak=   -3.761 closest distance to " O   HOH Z 435 " =    2.763
peak=   -3.757 closest distance to " CD  ARG A 139 " =    1.519
peak=   -3.753 closest distance to " O   PRO A 163 " =    2.057
peak=   -3.746 closest distance to " O   HOH Z 165 " =    1.968
peak=   -3.736 closest distance to " O   HOH Z 114 " =    3.222
peak=   -3.727 closest distance to " N   GLN A  58 " =    1.634
peak=   -3.709 closest distance to " O   HOH Z 389 " =    1.746
peak=   -3.704 closest distance to " CB  ASP A 132 " =    2.297
peak=   -3.680 closest distance to " O   HOH Z 102 " =    1.573
peak=   -3.670 closest distance to " O   HOH Z 185 " =    2.323
peak=   -3.662 closest distance to " CB  PHE A 192 " =    1.962
peak=   -3.658 closest distance to " C   LEU A 143 " =    1.003
peak=   -3.655 closest distance to " CG  PHE A 283 " =    2.671
peak=   -3.654 closest distance to " OD1 ASN A 187 " =    1.673
peak=   -3.649 closest distance to " O   HOH Z 351 " =    1.538
peak=   -3.643 closest distance to " CZ  TYR A 169 " =    1.749
peak=   -3.629 closest distance to " O   HOH Z  10 " =    1.494
peak=   -3.624 closest distance to " OG  SER A  62 " =    1.739
peak=   -3.620 closest distance to " CB  ALA A 291 " =    2.255
peak=   -3.619 closest distance to " CB  ALA A 291 " =    2.351
peak=   -3.603 closest distance to " CB  ALA A 248 " =    2.269
peak=   -3.603 closest distance to " CA  GLY A 203 " =    2.358
peak=   -3.587 closest distance to " CD  ARG A 195 " =    5.208
peak=   -3.582 closest distance to " CD1 LEU A 101 " =    2.364
peak=   -3.576 closest distance to " O   HOH Z 362 " =    5.969
peak=   -3.559 closest distance to " O   HOH Z 166 " =    1.512
peak=   -3.555 closest distance to " CA  ASP A 298 " =    1.042
peak=   -3.549 closest distance to " N   ALA A 248 " =    1.592
peak=   -3.535 closest distance to " CD2 LEU A 300 " =    2.890
peak=   -3.531 closest distance to " CD1 PHE A  59 " =    1.911
peak=   -3.524 closest distance to " O   PHE A 218 " =    1.629
peak=   -3.523 closest distance to " O   ALA A 161 " =    1.681
peak=   -3.518 closest distance to " O   HOH Z 211 " =    1.699
peak=   -3.511 closest distance to " O   HOH Z 311 " =    3.590
peak=   -3.509 closest distance to " OD2 ASP A 171 " =    2.367
peak=   -3.506 closest distance to " CB  ASP A 286 " =    1.900
peak=   -3.479 closest distance to " ND2 ASN A 187 " =    1.510
peak=   -3.475 closest distance to " O   HOH Z  43 " =    1.672
peak=   -3.467 closest distance to " O   SER A 210 " =    1.981
peak=   -3.466 closest distance to " O   MET A  40 " =    2.766
peak=   -3.462 closest distance to " O   HOH Z 166 " =    1.849
peak=   -3.462 closest distance to " CD1 LEU A  25 " =    2.477
peak=   -3.461 closest distance to " NE2 GLN A  88 " =    1.791
peak=   -3.460 closest distance to " CB  TYR A  15 " =    2.163
peak=   -3.457 closest distance to " OD2 ASP A 191 " =    1.453
peak=   -3.453 closest distance to " O   HOH Z  11 " =    1.744
peak=   -3.434 closest distance to " O   SER A  95 " =    1.586
peak=   -3.429 closest distance to " O   HOH Z  52 " =    1.386
peak=   -3.429 closest distance to " O   ALA A  34 " =    2.406
peak=   -3.429 closest distance to " CB  ALA A 248 " =    2.058
peak=   -3.428 closest distance to " N   ALA A 226 " =    1.994
peak=   -3.427 closest distance to " CD1 LEU A 228 " =    2.121
peak=   -3.426 closest distance to " O   HOH Z 313 " =    1.891
peak=   -3.425 closest distance to " CE3 TRP A 150 " =    2.179
peak=   -3.420 closest distance to " O   HOH Z 244 " =    2.072
peak=   -3.417 closest distance to " OD1 ASP A 171 " =    1.608
peak=   -3.413 closest distance to " CZ  PHE A  59 " =    1.539
peak=   -3.413 closest distance to " O   LEU A 167 " =    1.474
peak=   -3.413 closest distance to " OD2 ASP A  50 " =    2.285
peak=   -3.408 closest distance to " CG  GLU A   2 " =    1.866
peak=   -3.402 closest distance to " NH1 ARG A 195 " =    2.564
peak=   -3.398 closest distance to " C   PRO A  90 " =    1.508
peak=   -3.398 closest distance to " O   HOH Z   6 " =    2.146
peak=   -3.398 closest distance to " O   HOH Z 394 " =    1.490
peak=   -3.397 closest distance to " O   HOH Z  44 " =    2.179
peak=   -3.395 closest distance to " NH2AARG A 275 " =    5.167
peak=   -3.391 closest distance to " CD1 ILE A 239 " =    2.328
peak=   -3.390 closest distance to " CB  PHE A 208 " =    2.240
peak=   -3.382 closest distance to " CD2 LEU A 300 " =    2.922
peak=   -3.379 closest distance to " CB  GLN A  11 " =    1.801
peak=   -3.375 closest distance to " O   HOH Z 198 " =    1.441
peak=   -3.365 closest distance to " OG BSER A 134 " =    1.767
peak=   -3.365 closest distance to " SG ACYS A 201 " =    2.016
peak=   -3.365 closest distance to " O   HOH Z 134 " =    2.925
peak=   -3.356 closest distance to " CG  GLU A 277 " =    1.165
peak=   -3.351 closest distance to " CG  ARG A 269 " =    2.320
peak=   -3.344 closest distance to " CA  TYR A  68 " =    2.921
peak=   -3.340 closest distance to " CB  PRO A 163 " =    2.440
peak=   -3.338 closest distance to " O   HOH Z 414 " =    1.590
peak=   -3.337 closest distance to " O   HOH Z   6 " =    1.513
peak=   -3.337 closest distance to " OD1 ASN A 148 " =    1.511
peak=   -3.334 closest distance to " NH2 ARG A  79 " =    2.024
peak=   -3.332 closest distance to " O   HOH Z 234 " =    3.929
peak=   -3.317 closest distance to " O   HOH Z 292 " =    4.513
peak=   -3.312 closest distance to " C   ALA A 158 " =    1.253
peak=   -3.308 closest distance to " O   HOH Z 385 " =    1.996
peak=   -3.307 closest distance to " CD1 LEU A 297 " =    2.277
peak=   -3.305 closest distance to " O   SER A 135 " =    1.505
peak=   -3.303 closest distance to " O   HOH Z 283 " =    2.309
peak=   -3.292 closest distance to " CG1 VAL A 230 " =    2.034
peak=   -3.289 closest distance to " CD2 LEU A 237 " =    2.616
peak=   -3.285 closest distance to " O   HOH Z 298 " =    1.334
peak=   -3.280 closest distance to " O   HOH Z  38 " =    1.612
peak=   -3.274 closest distance to " CE  MET A 105 " =    2.044
peak=   -3.274 closest distance to " CG1 VAL A 112 " =    2.603
peak=   -3.273 closest distance to " O   HOH Z 322 " =    1.735
peak=   -3.270 closest distance to " O   VAL A 174 " =    2.082
peak=   -3.270 closest distance to " O   HOH Z  60 " =    2.240
peak=   -3.266 closest distance to " O   HOH Z  63 " =    1.527
peak=   -3.264 closest distance to " C   ASP A 231 " =    2.665
peak=   -3.258 closest distance to " C   MET A 188 " =    1.450
peak=   -3.255 closest distance to " CZ  PHE A 130 " =    0.981
peak=   -3.246 closest distance to " O   HOH Z 417 " =    2.475
peak=   -3.245 closest distance to " O   ALA A  10 " =    1.732
peak=   -3.242 closest distance to " OG ASER A 134 " =    1.110
peak=   -3.242 closest distance to " O   HOH Z  93 " =    2.015
peak=   -3.239 closest distance to " CA  GLY A 133 " =    1.968
peak=   -3.236 closest distance to " CG  GLU A  53 " =    1.474
peak=   -3.233 closest distance to " O   HOH Z  37 " =    1.745
peak=   -3.233 closest distance to " CZ  PHE A 155 " =    1.206
peak=   -3.232 closest distance to " CD1 TYR A 247 " =    2.746
peak=   -3.224 closest distance to " O   ALA A  51 " =    1.343
peak=   -3.223 closest distance to " O   TRP A  70 " =    1.481
peak=   -3.215 closest distance to " OG  SER A 206 " =    1.710
peak=   -3.212 closest distance to " ND2 ASN A 249 " =    2.142
peak=   -3.212 closest distance to " OG  SER A  26 " =    1.242
peak=   -3.212 closest distance to " O   ARG A 145 " =    1.650
peak=   -3.211 closest distance to " CG1AVAL A  41 " =    2.876
peak=   -3.209 closest distance to " O   HOH Z 385 " =    1.910
peak=   -3.209 closest distance to " CE2 PHE A 218 " =    2.435
peak=   -3.209 closest distance to " O   HOH Z 200 " =    4.811
peak=   -3.202 closest distance to " CD1 ILE A 199 " =    2.421
peak=   -3.198 closest distance to " NH2 ARG A 159 " =    2.376
peak=   -3.193 closest distance to " O   TRP A  92 " =    1.732
peak=   -3.190 closest distance to " CG1 VAL A 250 " =    2.617
peak=   -3.181 closest distance to " N   GLY A  23 " =    2.206
peak=   -3.178 closest distance to " O   HOH Z 357 " =    2.015
peak=   -3.175 closest distance to " O   VAL A 189 " =    2.568
peak=   -3.174 closest distance to " O   HOH Z 191 " =    5.744
peak=   -3.174 closest distance to " N   THR A  52 " =    1.751
peak=   -3.172 closest distance to " O   HOH Z 369 " =    2.200
peak=   -3.171 closest distance to " O   HOH Z  24 " =    1.558
peak=   -3.171 closest distance to " O   PRO A 198 " =    1.632
peak=   -3.167 closest distance to " O   HOH Z 111 " =    1.763
peak=   -3.167 closest distance to " O   HOH Z 250 " =    1.392
peak=   -3.166 closest distance to " OD1 ASP A 191 " =    1.584
peak=   -3.166 closest distance to " O   HOH Z  19 " =    2.297
peak=   -3.158 closest distance to " NH2 ARG A  66 " =    5.305
peak=   -3.158 closest distance to " NH2 ARG A  79 " =    1.601
peak=   -3.157 closest distance to " CG  PRO A 163 " =    2.613
peak=   -3.155 closest distance to " O   HOH Z 427 " =    1.436
peak=   -3.150 closest distance to " NH2BARG A 275 " =    2.231
peak=   -3.149 closest distance to " O   ILE A 106 " =    1.851
peak=   -3.146 closest distance to " OG BSER A 210 " =    2.136
peak=   -3.143 closest distance to " O   HOH Z 123 " =    2.200
peak=   -3.142 closest distance to " CD2 PHE A  61 " =    2.517
peak=   -3.138 closest distance to " O   GLY A  80 " =    2.588
peak=   -3.135 closest distance to " O   HOH Z  41 " =    2.349
peak=   -3.128 closest distance to " O   HOH Z 421 " =    3.192
peak=   -3.124 closest distance to " CD  GLN A 223 " =    1.028
peak=   -3.120 closest distance to " O   HOH Z 377 " =    1.831
peak=   -3.114 closest distance to " OE2 GLU A 152 " =    1.202
peak=   -3.105 closest distance to " CG2 THR A 221 " =    2.251
peak=   -3.102 closest distance to " O   ALA A 292 " =    2.006
peak=   -3.095 closest distance to " O   HOH Z 351 " =    1.308
peak=   -3.094 closest distance to " CG  GLU A 152 " =    1.120
peak=   -3.091 closest distance to " CZ3 TRP A 274 " =    2.386
peak=   -3.090 closest distance to " O   HOH Z 193 " =    1.852
peak=   -3.088 closest distance to " OXT GLY A 302 " =    3.254
peak=   -3.081 closest distance to " O   HOH Z  76 " =    2.012
peak=   -3.074 closest distance to " O   PRO A 198 " =    1.274
peak=   -3.069 closest distance to " O   HOH Z 378 " =    1.438
peak=   -3.060 closest distance to " CG  GLU A 152 " =    0.985
peak=   -3.055 closest distance to " O   HOH Z 361 " =    3.419
peak=   -3.054 closest distance to " ND2 ASN A  60 " =    1.392
peak=   -3.043 closest distance to " O   HOH Z 265 " =    1.924
peak=   -3.024 closest distance to " O   HOH Z 357 " =    2.154
peak=   -3.022 closest distance to " CB  ASP A 132 " =    2.364
peak=   -3.021 closest distance to " O   HOH Z 353 " =    2.094
peak=   -3.021 closest distance to " CG2 VAL A 189 " =    2.155

================= 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    :  0.2579 0.2533   5.832896e+00   5.797800e+00
   1_bss:  0.2424 0.2340   5.800660e+00   5.752943e+00
   1_xyz:  0.1433 0.1595   5.293735e+00   5.387717e+00
   1_adp:  0.1317 0.1621   5.237591e+00   5.408771e+00
   1_occ:  0.1312 0.1622   5.236093e+00   5.407773e+00
   2_bss:  0.1309 0.1612   5.236673e+00   5.405145e+00
   2_xyz:  0.1135 0.1504   5.130685e+00   5.342606e+00
   2_adp:  0.1113 0.1495   5.117733e+00   5.337962e+00
   2_occ:  0.1111 0.1494   5.117236e+00   5.337772e+00
   3_bss:  0.1110 0.1495   5.117476e+00   5.338029e+00
   3_xyz:  0.1087 0.1499   5.108457e+00   5.342553e+00
   3_adp:  0.1069 0.1519   5.106128e+00   5.352129e+00
   3_occ:  0.1068 0.1519   5.106199e+00   5.352460e+00
   4_bss:  0.1067 0.1518   5.105972e+00   5.352093e+00
   4_xyz:  0.1062 0.1530   5.108670e+00   5.359258e+00
   4_adp:  0.1082 0.1514   5.111112e+00   5.350738e+00
   4_occ:  0.1082 0.1515   5.111494e+00   5.351608e+00
   5_bss:  0.1084 0.1509   5.112546e+00   5.349560e+00
   5_xyz:  0.1069 0.1517   5.106921e+00   5.353255e+00
   5_adp:  0.1056 0.1534   5.106224e+00   5.361802e+00
   5_occ:  0.1056 0.1534   5.106198e+00   5.361868e+00
   5_bss:  0.1055 0.1534   5.106063e+00   5.361686e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.314  38.858  -2.083  -1.711  -1.372  -0.000  -0.000  -0.000
   1_xyz:  0.314  38.858  -2.083  -1.711  -1.372  -0.000  -0.000  -0.000
   1_adp:  0.314  38.858  -2.083  -1.711  -1.372  -0.000  -0.000  -0.000
   1_occ:  0.314  38.858  -2.083  -1.711  -1.372  -0.000  -0.000  -0.000
   2_bss:  0.322  43.717  -3.055  -2.350  -1.746  -0.000  -0.000  -0.000
   2_xyz:  0.322  43.717  -3.055  -2.350  -1.746  -0.000  -0.000  -0.000
   2_adp:  0.322  43.717  -3.055  -2.350  -1.746  -0.000  -0.000  -0.000
   2_occ:  0.322  43.717  -3.055  -2.350  -1.746  -0.000  -0.000  -0.000
   3_bss:  0.325  43.705  -2.922  -2.185  -1.481  -0.000  -0.000  -0.000
   3_xyz:  0.325  43.705  -2.922  -2.185  -1.481  -0.000  -0.000  -0.000
   3_adp:  0.325  43.705  -2.922  -2.185  -1.481  -0.000  -0.000  -0.000
   3_occ:  0.325  43.705  -2.922  -2.185  -1.481  -0.000  -0.000  -0.000
   4_bss:  0.324  45.786  -2.685  -1.964  -1.228  -0.000  -0.000  -0.000
   4_xyz:  0.324  45.786  -2.685  -1.964  -1.228  -0.000  -0.000  -0.000
   4_adp:  0.324  45.786  -2.685  -1.964  -1.228  -0.000  -0.000  -0.000
   4_occ:  0.324  45.786  -2.685  -1.964  -1.228  -0.000  -0.000  -0.000
   5_bss:  0.324  45.786  -2.600  -1.862  -1.106  -0.000  -0.000  -0.000
   5_xyz:  0.324  45.786  -2.600  -1.862  -1.106  -0.000  -0.000  -0.000
   5_adp:  0.324  45.786  -2.600  -1.862  -1.106  -0.000  -0.000  -0.000
   5_occ:  0.324  45.786  -2.600  -1.862  -1.106  -0.000  -0.000  -0.000
   5_bss:  0.320  45.770  -2.379  -1.650  -0.901  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  23.568 0.8304  1.0003    17020.410
   1_bss:  22.108 0.8437  0.9554    13848.007
   1_xyz:  13.940 0.9161  0.9995     6386.075
   1_adp:  14.427 0.9119  0.9969     6584.689
   1_occ:  14.421 0.9120  0.9967     6570.751
   2_bss:  14.355 0.9125  0.9733     6510.115
   2_xyz:  13.170 0.9216  0.9754     5797.718
   2_adp:  13.068 0.9224  0.9707     5746.465
   2_occ:  13.065 0.9224  0.9706     5738.329
   3_bss:  13.073 0.9223  0.9773     5744.602
   3_xyz:  13.085 0.9224  0.9776     5802.168
   3_adp:  13.268 0.9210  0.9707     5877.070
   3_occ:  13.273 0.9210  0.9705     5879.587
   4_bss:  13.268 0.9210  0.9790     5873.858
   4_xyz:  13.397 0.9201  0.9780     5972.417
   4_adp:  13.220 0.9214  0.9741     5905.311
   4_occ:  13.232 0.9213  0.9740     5912.644
   5_bss:  13.203 0.9215  0.9774     5869.377
   5_xyz:  13.235 0.9213  0.9780     5921.835
   5_adp:  13.412 0.9200  0.9712     5982.712
   5_occ:  13.413 0.9200  0.9711     5984.054
   5_bss:  13.410 0.9200  0.9781     5979.473
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6255e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6255e-01
   1_xyz:   0.981  0.006  0.068 15.155  0.004  4.110   5.7072e-02
   1_adp:   0.981  0.006  0.068 15.155  0.004  4.110   5.7072e-02
   1_occ:   0.981  0.006  0.068 15.155  0.004  4.110   5.7072e-02
   2_bss:   0.981  0.006  0.068 15.155  0.004  4.110   5.7072e-02
   2_xyz:   0.995  0.007  0.074 14.877  0.004  4.117   5.8413e-02
   2_adp:   0.995  0.007  0.074 14.877  0.004  4.117   5.8413e-02
   2_occ:   0.995  0.007  0.074 14.877  0.004  4.117   5.8413e-02
   3_bss:   0.995  0.007  0.074 14.877  0.004  4.117   5.8413e-02
   3_xyz:   0.984  0.007  0.075 14.867  0.004  4.117   5.8438e-02
   3_adp:   0.984  0.007  0.075 14.867  0.004  4.117   5.8438e-02
   3_occ:   0.984  0.007  0.075 14.867  0.004  4.117   5.8438e-02
   4_bss:   0.984  0.007  0.075 14.867  0.004  4.117   5.8438e-02
   4_xyz:   0.968  0.007  0.075 14.789  0.004  4.117   5.6762e-02
   4_adp:   0.968  0.007  0.075 14.789  0.004  4.117   5.6762e-02
   4_occ:   0.968  0.007  0.075 14.789  0.004  4.117   5.6762e-02
   5_bss:   0.968  0.007  0.075 14.789  0.004  4.117   5.6762e-02
   5_xyz:   1.000  0.007  0.077 14.836  0.004  4.118   6.0267e-02
   5_adp:   1.000  0.007  0.077 14.836  0.004  4.118   6.0267e-02
   5_occ:   1.000  0.007  0.077 14.836  0.004  4.118   6.0267e-02
   5_bss:   1.000  0.007  0.077 14.836  0.004  4.118   6.0267e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4016e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4016e-01
   1_xyz:   6.839  0.037  0.217 83.321  0.034  2.304   4.5247e-02
   1_adp:   6.839  0.037  0.217 83.321  0.034  2.304   4.5247e-02
   1_occ:   6.839  0.037  0.217 83.321  0.034  2.304   4.5247e-02
   2_bss:   6.839  0.037  0.217 83.321  0.034  2.304   4.5247e-02
   2_xyz:   6.839  0.038  0.239 82.761  0.041  2.340   4.0981e-02
   2_adp:   6.839  0.038  0.239 82.761  0.041  2.340   4.0981e-02
   2_occ:   6.839  0.038  0.239 82.761  0.041  2.340   4.0981e-02
   3_bss:   6.839  0.038  0.239 82.761  0.041  2.340   4.0981e-02
   3_xyz:   7.079  0.037  0.244 82.571  0.039  2.337   4.1039e-02
   3_adp:   7.079  0.037  0.244 82.571  0.039  2.337   4.1039e-02
   3_occ:   7.079  0.037  0.244 82.571  0.039  2.337   4.1039e-02
   4_bss:   7.079  0.037  0.244 82.571  0.039  2.337   4.1039e-02
   4_xyz:   6.756  0.035  0.239 82.575  0.038  2.346   3.8497e-02
   4_adp:   6.756  0.035  0.239 82.575  0.038  2.346   3.8497e-02
   4_occ:   6.756  0.035  0.239 82.575  0.038  2.346   3.8497e-02
   5_bss:   6.756  0.035  0.239 82.575  0.038  2.346   3.8497e-02
   5_xyz:   7.144  0.038  0.249 83.147  0.038  2.301   4.7342e-02
   5_adp:   7.144  0.038  0.249 83.147  0.038  2.301   4.7342e-02
   5_occ:   7.144  0.038  0.249 83.147  0.038  2.301   4.7342e-02
   5_bss:   7.144  0.038  0.249 83.147  0.038  2.301   4.7342e-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:  62.46   0.00  16.57  53.79   0.00  12.77  62.46   6.88  37.28
   1_occ:  62.46   0.00  16.57  53.79   0.00  12.77  62.46   6.88  37.28
   2_bss:  62.46   0.00  16.57  53.79   0.00  12.77  62.46   6.88  37.28
   2_xyz:  62.46   0.00  16.57  53.79   0.00  12.77  62.46   6.88  37.28
   2_adp:  63.34   2.19  16.46  63.34   2.19  12.76  63.28   6.00  36.60
   2_occ:  63.34   2.19  16.46  63.34   2.19  12.76  63.28   6.00  36.60
   3_bss:  63.34   2.19  16.46  63.34   2.19  12.76  63.28   6.00  36.60
   3_xyz:  63.34   2.19  16.46  63.34   2.19  12.76  63.28   6.00  36.60
   3_adp:  81.55   0.79  16.93  81.55   0.79  12.85  74.41   5.85  39.15
   3_occ:  81.55   0.79  16.93  81.55   0.79  12.85  74.41   5.85  39.15
   4_bss:  81.55   0.79  16.93  81.55   0.79  12.85  74.41   5.85  39.15
   4_xyz:  81.55   0.79  16.93  81.55   0.79  12.85  74.41   5.85  39.15
   4_adp:  78.44   2.19  16.24  78.44   2.19  12.55  67.88   5.50  36.29
   4_occ:  78.44   2.19  16.24  78.44   2.19  12.55  67.88   5.50  36.29
   5_bss:  78.44   2.19  16.24  78.44   2.19  12.55  67.88   5.50  36.29
   5_xyz:  78.44   2.19  16.24  78.44   2.19  12.55  67.88   5.50  36.29
   5_adp:  86.03   0.48  16.54  86.03   0.48  12.52  74.42   5.42  38.42
   5_occ:  86.03   0.48  16.54  86.03   0.48  12.52  74.42   5.42  38.42
   5_bss:  86.02   0.47  16.52  86.02   0.47  12.50  74.40   5.40  38.40
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.879    0.015    0.219
   1_adp:    0.879    0.015    0.219
   1_occ:    0.879    0.015    0.219
   2_bss:    0.879    0.015    0.219
   2_xyz:    0.690    0.025    0.258
   2_adp:    0.690    0.025    0.258
   2_occ:    0.690    0.025    0.258
   3_bss:    0.690    0.025    0.258
   3_xyz:    0.769    0.048    0.271
   3_adp:    0.769    0.048    0.271
   3_occ:    0.769    0.048    0.271
   4_bss:    0.769    0.048    0.271
   4_xyz:    0.842    0.049    0.277
   4_adp:    0.842    0.049    0.277
   4_occ:    0.842    0.049    0.277
   5_bss:    0.842    0.049    0.277
   5_xyz:    1.010    0.047    0.282
   5_adp:    1.010    0.047    0.282
   5_occ:    1.010    0.047    0.282
   5_bss:    1.010    0.047    0.282
------------------------------------------------------------------------

CPU time actual refinement: 322.35


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_433/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_433/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_433/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_433/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_433/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.18 
  Macro-tasks:
    bulk solvent and scale       = 38.81  
    individual site refinement   = 131.03 
    weights calculation          = 29.46  
    collect and process          = 6.61   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 206.02 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 101.09 
    alpha_beta                      = 7.70   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 110.55 
    fmodel                         = 6.66   
    r_factors                      = 0.20   
    phase_errors                   = 11.37  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 240.17 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.565 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    648 calls, 100.75 s
gradients_fft:          593 calls,  97.09 s

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

# Date 2008-01-16 Time 04:49:13 PST -0800 (1200487753.39 s)
Start R-work = 0.2579, R-free = 0.2533 (no bulk solvent and anisotropic scale)
Final R-work = 0.1294, R-free = 0.1727 (no bulk solvent and anisotropic scale)

Start R-work = 0.2424, R-free = 0.2340
Final R-work = 0.1055, R-free = 0.1534