# Date 2008-01-16 Time 06:38:13 PST -0800 (1200494293.67 s)
#phil __OFF__

Command line arguments: "../1228.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21804
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1228

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (72.0062, 45.9914, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.96442
Completeness in resolution range: 0.921445
Completeness with d_max=infinity: 0.918852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3069
                             d_min =   1.9644

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.96442
Completeness in resolution range: 0.921445
Completeness with d_max=infinity: 0.918852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3073 -  4.2057 [2231/2258]  2009   222  10.0%
  bin  2:  4.2057 -  3.3497 [2153/2173]  1940   213   9.9%
  bin  3:  3.3497 -  2.9296 [2114/2133]  1899   215  10.2%
  bin  4:  2.9296 -  2.6633 [2077/2107]  1867   210  10.1%
  bin  5:  2.6633 -  2.4733 [2101/2120]  1899   202   9.6%
  bin  6:  2.4733 -  2.3280 [2084/2109]  1870   214  10.3%
  bin  7:  2.3280 -  2.2118 [2069/2097]  1852   217  10.5%
  bin  8:  2.2118 -  2.1157 [2048/2084]  1848   200   9.8%
  bin  9:  2.1157 -  2.0345 [2012/2099]  1820   192   9.5%
  bin 10:  2.0345 -  1.9644 [ 700/2079]   626    74  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1228/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 34
        2.41 -     3.04: 2141
        3.04 -     3.66: 4649
        3.66 -     4.28: 9024
        4.28 -     4.90: 12298
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.792 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28141 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_1228/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1228/model_refine_001.geo

CPU time processing inputs: 9.50


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 72.00625 45.9914 87.2539 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: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4719   r_free= 0.4736   ksol= 0.00   Bsol= 0.00   scale= 0.881    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.283274                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6919 0.99   1447  163 0.3798 0.3682      6.5723      6.5501|
|  2:  4.6919 -  3.7420 0.99   1402  154 0.4132 0.3992      6.8339      6.8073|
|  3:  3.7420 -  3.2743 0.99   1362  148 0.4344 0.4234       6.648       6.649|
|  4:  3.2743 -  2.9773 0.99   1362  157 0.4713 0.5029      6.5225       6.536|
|  5:  2.9773 -  2.7653 0.99   1354  146 0.4967 0.5211      6.3595      6.3749|
|  6:  2.7653 -  2.6031 0.99   1346  153 0.4980 0.4780      6.2648      6.2156|
|  7:  2.6031 -  2.4733 0.99   1341  141 0.5182 0.4845      6.2358      6.1604|
|  8:  2.4733 -  2.3660 0.98   1331  155 0.5277 0.5773      6.1621      6.2236|
|  9:  2.3660 -  2.2752 0.98   1328  149 0.5104 0.5341      6.1242      6.1322|
| 10:  2.2752 -  2.1970 1.00   1322  152 0.5293 0.4989       6.073      6.0356|
| 11:  2.1970 -  2.1284 0.98   1328  145 0.5281 0.5494      6.0251      6.0734|
| 12:  2.1284 -  2.0678 0.98   1327  144 0.5162 0.5464      5.9341      5.9316|
| 13:  2.0678 -  2.0134 0.83   1100  123 0.5183 0.4542      5.8736      5.7846|
| 14:  2.0134 -  1.9644 0.21    280   29 0.5030 0.6610      5.8545      5.9704|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.6919  1447   163  0.72  32.21   0.81     0.78      65939.77|
|  2:  4.6919 -  3.7420  1402   154  0.71  34.57   0.89     0.81     104956.68|
|  3:  3.7420 -  3.2743  1362   148  0.56  47.20   0.92     0.74     120542.38|
|  4:  3.2743 -  2.9773  1362   157  0.45  55.96   0.88     0.63     115629.09|
|  5:  2.9773 -  2.7653  1354   146  0.36  63.18   0.87     0.52      92585.35|
|  6:  2.7653 -  2.6031  1346   153  0.34  64.36   0.89     0.50      77902.33|
|  7:  2.6031 -  2.4733  1341   141  0.33  65.60   0.89     0.46      68278.30|
|  8:  2.4733 -  2.3660  1331   155  0.31  66.63   0.87     0.46      61816.01|
|  9:  2.3660 -  2.2752  1328   149  0.33  65.52   0.92     0.47      55675.58|
| 10:  2.2752 -  2.1970  1322   152  0.33  65.65   0.92     0.49      49790.84|
| 11:  2.1970 -  2.1284  1328   145  0.31  66.89   0.91     0.49      49005.13|
| 12:  2.1284 -  2.0678  1327   144  0.28  69.12   0.92     0.44      44668.05|
| 13:  2.0678 -  2.0134  1100   123  0.27  69.70   0.93     0.46      39712.25|
| 14:  2.0134 -  1.9644   280    29  0.37  62.73   0.98     0.51      30657.14|
|alpha:            min =        0.44 max =            0.81 mean =         0.56|
|beta:             min =    30657.14 max =       120542.38 mean =     72868.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.59|
|phase err.(test): min =        0.00 max =           89.98 mean =        58.85|
|-----------------------------------------------------------------------------|

============================== 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 = 13.776194             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.860   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.117981              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.513   (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 |  1.792 -  2.103:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.103 -  2.413:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.413 -  2.724:      164 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.724 -  3.035:     1977 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.035 -  3.346:     1875 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.346 -  3.657:     2774 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.657 -  3.968:     4673 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.968 -  4.278:     4351 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.278 -  4.589:     5605 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.589 -  4.900:     6693 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.792 |       0.312 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    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: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4719   r_free= 0.4736   ksol= 0.00   Bsol= 0.00   scale= 0.881    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.283274                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4646   r_free= 0.4680   ksol= 0.34   Bsol= 65.16   scale= 0.920   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,1.10,-0.69,0.00,-0.00,-0.00); trace/3= 0.55                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.279051                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.507570             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.851   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.467913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.148   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4646      final r-factor (work) = 0.3602          |
| start r-factor (free) = 0.4680      final r-factor (free) = 0.4012          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2725 = 11.51 * 0.50 * 6.2742 + 1.00 * 0.1723                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.6766 = 11.51 * 0.50 * 6.1769 + 1.00 * 0.1360                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3602      final r-factor (work) = 0.3258          |
| start r-factor (free) = 0.4012      final r-factor (free) = 0.4116          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0733 = 1.47 * 1.00 * 6.1769 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9287 = 1.47 * 1.00 * 6.0674 + 1.00 * 0.0223                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.49  19.70    None  None   None       |
|    all(noH): 2823   0      0.00    106.49  19.70    None  None   None       |
|    Sol.    : 438    0      0.00    106.49  39.57    None  None   None       |
|    Mac.    : 2385   0      0.00    71.23   16.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.649:  956   |   5:    53.246 -  63.895:   80        |
|      1:    10.649 -  21.298:  870   |   6:    63.895 -  74.544:   49        |
|      2:    21.298 -  31.947:  477   |   7:    74.544 -  85.193:   11        |
|      3:    31.947 -  42.597:  250   |   8:    85.193 -  95.842:    2        |
|      4:    42.597 -  53.246:  127   |   9:    95.842 - 106.491:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3258 r_free = 0.4116             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3253 r_free = 0.4116             target_work(ml) = 6.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3253   r_free= 0.4116   ksol= 0.34   Bsol= 65.16   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,1.10,-0.69,0.00,-0.00,-0.00); trace/3= 0.55                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.074534                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3258   r_free= 0.4093   ksol= 0.36   Bsol= 79.61   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.54,-0.07,0.21,-0.00,0.00,0.00); trace/3= 0.23                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.074366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.556399              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.727   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659613              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.775  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3258      final r-factor (work) = 0.2627          |
| start r-factor (free) = 0.4093      final r-factor (free) = 0.3391          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.0986 = 8.56 * 0.50 * 6.0686 + 1.00 * 0.1360                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7626 = 8.56 * 0.50 * 6.0018 + 1.00 * 0.0857                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2627      final r-factor (work) = 0.2476          |
| start r-factor (free) = 0.3391      final r-factor (free) = 0.3243          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9808 = 0.66 * 1.00 * 6.0018 + 1.00 * 0.0219                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8914 = 0.66 * 1.00 * 5.8744 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.41  19.34    None  None   None       |
|    all(noH): 2823   0      0.00    106.41  19.34    None  None   None       |
|    Sol.    : 438    0      0.00    106.41  41.36    None  None   None       |
|    Mac.    : 2385   0      0.00    74.08   15.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.641:  982   |   5:    53.207 -  63.848:   74        |
|      1:    10.641 -  21.283:  945   |   6:    63.848 -  74.489:   44        |
|      2:    21.283 -  31.924:  393   |   7:    74.489 -  85.131:   10        |
|      3:    31.924 -  42.565:  221   |   8:    85.131 -  95.772:    1        |
|      4:    42.565 -  53.207:  152   |   9:    95.772 - 106.413:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2476 r_free = 0.3243             target_work(ml) = 5.860         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2476 r_free = 0.3238             target_work(ml) = 5.859         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2476   r_free= 0.3238   ksol= 0.36   Bsol= 79.61   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.54,-0.07,0.21,-0.00,0.00,0.00); trace/3= 0.23                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.858943                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2479   r_free= 0.3238   ksol= 0.35   Bsol= 72.79   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.90,0.09,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.859163                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.812395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.626   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.114244              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.347  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2479      final r-factor (work) = 0.2039          |
| start r-factor (free) = 0.3238      final r-factor (free) = 0.2688          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2839 = 3.81 * 0.50 * 5.8747 + 1.00 * 0.0857                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0816 = 3.81 * 0.50 * 5.7818 + 1.00 * 0.0604                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2039      final r-factor (work) = 0.1849          |
| start r-factor (free) = 0.2688      final r-factor (free) = 0.2533          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2409 = 2.11 * 1.00 * 5.7818 + 1.00 * 0.0168                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.9254 = 2.11 * 1.00 * 5.6320 + 1.00 * 0.0179                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    118.09  19.90    None  None   None       |
|    all(noH): 2823   0      0.00    118.09  19.90    None  None   None       |
|    Sol.    : 438    0      4.23    118.09  49.67    None  None   None       |
|    Mac.    : 2385   0      0.00    98.85   14.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.809: 1258   |   5:    59.046 -  70.855:   90        |
|      1:    11.809 -  23.618:  874   |   6:    70.855 -  82.664:   62        |
|      2:    23.618 -  35.427:  252   |   7:    82.664 -  94.473:   20        |
|      3:    35.427 -  47.236:  138   |   8:    94.473 - 106.282:    8        |
|      4:    47.236 -  59.046:  119   |   9:   106.282 - 118.091:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1849 r_free = 0.2533             target_work(ml) = 5.606         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1848 r_free = 0.2530             target_work(ml) = 5.605         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1848   r_free= 0.2530   ksol= 0.35   Bsol= 72.79   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.90,0.09,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.605378                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1849   r_free= 0.2531   ksol= 0.34   Bsol= 78.83   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.08,-1.91,-0.42,-0.00,-0.00,-0.00); trace/3= -1.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.604744                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.772152              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.325   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287995              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.416  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1849      final r-factor (work) = 0.1553          |
| start r-factor (free) = 0.2531      final r-factor (free) = 0.2185          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8712 = 2.77 * 0.50 * 5.6352 + 1.00 * 0.0604                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7261 = 2.77 * 0.50 * 5.5334 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1553      final r-factor (work) = 0.1477          |
| start r-factor (free) = 0.2185      final r-factor (free) = 0.2016          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6116 = 0.29 * 1.00 * 5.5334 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5922 = 0.29 * 1.00 * 5.4354 + 1.00 * 0.0268                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.32  18.81    None  None   None       |
|    all(noH): 2823   0      0.00    113.32  18.81    None  None   None       |
|    Sol.    : 438    0      5.85    113.32  47.66    None  None   None       |
|    Mac.    : 2385   0      0.00    95.78   13.51    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 -  11.332: 1306   |   5:    56.658 -  67.990:   83        |
|      1:    11.332 -  22.663:  910   |   6:    67.990 -  79.321:   63        |
|      2:    22.663 -  33.995:  195   |   7:    79.321 -  90.653:   22        |
|      3:    33.995 -  45.327:  119   |   8:    90.653 - 101.985:   10        |
|      4:    45.327 -  56.658:  113   |   9:   101.985 - 113.316:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1477 r_free = 0.2016             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1476 r_free = 0.2014             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1476   r_free= 0.2014   ksol= 0.34   Bsol= 78.83   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.08,-1.91,-0.42,-0.00,-0.00,-0.00); trace/3= -1.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.390607                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1477   r_free= 0.2011   ksol= 0.33   Bsol= 69.81   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,-2.43,-0.78,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.390087                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.913866              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.987  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.238187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.186   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1477      final r-factor (work) = 0.1354          |
| start r-factor (free) = 0.2011      final r-factor (free) = 0.1840          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2580 = 1.91 * 0.50 * 5.4357 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1741 = 1.91 * 0.50 * 5.3544 + 1.00 * 0.0503                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1354      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.1840      final r-factor (free) = 0.1789          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2901 = 0.24 * 1.00 * 5.3544 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3755 = 0.24 * 1.00 * 5.2985 + 1.00 * 0.1134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.03  18.43    None  None   None       |
|    all(noH): 2823   0      0.00    111.03  18.43    None  None   None       |
|    Sol.    : 438    0      6.02    111.03  46.25    None  None   None       |
|    Mac.    : 2385   0      0.00    93.86   13.32    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 -  11.103: 1260   |   5:    55.515 -  66.618:   81        |
|      1:    11.103 -  22.206:  977   |   6:    66.618 -  77.721:   56        |
|      2:    22.206 -  33.309:  185   |   7:    77.721 -  88.824:   24        |
|      3:    33.309 -  44.412:  114   |   8:    88.824 -  99.927:   10        |
|      4:    44.412 -  55.515:  114   |   9:    99.927 - 111.030:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1331 r_free = 0.1789             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1330 r_free = 0.1788             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1788   ksol= 0.33   Bsol= 69.81   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.59,-2.43,-0.78,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.284634                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6919 0.99   1447  163 0.1004 0.1386      5.4021      5.6264|
|  2:  4.6919 -  3.7420 0.99   1402  154 0.0919 0.1243      5.5108      5.7517|
|  3:  3.7420 -  3.2743 0.99   1362  148 0.1251 0.1694      5.5896      5.8671|
|  4:  3.2743 -  2.9773 0.99   1362  157 0.1512 0.1908      5.6007       5.739|
|  5:  2.9773 -  2.7653 0.99   1354  146 0.1620 0.2117      5.4753        5.69|
|  6:  2.7653 -  2.6031 0.99   1346  153 0.1550 0.2186      5.3553      5.5887|
|  7:  2.6031 -  2.4733 0.99   1341  141 0.1540 0.1894      5.3086      5.4374|
|  8:  2.4733 -  2.3660 0.98   1331  155 0.1477 0.1844       5.221      5.4234|
|  9:  2.3660 -  2.2752 0.98   1328  149 0.1451 0.2066      5.1838      5.3953|
| 10:  2.2752 -  2.1970 1.00   1322  152 0.1352 0.1822      5.0675      5.2782|
| 11:  2.1970 -  2.1284 0.98   1328  145 0.1354 0.1899      5.0546      5.4088|
| 12:  2.1284 -  2.0678 0.98   1327  144 0.1386 0.2128      5.0076      5.2419|
| 13:  2.0678 -  2.0134 0.83   1100  123 0.1382 0.1885      4.9214       5.119|
| 14:  2.0134 -  1.9644 0.21    280   29 0.1210 0.1696      4.7852      5.0643|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.6919  1447   163  0.94   9.50   0.97     0.94       7711.23|
|  2:  4.6919 -  3.7420  1402   154  0.95   9.02   1.02     1.00      10563.73|
|  3:  3.7420 -  3.2743  1362   148  0.92  13.40   1.04     1.03      12802.69|
|  4:  3.2743 -  2.9773  1362   157  0.89  17.13   1.02     1.00      13483.51|
|  5:  2.9773 -  2.7653  1354   146  0.88  18.06   1.01     1.00      10514.40|
|  6:  2.7653 -  2.6031  1346   153  0.87  18.84   0.99     0.95       8781.07|
|  7:  2.6031 -  2.4733  1341   141  0.88  18.13   1.01     0.99       8056.98|
|  8:  2.4733 -  2.3660  1331   155  0.88  18.17   1.00     0.96       6818.90|
|  9:  2.3660 -  2.2752  1328   149  0.88  18.65   1.01     0.97       6484.51|
| 10:  2.2752 -  2.1970  1322   152  0.89  17.66   1.01     0.98       5337.59|
| 11:  2.1970 -  2.1284  1328   145  0.88  18.50   1.00     0.95       5243.13|
| 12:  2.1284 -  2.0678  1327   144  0.88  18.78   1.01     1.00       5084.23|
| 13:  2.0678 -  2.0134  1100   123  0.87  19.62   1.00     0.98       4376.36|
| 14:  2.0134 -  1.9644   280    29  0.91  15.65   0.99     0.96       3206.70|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3206.70 max =        13483.51 mean =      8099.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.89 mean =        16.44|
|phase err.(test): min =        0.00 max =           89.28 mean =        15.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1789   ksol= 0.32   Bsol= 64.05   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-2.78,-1.07,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.284307                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1789   ksol= 0.32   Bsol= 64.05   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-2.78,-1.07,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.284307                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.6919 0.99   1447  163 0.1000 0.1381      5.3986      5.6232|
|  2:  4.6919 -  3.7420 0.99   1402  154 0.0916 0.1241      5.5087      5.7496|
|  3:  3.7420 -  3.2743 0.99   1362  148 0.1250 0.1691      5.5886      5.8657|
|  4:  3.2743 -  2.9773 0.99   1362  157 0.1513 0.1909       5.601      5.7393|
|  5:  2.9773 -  2.7653 0.99   1354  146 0.1621 0.2118       5.476      5.6908|
|  6:  2.7653 -  2.6031 0.99   1346  153 0.1551 0.2187      5.3555      5.5889|
|  7:  2.6031 -  2.4733 0.99   1341  141 0.1541 0.1894      5.3091      5.4378|
|  8:  2.4733 -  2.3660 0.98   1331  155 0.1479 0.1848      5.2214      5.4245|
|  9:  2.3660 -  2.2752 0.98   1328  149 0.1451 0.2066       5.184      5.3947|
| 10:  2.2752 -  2.1970 1.00   1322  152 0.1353 0.1825      5.0678      5.2796|
| 11:  2.1970 -  2.1284 0.98   1328  145 0.1354 0.1898      5.0542      5.4082|
| 12:  2.1284 -  2.0678 0.98   1327  144 0.1386 0.2128      5.0081      5.2426|
| 13:  2.0678 -  2.0134 0.83   1100  123 0.1382 0.1883      4.9213      5.1192|
| 14:  2.0134 -  1.9644 0.21    280   29 0.1211 0.1693      4.7848      5.0627|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.6919  1447   163  0.94   9.48   0.96     0.94       7671.59|
|  2:  4.6919 -  3.7420  1402   154  0.95   9.00   1.01     1.00      10517.69|
|  3:  3.7420 -  3.2743  1362   148  0.92  13.37   1.03     1.03      12765.10|
|  4:  3.2743 -  2.9773  1362   157  0.89  17.12   1.01     0.99      13471.38|
|  5:  2.9773 -  2.7653  1354   146  0.88  18.06   1.00     0.99      10514.34|
|  6:  2.7653 -  2.6031  1346   153  0.88  18.84   0.98     0.94       8786.27|
|  7:  2.6031 -  2.4733  1341   141  0.88  18.13   1.00     0.98       8061.40|
|  8:  2.4733 -  2.3660  1331   155  0.88  18.18   0.98     0.95       6826.96|
|  9:  2.3660 -  2.2752  1328   149  0.88  18.66   1.00     0.95       6490.45|
| 10:  2.2752 -  2.1970  1322   152  0.89  17.66   1.00     0.96       5343.52|
| 11:  2.1970 -  2.1284  1328   145  0.88  18.50   0.99     0.93       5249.33|
| 12:  2.1284 -  2.0678  1327   144  0.88  18.78   0.99     0.99       5088.94|
| 13:  2.0678 -  2.0134  1100   123  0.87  19.61   0.98     0.96       4376.96|
| 14:  2.0134 -  1.9644   280    29  0.91  15.62   0.97     0.94       3202.19|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3202.19 max =        13471.38 mean =      8091.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.91 mean =        16.43|
|phase err.(test): min =        0.00 max =           89.32 mean =        15.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.03  18.43    None  None   None       |
|    all(noH): 2823   0      0.00    111.03  18.43    None  None   None       |
|    Sol.    : 438    0      6.02    111.03  46.25    None  None   None       |
|    Mac.    : 2385   0      0.00    93.86   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.106: 1260   |   5:    55.518 -  66.621:   81        |
|      1:    11.106 -  22.209:  977   |   6:    66.621 -  77.724:   56        |
|      2:    22.209 -  33.312:  185   |   7:    77.724 -  88.827:   24        |
|      3:    33.312 -  44.415:  114   |   8:    88.827 -  99.930:   10        |
|      4:    44.415 -  55.518:  114   |   9:    99.930 - 111.033:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.054 - 5.026
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 339 from: 346
   mapped sites are within: 0.716 - 5.026

peak=    5.786 closest distance to " O   HOH Z 245 " =    1.135
peak=    5.674 closest distance to " O   HOH Z 222 " =    1.351
peak=    5.436 closest distance to " O   HOH Z 417 " =    1.998
peak=    5.397 closest distance to " NE2 GLN A  11 " =    1.233
peak=    5.387 closest distance to " O   HOH Z   7 " =    1.883
peak=    5.220 closest distance to " CB  PRO A  54 " =    1.446
peak=    5.120 closest distance to " O   HOH Z 403 " =    1.601
peak=    5.108 closest distance to " O   HOH Z  63 " =    1.619
peak=    4.867 closest distance to " O   HOH Z 130 " =    0.973
peak=    4.798 closest distance to " CB  PRO A  54 " =    1.115
peak=    4.796 closest distance to " O   HOH Z  65 " =    1.013
peak=    4.752 closest distance to " CB  SER A  63 " =    1.403
peak=    4.711 closest distance to " CB  SER A 216 " =    1.084
peak=    4.703 closest distance to " CB  GLN A 223 " =    1.534
peak=    4.638 closest distance to " O   HOH Z 120 " =    0.925
peak=    4.623 closest distance to " O   HOH Z 144 " =    1.815
peak=    4.587 closest distance to " O   HOH Z 232 " =    2.085
peak=    4.559 closest distance to " O   HOH Z 425 " =    1.670
peak=    4.534 closest distance to " O   HOH Z  97 " =    1.439
peak=    4.516 closest distance to " O   HOH Z 423 " =    2.259
peak=    4.473 closest distance to " O   HOH Z 272 " =    1.906
peak=    4.471 closest distance to " CG  PRO A  90 " =    1.248
peak=    4.444 closest distance to " CB  ASN A 148 " =    1.241
peak=    4.414 closest distance to " O   HOH Z  49 " =    1.317
peak=    4.407 closest distance to " O   HOH Z 126 " =    1.975
peak=    4.381 closest distance to " O   HOH Z 147 " =    1.031
peak=    4.362 closest distance to " O   HOH Z 369 " =    1.937
peak=    4.330 closest distance to " NZ ALYS A 290 " =    1.004
peak=    4.321 closest distance to " O   HOH Z 316 " =    3.150
peak=    4.312 closest distance to " O   PRO A 198 " =    1.322
peak=    4.296 closest distance to " O   HOH Z  51 " =    2.208
peak=    4.292 closest distance to " CG  PRO A 198 " =    1.299
peak=    4.278 closest distance to " NH1AARG A 145 " =    1.191
peak=    4.277 closest distance to " CA  ARG A 195 " =    1.458
peak=    4.277 closest distance to " CB  TRP A 266 " =    0.994
peak=    4.276 closest distance to " O   HOH Z 427 " =    2.229
peak=    4.273 closest distance to " O   HOH Z 139 " =    1.192
peak=    4.268 closest distance to " O   HOH Z  39 " =    1.229
peak=    4.247 closest distance to " O   HOH Z 390 " =    1.255
peak=    4.222 closest distance to " O   HOH Z 295 " =    1.098
peak=    4.214 closest distance to " O   HOH Z 117 " =    0.719
peak=    4.205 closest distance to " NZ  LYS A 119 " =    2.553
peak=    4.192 closest distance to " CB  PRO A  90 " =    1.217
peak=    4.171 closest distance to " CB  SER A   3 " =    1.536
peak=    4.143 closest distance to " O   HOH Z 258 " =    2.168
peak=    4.069 closest distance to " CB  GLU A 128 " =    1.097
peak=    4.068 closest distance to " CD  ARG A 159 " =    0.833
peak=    4.067 closest distance to " O   HOH Z 236 " =    2.396
peak=    4.067 closest distance to " CG  LEU A 167 " =    1.327
peak=    4.063 closest distance to " CA  SER A  95 " =    0.955
peak=    4.062 closest distance to " CB  ASP A 124 " =    0.883
peak=    4.054 closest distance to " CB  MET A  40 " =    0.805
peak=    4.040 closest distance to " CD BLYS A 290 " =    1.073
peak=    4.037 closest distance to " O   HOH Z 437 " =    1.954
peak=    4.035 closest distance to " O   HOH Z 126 " =    1.560
peak=    4.034 closest distance to " O   HOH Z 298 " =    2.271
peak=    4.025 closest distance to " CG  PRO A 280 " =    1.009
peak=    4.024 closest distance to " O   HOH Z  11 " =    1.237
peak=    3.999 closest distance to " CZ  PHE A 192 " =    1.041
peak=    3.992 closest distance to " CE3 TRP A 274 " =    1.490
peak=    3.991 closest distance to " CB  LYS A 290 " =    0.869
peak=    3.979 closest distance to " O   HOH Z 419 " =    1.985
peak=    3.972 closest distance to " O   HOH Z 183 " =    1.725
peak=    3.964 closest distance to " CA  TYR A  30 " =    1.148
peak=    3.963 closest distance to " CB  SER A 276 " =    1.148
peak=    3.960 closest distance to " O   HOH Z   4 " =    1.031
peak=    3.956 closest distance to " CA  ALA A  51 " =    1.012
peak=    3.949 closest distance to " CB  ASN A  60 " =    0.922
peak=    3.946 closest distance to " O   HOH Z 389 " =    1.975
peak=    3.922 closest distance to " C   ASN A 209 " =    1.592
peak=    3.914 closest distance to " O   HOH Z 170 " =    1.393
peak=    3.912 closest distance to " CA  ILE A 234 " =    1.133
peak=    3.902 closest distance to " CG  GLN A  88 " =    0.959
peak=    3.879 closest distance to " CB  ARG A 275 " =    1.055
peak=    3.872 closest distance to " NH1 ARG A  56 " =    1.278
peak=    3.869 closest distance to " O   HOH Z 380 " =    1.848
peak=    3.864 closest distance to " CG  PRO A 213 " =    1.372
peak=    3.862 closest distance to " O   HOH Z 201 " =    1.740
peak=    3.861 closest distance to " CG2 VAL A 257 " =    0.981
peak=    3.855 closest distance to " CA  ASP A  50 " =    1.203
peak=    3.853 closest distance to " N   TYR A  15 " =    0.983
peak=    3.850 closest distance to " O   HOH Z 158 " =    1.080
peak=    3.846 closest distance to " O   HOH Z  59 " =    1.719
peak=    3.834 closest distance to " O   TYR A 116 " =    1.251
peak=    3.828 closest distance to " N   GLN A 278 " =    0.980
peak=    3.820 closest distance to " O   HOH Z 211 " =    1.389
peak=    3.816 closest distance to " O   HOH Z 217 " =    2.723
peak=    3.808 closest distance to " CA  ASN A 127 " =    1.051
peak=    3.804 closest distance to " O   HOH Z   9 " =    1.490
peak=    3.801 closest distance to " O   HOH Z 361 " =    1.425
peak=    3.801 closest distance to " O   HOH Z  61 " =    1.843
peak=    3.799 closest distance to " O   GLN A  55 " =    1.767
peak=    3.798 closest distance to " CB  ARG A  79 " =    1.181
peak=    3.794 closest distance to " O   HOH Z 411 " =    3.013
peak=    3.790 closest distance to " CD1 LEU A 300 " =    1.182
peak=    3.784 closest distance to " O   HOH Z 167 " =    1.797
peak=    3.779 closest distance to " CB  ASP A 132 " =    3.999
peak=    3.776 closest distance to " CD  ARG A 269 " =    0.963
peak=    3.770 closest distance to " OH  TYR A 186 " =    1.049
peak=    3.768 closest distance to " CB  LEU A 228 " =    1.114
peak=    3.768 closest distance to " O   HOH Z 111 " =    1.595
peak=    3.768 closest distance to " CA  TRP A  92 " =    1.054
peak=    3.767 closest distance to " CB  TYR A 169 " =    0.725
peak=    3.756 closest distance to " O   HOH Z 427 " =    1.257
peak=    3.742 closest distance to " O   HOH Z 225 " =    1.639
peak=    3.739 closest distance to " O   HOH Z 393 " =    1.502
peak=    3.736 closest distance to " CG2 ILE A 120 " =    0.953
peak=    3.729 closest distance to " O   HOH Z 352 " =    1.667
peak=    3.722 closest distance to " CB  SER A 210 " =    0.895
peak=    3.721 closest distance to " N   CYS A 260 " =    0.921
peak=    3.719 closest distance to " CZ  PHE A  38 " =    1.283
peak=    3.716 closest distance to " CG2 THR A 221 " =    1.120
peak=    3.703 closest distance to " OE1 GLN A 240 " =    1.672
peak=    3.689 closest distance to " CZ  PHE A 218 " =    1.169
peak=    3.684 closest distance to " OD1 ASN A  60 " =    0.938
peak=    3.674 closest distance to " O   HOH Z  78 " =    1.621
peak=    3.672 closest distance to " O   HOH Z 287 " =    2.086
peak=    3.669 closest distance to " O   HOH Z 207 " =    2.349
peak=    3.668 closest distance to " CA  ARG A 102 " =    1.114
peak=    3.666 closest distance to " O   HOH Z 193 " =    1.684
peak=    3.664 closest distance to " O   HOH Z 394 " =    1.765
peak=    3.663 closest distance to " O   HOH Z 171 " =    1.853
peak=    3.660 closest distance to " CA  ARG A  36 " =    1.277
peak=    3.658 closest distance to " CB  GLN A  89 " =    1.256
peak=    3.655 closest distance to " O   HOH Z 145 " =    2.022
peak=    3.651 closest distance to " O   HOH Z 186 " =    1.148
peak=    3.648 closest distance to " CB  TYR A  30 " =    1.352
peak=    3.644 closest distance to " O   HOH Z  46 " =    1.087
peak=    3.643 closest distance to " N   GLU A   2 " =    1.482
peak=    3.633 closest distance to " CD2 TRP A 179 " =    2.108
peak=    3.620 closest distance to " O   HOH Z 422 " =    2.552
peak=    3.617 closest distance to " O   HOH Z  78 " =    2.322
peak=    3.616 closest distance to " O   HOH Z 148 " =    1.612
peak=    3.616 closest distance to " CB  ALA A  43 " =    0.912
peak=    3.613 closest distance to " CG  PRO A 243 " =    1.093
peak=    3.612 closest distance to " O   HOH Z  42 " =    1.710
peak=    3.595 closest distance to " CB  VAL A 202 " =    1.558
peak=    3.594 closest distance to " O   HOH Z 175 " =    3.819
peak=    3.583 closest distance to " ND2 ASN A  60 " =    2.929
peak=    3.580 closest distance to " CA  GLY A 196 " =    0.926
peak=    3.579 closest distance to " CG1 ILE A  33 " =    1.228
peak=    3.579 closest distance to " CG1 ILE A 120 " =    1.416
peak=    3.576 closest distance to " CB  GLU A 152 " =    1.124
peak=    3.570 closest distance to " CA  ASP A 124 " =    0.801
peak=    3.568 closest distance to " N   ARG A 156 " =    1.334
peak=    3.568 closest distance to " CG  GLU A 277 " =    1.976
peak=    3.565 closest distance to " O   HOH Z 410 " =    1.416
peak=    3.564 closest distance to " CB  VAL A 265 " =    1.332
peak=    3.560 closest distance to " CB  MET A  47 " =    1.054
peak=    3.549 closest distance to " O   HOH Z 172 " =    2.389
peak=    3.545 closest distance to " O   HOH Z  40 " =    2.159
peak=    3.542 closest distance to " O   HOH Z 293 " =    2.191
peak=    3.535 closest distance to " N   VAL A 296 " =    1.796
peak=    3.531 closest distance to " CB  ALA A 114 " =    0.907
peak=    3.531 closest distance to " CA  GLU A 152 " =    1.124
peak=    3.530 closest distance to " O   HOH Z   1 " =    1.857
peak=    3.526 closest distance to " OE1 GLN A  11 " =    2.067
peak=    3.525 closest distance to " CG  ARG A 159 " =    0.832
peak=    3.519 closest distance to " OE2 GLU A  53 " =    1.383
peak=    3.515 closest distance to " NE  ARG A  66 " =    3.237
peak=    3.514 closest distance to " CG1 ILE A 151 " =    1.084
peak=    3.512 closest distance to " O   HOH Z 234 " =    3.983
peak=    3.512 closest distance to " CB  GLN A 183 " =    1.114
peak=    3.511 closest distance to " O   HOH Z  91 " =    2.394
peak=    3.507 closest distance to " OD2 ASP A 286 " =    2.921
peak=    3.503 closest distance to " ND2AASN A 224 " =    0.987
peak=    3.500 closest distance to " CE3 TRP A  85 " =    0.953
peak=    3.498 closest distance to " CB  PHE A  61 " =    1.259
peak=    3.495 closest distance to " O   HOH Z 434 " =    1.531
peak=    3.492 closest distance to " N   ASN A 127 " =    1.447
peak=    3.491 closest distance to " CB  ARG A 156 " =    1.003
peak=    3.487 closest distance to " OG BSER A 134 " =    2.696
peak=    3.476 closest distance to " CD1 ILE A  33 " =    1.723
peak=    3.475 closest distance to " CG2 ILE A 151 " =    0.917
peak=    3.473 closest distance to " O   HOH Z  30 " =    1.793
peak=    3.464 closest distance to " O   HOH Z  67 " =    1.725
peak=    3.463 closest distance to " CG BARG A 275 " =    1.520
peak=    3.463 closest distance to " CB  ASN A  39 " =    0.943
peak=    3.462 closest distance to " O   HOH Z 329 " =    3.893
peak=    3.461 closest distance to " O   HOH Z 132 " =    2.459
peak=    3.461 closest distance to " CD  ARG A  66 " =    2.239
peak=    3.457 closest distance to " O   HOH Z  69 " =    2.249
peak=    3.455 closest distance to " CZ3 TRP A 266 " =    1.117
peak=    3.448 closest distance to " O   HOH Z 385 " =    3.755
peak=    3.445 closest distance to " O   HOH Z 105 " =    1.171
peak=    3.441 closest distance to " CA  GLY A 267 " =    1.178
peak=    3.441 closest distance to " NZ  LYS A 117 " =    1.357
peak=    3.436 closest distance to " CA  ASN A 284 " =    1.005
peak=    3.432 closest distance to " O   HOH Z 112 " =    1.294
peak=    3.430 closest distance to " O   HOH Z 180 " =    2.085
peak=    3.428 closest distance to " CB  ARG A 190 " =    1.630
peak=    3.427 closest distance to " O   HOH Z 421 " =    2.907
peak=    3.425 closest distance to " O   HOH Z 290 " =    1.211
peak=    3.425 closest distance to " CB  ALA A  21 " =    1.051
peak=    3.424 closest distance to " O   THR A 220 " =    1.437
peak=    3.421 closest distance to " CG  LYS A  76 " =    1.671
peak=    3.419 closest distance to " O   HOH Z   2 " =    1.671
peak=    3.416 closest distance to " SD  MET A  93 " =    0.835
peak=    3.414 closest distance to " CA  ILE A 263 " =    1.110
peak=    3.412 closest distance to " CB  ALA A  10 " =    1.049
peak=    3.406 closest distance to " N   SER A 271 " =    1.083
peak=    3.404 closest distance to " CA  SER A  87 " =    0.961
peak=    3.403 closest distance to " O   HOH Z 313 " =    1.629
peak=    3.394 closest distance to " O   HOH Z 409 " =    2.065
peak=    3.394 closest distance to " O   HOH Z  44 " =    2.584
peak=    3.393 closest distance to " O   HOH Z 217 " =    1.430
peak=    3.392 closest distance to " N   PHE A 130 " =    1.279
peak=    3.389 closest distance to " CA  ALA A 154 " =    0.971
peak=    3.389 closest distance to " O   HOH Z 122 " =    1.915
peak=    3.375 closest distance to " CD  LYS A 119 " =    1.240
peak=    3.373 closest distance to " O   HOH Z 299 " =    3.270
peak=    3.373 closest distance to " CA  THR A 264 " =    0.898
peak=    3.372 closest distance to " CA  ALA A 160 " =    0.920
peak=    3.369 closest distance to " CB  TYR A 169 " =    1.006
peak=    3.366 closest distance to " CA  VAL A 121 " =    1.064
peak=    3.358 closest distance to " O   HOH Z 153 " =    3.729
peak=    3.355 closest distance to " O   HOH Z  88 " =    3.319
peak=    3.353 closest distance to " O   HOH Z 390 " =    2.801
peak=    3.353 closest distance to " NE2 HIS A 207 " =    1.026
peak=    3.350 closest distance to " OG BSER A 258 " =    0.953
peak=    3.348 closest distance to " CD  LYS A 166 " =    1.397
peak=    3.346 closest distance to " OD1 ASN A 217 " =    1.489
peak=    3.341 closest distance to " NE1 TRP A 274 " =    0.961
peak=    3.341 closest distance to " O   HOH Z 431 " =    1.089
peak=    3.341 closest distance to " N   SER A  97 " =    0.954
peak=    3.340 closest distance to " O   HOH Z 184 " =    2.190
peak=    3.339 closest distance to " O   HOH Z 124 " =    1.842
peak=    3.338 closest distance to " CE2 PHE A  16 " =    1.196
peak=    3.337 closest distance to " O   HOH Z 218 " =    2.011
peak=    3.337 closest distance to " O   HOH Z 128 " =    3.070
peak=    3.336 closest distance to " O   HOH Z 222 " =    1.904
peak=    3.333 closest distance to " CE3 TRP A 150 " =    1.408
peak=    3.328 closest distance to " O   HOH Z 124 " =    2.548
peak=    3.328 closest distance to " O   HOH Z 344 " =    3.536
peak=    3.319 closest distance to " CG  GLN A 144 " =    0.884
peak=    3.319 closest distance to " O  BHOH Z 338 " =    2.055
peak=    3.317 closest distance to " CB  LEU A  83 " =    0.818
peak=    3.317 closest distance to " O   ALA A  71 " =    1.182
peak=    3.311 closest distance to " O   HOH Z 409 " =    3.592
peak=    3.310 closest distance to " CD  ARG A 195 " =    3.449
peak=    3.303 closest distance to " CG2 THR A  29 " =    1.483
peak=    3.303 closest distance to " O   HOH Z  26 " =    1.493
peak=    3.301 closest distance to " CB  THR A 157 " =    1.114
peak=    3.298 closest distance to " CG  GLU A   2 " =    1.090
peak=    3.294 closest distance to " CZ3 TRP A 123 " =    1.378
peak=    3.293 closest distance to " CB  ALA A 184 " =    1.037
peak=    3.285 closest distance to " O   HOH Z 276 " =    0.999
peak=    3.284 closest distance to " NE AARG A 275 " =    1.736
peak=    3.284 closest distance to " O   HOH Z 285 " =    2.629
peak=    3.281 closest distance to " O   HOH Z 153 " =    1.659
peak=    3.279 closest distance to " CB BSER A 164 " =    1.279
peak=    3.279 closest distance to " O   MET A 105 " =    1.830
peak=    3.278 closest distance to " O   HOH Z 223 " =    1.461
peak=    3.271 closest distance to " O   HOH Z 128 " =    2.268
peak=    3.271 closest distance to " CB  LEU A 237 " =    0.931
peak=    3.267 closest distance to " O   HOH Z 177 " =    2.077
peak=    3.267 closest distance to " CA  CYS A 260 " =    0.716
peak=    3.266 closest distance to " CB  SER A 212 " =    1.236
peak=    3.263 closest distance to " CA  VAL A 125 " =    1.114
peak=    3.259 closest distance to " CB  ASN A 187 " =    1.009
peak=    3.248 closest distance to " CA  GLY A  23 " =    0.870
peak=    3.246 closest distance to " O   HOH Z 153 " =    4.056
peak=    3.244 closest distance to " NE2 GLN A  58 " =    4.018
peak=    3.243 closest distance to " CA  LEU A 282 " =    1.170
peak=    3.242 closest distance to " ND2 ASN A 187 " =    1.432
peak=    3.241 closest distance to " O   HOH Z  57 " =    1.280
peak=    3.241 closest distance to " O   HOH Z 288 " =    1.979
peak=    3.234 closest distance to " CB  ALA A 161 " =    1.042
peak=    3.228 closest distance to " CA  CYS A 201 " =    1.638
peak=    3.228 closest distance to " C   GLU A 277 " =    1.312
peak=    3.226 closest distance to " O   HOH Z   3 " =    2.492
peak=    3.224 closest distance to " CB  HIS A  86 " =    1.022
peak=    3.221 closest distance to " CA  TYR A  15 " =    1.141
peak=    3.214 closest distance to " CA  MET A 105 " =    0.887
peak=    3.211 closest distance to " O   HOH Z 172 " =    5.026
peak=    3.211 closest distance to " CA  ASP A 149 " =    1.379
peak=    3.210 closest distance to " CG  GLN A 278 " =    3.606
peak=    3.208 closest distance to " O   HOH Z 154 " =    1.834
peak=    3.207 closest distance to " O   HOH Z  68 " =    1.814
peak=    3.207 closest distance to " N   PHE A 218 " =    0.979
peak=    3.204 closest distance to " O   HOH Z 302 " =    1.679
peak=    3.203 closest distance to " O   HOH Z 284 " =    1.322
peak=    3.198 closest distance to " CA  GLU A  46 " =    0.810
peak=    3.198 closest distance to " CB  ASN A 142 " =    0.861
peak=    3.194 closest distance to " O   HOH Z 281 " =    1.862
peak=    3.193 closest distance to " CB  PHE A 225 " =    1.400
peak=    3.192 closest distance to " CB  ASN A 285 " =    0.920
peak=    3.191 closest distance to " OE1 GLU A 236 " =    1.327
peak=    3.184 closest distance to " O   HOH Z 282 " =    2.118
peak=    3.182 closest distance to " O   THR A 251 " =    1.311
peak=    3.181 closest distance to " CA  ASP A 191 " =    0.802
peak=    3.179 closest distance to " CB  ALA A 104 " =    0.780
peak=    3.175 closest distance to " CE3 TRP A 274 " =    2.266
peak=    3.173 closest distance to " O   HOH Z 145 " =    2.098
peak=    3.173 closest distance to " O   HOH Z 362 " =    2.018
peak=    3.172 closest distance to " O   HOH Z 236 " =    1.720
peak=    3.170 closest distance to " CB  GLU A 236 " =    1.456
peak=    3.170 closest distance to " O   HOH Z 103 " =    0.721
peak=    3.169 closest distance to " CB  ASP A 140 " =    0.800
peak=    3.162 closest distance to " CB  ASN A 215 " =    1.272
peak=    3.160 closest distance to " CB  ALA A 114 " =    1.457
peak=    3.160 closest distance to " CA  GLY A  13 " =    0.950
peak=    3.155 closest distance to " CG2 THR A 279 " =    0.829
peak=    3.154 closest distance to " O   HOH Z 186 " =    3.136
peak=    3.153 closest distance to " CB  LEU A 300 " =    0.894
peak=    3.151 closest distance to " O   HOH Z 367 " =    2.295
peak=    3.146 closest distance to " O   HOH Z 148 " =    2.330
peak=    3.144 closest distance to " CB  GLU A 277 " =    3.621
peak=    3.144 closest distance to " NH2AARG A 190 " =    1.747
peak=    3.143 closest distance to " O   HOH Z 133 " =    2.633
peak=    3.137 closest distance to " CA  GLY A  98 " =    1.066
peak=    3.133 closest distance to " CB  TRP A 179 " =    1.366
peak=    3.131 closest distance to " CG1 VAL A 153 " =    0.965
peak=    3.124 closest distance to " O   HOH Z 325 " =    2.192
peak=    3.122 closest distance to " O   GLU A   2 " =    1.720
peak=    3.120 closest distance to " CB  TRP A 274 " =    1.094
peak=    3.120 closest distance to " CD2 LEU A   5 " =    1.311
peak=    3.118 closest distance to " O   HOH Z 298 " =    4.057
peak=    3.114 closest distance to " O   THR A 294 " =    1.068
peak=    3.112 closest distance to " ND2 ASN A  60 " =    3.822
peak=    3.107 closest distance to " CA  PHE A 283 " =    1.254
peak=    3.107 closest distance to " CH2 TRP A 150 " =    1.186
peak=    3.106 closest distance to " O   HOH Z 332 " =    1.582
peak=    3.106 closest distance to " OE1 GLN A  77 " =    1.048
peak=    3.103 closest distance to " O   HOH Z 319 " =    2.084
peak=    3.098 closest distance to " N   ASP A 162 " =    1.322
peak=    3.096 closest distance to " O   HOH Z  64 " =    2.279
peak=    3.087 closest distance to " NZ  LYS A 119 " =    1.391
peak=    3.084 closest distance to " NE2 GLN A 205 " =    1.097
peak=    3.081 closest distance to " CB  ALA A 291 " =    1.239
peak=    3.074 closest distance to " CB  PRO A 163 " =    4.184
peak=    3.058 closest distance to " CB  ALA A  34 " =    1.319
peak=    3.054 closest distance to " OG ASER A 212 " =    1.514
peak=    3.050 closest distance to " ND2 ASN A 110 " =    1.704
peak=    3.038 closest distance to " CG1 ILE A 120 " =    1.440
peak=    3.033 closest distance to " CB  ASP A 171 " =    0.889
peak=    3.019 closest distance to " ND1 HIS A  81 " =    1.552
peak=    3.018 closest distance to " O   HOH Z 411 " =    1.275
peak=    3.014 closest distance to " CA  ALA A 100 " =    1.149

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.354 - 5.796
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 218
   mapped sites are within: 0.777 - 5.796

peak=   -5.102 closest distance to " O   PRO A 198 " =    1.120
peak=   -4.412 closest distance to " CG  GLN A  88 " =    0.904
peak=   -4.401 closest distance to " CD  ARG A  14 " =    3.367
peak=   -4.352 closest distance to " CG  MET A 105 " =    0.983
peak=   -4.114 closest distance to " CZ3 TRP A 179 " =    1.189
peak=   -4.099 closest distance to " O   HOH Z  60 " =    1.667
peak=   -3.997 closest distance to " CA  GLY A 203 " =    2.282
peak=   -3.982 closest distance to " O   HOH Z 111 " =    1.836
peak=   -3.946 closest distance to " CB  ASP A  27 " =    2.598
peak=   -3.889 closest distance to " OG  SER A  97 " =    2.003
peak=   -3.874 closest distance to " O   HOH Z 290 " =    1.202
peak=   -3.871 closest distance to " O   HOH Z 211 " =    1.007
peak=   -3.859 closest distance to " O   HOH Z  24 " =    1.152
peak=   -3.856 closest distance to " O   HOH Z 188 " =    0.811
peak=   -3.848 closest distance to " OG BSER A 134 " =    1.632
peak=   -3.828 closest distance to " O   HOH Z  52 " =    2.241
peak=   -3.825 closest distance to " CD2 TYR A 293 " =    1.881
peak=   -3.801 closest distance to " O   HOH Z 318 " =    1.580
peak=   -3.798 closest distance to " CB  ALA A 291 " =    2.078
peak=   -3.778 closest distance to " OE1 GLN A  88 " =    1.359
peak=   -3.774 closest distance to " O   HOH Z 231 " =    1.921
peak=   -3.763 closest distance to " O   HOH Z 185 " =    2.241
peak=   -3.760 closest distance to " CB  ASN A 285 " =    2.437
peak=   -3.752 closest distance to " O   HOH Z 316 " =    1.917
peak=   -3.752 closest distance to " O   HOH Z 313 " =    1.724
peak=   -3.735 closest distance to " ND2 ASN A 209 " =    1.986
peak=   -3.730 closest distance to " O   HOH Z 118 " =    0.875
peak=   -3.708 closest distance to " CB  ALA A  43 " =    2.496
peak=   -3.697 closest distance to " CB  PRO A 243 " =    2.471
peak=   -3.689 closest distance to " O   HOH Z 404 " =    1.007
peak=   -3.689 closest distance to " OE1 GLN A  88 " =    1.127
peak=   -3.687 closest distance to " CG1 VAL A  78 " =    2.338
peak=   -3.654 closest distance to " O   ALA A  10 " =    1.735
peak=   -3.647 closest distance to " O   HOH Z 410 " =    2.349
peak=   -3.647 closest distance to " N   THR A 157 " =    1.517
peak=   -3.642 closest distance to " O   HOH Z 377 " =    1.479
peak=   -3.641 closest distance to " O   VAL A 125 " =    2.196
peak=   -3.629 closest distance to " O   HOH Z 407 " =    3.459
peak=   -3.622 closest distance to " O   HOH Z 389 " =    2.179
peak=   -3.616 closest distance to " O   HOH Z  76 " =    1.086
peak=   -3.615 closest distance to " CD  LYS A 289 " =    2.380
peak=   -3.610 closest distance to " O   HOH Z  85 " =    2.214
peak=   -3.604 closest distance to " N   ALA A  43 " =    2.469
peak=   -3.595 closest distance to " CG1 VAL A 112 " =    2.764
peak=   -3.585 closest distance to " O   HOH Z 166 " =    1.784
peak=   -3.585 closest distance to " CB  PRO A  54 " =    2.468
peak=   -3.581 closest distance to " CG2 VAL A 112 " =    2.551
peak=   -3.575 closest distance to " O   HOH Z  39 " =    0.842
peak=   -3.564 closest distance to " CA  GLY A  98 " =    1.796
peak=   -3.564 closest distance to " CB  ALA A 131 " =    1.913
peak=   -3.563 closest distance to " CE3 TRP A 150 " =    2.757
peak=   -3.562 closest distance to " CA  GLY A  23 " =    2.952
peak=   -3.559 closest distance to " O   ASN A 301 " =    1.295
peak=   -3.559 closest distance to " O   HOH Z 282 " =    4.477
peak=   -3.551 closest distance to " CA  GLY A 241 " =    3.094
peak=   -3.550 closest distance to " O   PRO A 163 " =    1.936
peak=   -3.549 closest distance to " CG2 VAL A 232 " =    1.986
peak=   -3.549 closest distance to " O   HOH Z 102 " =    1.755
peak=   -3.548 closest distance to " CG  GLN A  55 " =    1.459
peak=   -3.548 closest distance to " OE2 GLU A 152 " =    2.301
peak=   -3.546 closest distance to " CB  ALA A   9 " =    2.482
peak=   -3.542 closest distance to " CE3 TRP A 150 " =    1.872
peak=   -3.540 closest distance to " O   HOH Z 201 " =    1.560
peak=   -3.536 closest distance to " CD1 TRP A 179 " =    1.162
peak=   -3.524 closest distance to " O   GLY A  80 " =    2.452
peak=   -3.520 closest distance to " N   LEU A 282 " =    2.192
peak=   -3.519 closest distance to " O   HOH Z 371 " =    2.360
peak=   -3.514 closest distance to " O   HOH Z  28 " =    1.200
peak=   -3.514 closest distance to " CB  ALA A 248 " =    2.509
peak=   -3.504 closest distance to " O   ALA A 158 " =    2.230
peak=   -3.499 closest distance to " O   HOH Z  65 " =    1.351
peak=   -3.493 closest distance to " O   HOH Z 298 " =    2.555
peak=   -3.476 closest distance to " C   ALA A 158 " =    1.774
peak=   -3.471 closest distance to " O   HOH Z 384 " =    3.292
peak=   -3.471 closest distance to " CD2 LEU A 143 " =    2.519
peak=   -3.458 closest distance to " O   HOH Z  38 " =    1.051
peak=   -3.457 closest distance to " CG  LEU A  83 " =    2.126
peak=   -3.452 closest distance to " CD  GLN A 223 " =    1.437
peak=   -3.452 closest distance to " O   HOH Z 166 " =    1.294
peak=   -3.451 closest distance to " O   HOH Z  32 " =    1.661
peak=   -3.450 closest distance to " CE1 PHE A 225 " =    2.155
peak=   -3.448 closest distance to " CA  GLY A 133 " =    2.036
peak=   -3.443 closest distance to " O   HOH Z 163 " =    1.538
peak=   -3.434 closest distance to " O   HOH Z 411 " =    1.238
peak=   -3.429 closest distance to " C   ASP A 270 " =    1.087
peak=   -3.429 closest distance to " CB  PRO A  90 " =    1.411
peak=   -3.420 closest distance to " O   ALA A  51 " =    1.338
peak=   -3.412 closest distance to " CG2 THR A 178 " =    2.166
peak=   -3.409 closest distance to " CB  ASP A 132 " =    2.373
peak=   -3.400 closest distance to " O   HOH Z 276 " =    1.100
peak=   -3.398 closest distance to " CG2 ILE A  49 " =    2.777
peak=   -3.393 closest distance to " O   HOH Z 189 " =    2.917
peak=   -3.393 closest distance to " O   HOH Z  73 " =    1.918
peak=   -3.392 closest distance to " OG ASER A 134 " =    1.207
peak=   -3.391 closest distance to " CD  ARG A 156 " =    2.044
peak=   -3.390 closest distance to " CD2 LEU A 237 " =    2.886
peak=   -3.384 closest distance to " O   HOH Z 351 " =    1.453
peak=   -3.381 closest distance to " CD1 PHE A  59 " =    2.088
peak=   -3.377 closest distance to " OE1 GLU A  44 " =    1.406
peak=   -3.377 closest distance to " CG1 VAL A 112 " =    2.517
peak=   -3.376 closest distance to " CD  LYS A 166 " =    2.445
peak=   -3.376 closest distance to " N   ASP A 171 " =    2.386
peak=   -3.376 closest distance to " O   HOH Z  43 " =    1.299
peak=   -3.375 closest distance to " O   HOH Z 139 " =    3.072
peak=   -3.373 closest distance to " O   HOH Z 286 " =    1.535
peak=   -3.370 closest distance to " CD2 TRP A 274 " =    2.576
peak=   -3.367 closest distance to " CG2BVAL A  41 " =    1.231
peak=   -3.367 closest distance to " CD1 TYR A 169 " =    2.585
peak=   -3.362 closest distance to " OD2 ASP A  27 " =    1.684
peak=   -3.356 closest distance to " CB  TYR A  15 " =    2.048
peak=   -3.352 closest distance to " O   HOH Z 413 " =    3.411
peak=   -3.340 closest distance to " O   HOH Z  49 " =    1.542
peak=   -3.339 closest distance to " NH2AARG A 275 " =    5.796
peak=   -3.333 closest distance to " O   HOH Z 220 " =    1.230
peak=   -3.333 closest distance to " O   PHE A 218 " =    1.402
peak=   -3.332 closest distance to " CZ2 TRP A 274 " =    0.943
peak=   -3.330 closest distance to " O   HOH Z  88 " =    2.054
peak=   -3.328 closest distance to " CG  TRP A 266 " =    1.572
peak=   -3.322 closest distance to " O   HOH Z 390 " =    2.424
peak=   -3.314 closest distance to " O   HOH Z 275 " =    1.806
peak=   -3.314 closest distance to " O   LYS A  76 " =    1.320
peak=   -3.313 closest distance to " CA  GLY A 241 " =    2.222
peak=   -3.308 closest distance to " O   HOH Z 425 " =    1.010
peak=   -3.299 closest distance to " O   GLU A 152 " =    1.590
peak=   -3.298 closest distance to " CZ  TYR A 169 " =    1.842
peak=   -3.295 closest distance to " CG  GLN A  88 " =    1.028
peak=   -3.288 closest distance to " OE1 GLN A 183 " =    1.685
peak=   -3.285 closest distance to " O   HOH Z 348 " =    1.969
peak=   -3.282 closest distance to " CB  ALA A 114 " =    2.392
peak=   -3.276 closest distance to " O   HOH Z 281 " =    3.085
peak=   -3.271 closest distance to " O   HOH Z 275 " =    1.664
peak=   -3.271 closest distance to " CG2 ILE A 120 " =    1.119
peak=   -3.268 closest distance to " O   ALA A 180 " =    1.199
peak=   -3.261 closest distance to " O   HOH Z  52 " =    1.992
peak=   -3.260 closest distance to " CG  PRO A 163 " =    2.498
peak=   -3.256 closest distance to " O   HOH Z 198 " =    2.180
peak=   -3.253 closest distance to " O   HOH Z 138 " =    0.849
peak=   -3.252 closest distance to " O   HOH Z 431 " =    1.340
peak=   -3.252 closest distance to " O   HOH Z 259 " =    3.969
peak=   -3.252 closest distance to " CG1 VAL A 125 " =    1.780
peak=   -3.248 closest distance to " CB  ASP A  50 " =    2.454
peak=   -3.244 closest distance to " OG BSER A 134 " =    2.064
peak=   -3.242 closest distance to " CD1 LEU A 282 " =    2.543
peak=   -3.240 closest distance to " O   HOH Z 385 " =    1.536
peak=   -3.240 closest distance to " N   MET A 105 " =    2.533
peak=   -3.236 closest distance to " OG1 THR A  82 " =    1.920
peak=   -3.234 closest distance to " ND2 ASN A 217 " =    2.179
peak=   -3.232 closest distance to " OG  SER A  63 " =    1.144
peak=   -3.231 closest distance to " CZ  PHE A 130 " =    1.026
peak=   -3.230 closest distance to " C   PHE A  59 " =    1.102
peak=   -3.229 closest distance to " CD  GLN A  55 " =    1.202
peak=   -3.227 closest distance to " OE1 GLN A 278 " =    1.125
peak=   -3.227 closest distance to " O   SER A  87 " =    2.013
peak=   -3.226 closest distance to " CG2 THR A  52 " =    3.206
peak=   -3.225 closest distance to " O   HOH Z 359 " =    1.658
peak=   -3.225 closest distance to " N   ALA A  51 " =    1.669
peak=   -3.223 closest distance to " O   HOH Z 128 " =    4.143
peak=   -3.223 closest distance to " CG  ARG A 219 " =    2.438
peak=   -3.221 closest distance to " CB  PHE A 130 " =    1.263
peak=   -3.220 closest distance to " CD2 TYR A 169 " =    2.246
peak=   -3.220 closest distance to " OE2 GLU A 152 " =    1.120
peak=   -3.219 closest distance to " CE3 TRP A  70 " =    1.732
peak=   -3.217 closest distance to " O   HOH Z 364 " =    2.875
peak=   -3.217 closest distance to " O   SER A 135 " =    1.403
peak=   -3.214 closest distance to " O   HOH Z 216 " =    1.914
peak=   -3.207 closest distance to " OG  SER A 245 " =    1.344
peak=   -3.206 closest distance to " NE2 GLN A  55 " =    1.006
peak=   -3.202 closest distance to " O   PRO A 163 " =    1.327
peak=   -3.202 closest distance to " N   HIS A  81 " =    1.235
peak=   -3.198 closest distance to " O   HOH Z 368 " =    1.451
peak=   -3.197 closest distance to " O   HOH Z 414 " =    1.641
peak=   -3.194 closest distance to " ND2 ASN A  60 " =    4.019
peak=   -3.192 closest distance to " O   HOH Z 168 " =    2.026
peak=   -3.189 closest distance to " O   HOH Z  37 " =    1.297
peak=   -3.188 closest distance to " CB  ASN A 285 " =    2.152
peak=   -3.187 closest distance to " OD1 ASN A 176 " =    1.403
peak=   -3.187 closest distance to " O   HOH Z  11 " =    1.911
peak=   -3.186 closest distance to " O   HOH Z 131 " =    3.899
peak=   -3.183 closest distance to " NH2 ARG A  79 " =    1.914
peak=   -3.178 closest distance to " O   HOH Z 128 " =    2.518
peak=   -3.174 closest distance to " O   HOH Z  22 " =    2.229
peak=   -3.174 closest distance to " CA  GLY A 133 " =    2.215
peak=   -3.162 closest distance to " NH2 ARG A 219 " =    1.884
peak=   -3.159 closest distance to " CG  ASP A 231 " =    0.777
peak=   -3.157 closest distance to " OXT GLY A 302 " =    3.667
peak=   -3.153 closest distance to " O   ALA A   1 " =    1.320
peak=   -3.151 closest distance to " O   SER A  62 " =    2.392
peak=   -3.139 closest distance to " C   SER A 273 " =    1.213
peak=   -3.134 closest distance to " CB  TRP A  85 " =    2.244
peak=   -3.134 closest distance to " C   LEU A 222 " =    0.777
peak=   -3.134 closest distance to " CZ  PHE A 225 " =    1.190
peak=   -3.131 closest distance to " OD2 ASP A 171 " =    1.787
peak=   -3.128 closest distance to " O   HOH Z 417 " =    3.044
peak=   -3.128 closest distance to " CG2 VAL A 296 " =    2.099
peak=   -3.127 closest distance to " CZ  PHE A  38 " =    1.038
peak=   -3.124 closest distance to " C   LEU A 101 " =    1.078
peak=   -3.119 closest distance to " C   GLY A  13 " =    0.855
peak=   -3.116 closest distance to " O   HOH Z 212 " =    0.944
peak=   -3.103 closest distance to " CA  HIS A  86 " =    2.121
peak=   -3.100 closest distance to " CD1 LEU A 101 " =    2.720
peak=   -3.096 closest distance to " CB  ALA A 137 " =    1.646
peak=   -3.090 closest distance to " CD2 PHE A  61 " =    2.025
peak=   -3.090 closest distance to " O   TRP A  70 " =    1.532
peak=   -3.085 closest distance to " O   HOH Z 111 " =    1.469
peak=   -3.073 closest distance to " OD1 ASN A 301 " =    1.882
peak=   -3.068 closest distance to " CB  ASN A  39 " =    2.165
peak=   -3.068 closest distance to " CE3 TRP A 150 " =    2.586
peak=   -3.059 closest distance to " CA  ILE A 120 " =    1.093
peak=   -3.055 closest distance to " CB  ALA A 100 " =    2.325
peak=   -3.048 closest distance to " CZ  ARG A  24 " =    1.975
peak=   -3.045 closest distance to " O   HOH Z 368 " =    1.803
peak=   -3.028 closest distance to " CE2 TRP A  70 " =    2.440
peak=   -3.018 closest distance to " CD  ARG A 219 " =    2.533

================= 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    :  0.4719 0.4736   6.283274e+00   6.274494e+00
   1_bss:  0.4646 0.4680   6.279051e+00   6.269820e+00
   1_xyz:  0.3602 0.4012   6.119270e+00   6.174624e+00
   1_adp:  0.3258 0.4116   6.075029e+00   6.189364e+00
   1_occ:  0.3253 0.4116   6.074534e+00   6.189695e+00
   2_bss:  0.3258 0.4093   6.074366e+00   6.187832e+00
   2_xyz:  0.2627 0.3391   5.893871e+00   6.053547e+00
   2_adp:  0.2476 0.3243   5.859723e+00   6.026769e+00
   2_occ:  0.2476 0.3238   5.858943e+00   6.026105e+00
   3_bss:  0.2479 0.3238   5.859163e+00   6.025028e+00
   3_xyz:  0.2039 0.2688   5.675582e+00   5.865073e+00
   3_adp:  0.1849 0.2533   5.605867e+00   5.819882e+00
   3_occ:  0.1848 0.2530   5.605378e+00   5.819652e+00
   4_bss:  0.1849 0.2531   5.604744e+00   5.818188e+00
   4_xyz:  0.1553 0.2185   5.448965e+00   5.689310e+00
   4_adp:  0.1477 0.2016   5.391127e+00   5.615419e+00
   4_occ:  0.1476 0.2014   5.390607e+00   5.614693e+00
   5_bss:  0.1477 0.2011   5.390087e+00   5.613834e+00
   5_xyz:  0.1354 0.1840   5.304765e+00   5.528520e+00
   5_adp:  0.1331 0.1789   5.284702e+00   5.506457e+00
   5_occ:  0.1330 0.1788   5.284634e+00   5.506459e+00
   5_bss:  0.1330 0.1789   5.284307e+00   5.506189e+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:  0.338  65.159   1.246   1.098  -0.690   0.000  -0.000  -0.000
   1_xyz:  0.338  65.159   1.246   1.098  -0.690   0.000  -0.000  -0.000
   1_adp:  0.338  65.159   1.246   1.098  -0.690   0.000  -0.000  -0.000
   1_occ:  0.338  65.159   1.246   1.098  -0.690   0.000  -0.000  -0.000
   2_bss:  0.355  79.612   0.540  -0.074   0.215  -0.000   0.000   0.000
   2_xyz:  0.355  79.612   0.540  -0.074   0.215  -0.000   0.000   0.000
   2_adp:  0.355  79.612   0.540  -0.074   0.215  -0.000   0.000   0.000
   2_occ:  0.355  79.612   0.540  -0.074   0.215  -0.000   0.000   0.000
   3_bss:  0.346  72.794  -0.298  -0.896   0.088  -0.000   0.000   0.000
   3_xyz:  0.346  72.794  -0.298  -0.896   0.088  -0.000   0.000   0.000
   3_adp:  0.346  72.794  -0.298  -0.896   0.088  -0.000   0.000   0.000
   3_occ:  0.346  72.794  -0.298  -0.896   0.088  -0.000   0.000   0.000
   4_bss:  0.337  78.829  -1.085  -1.908  -0.418  -0.000  -0.000  -0.000
   4_xyz:  0.337  78.829  -1.085  -1.908  -0.418  -0.000  -0.000  -0.000
   4_adp:  0.337  78.829  -1.085  -1.908  -0.418  -0.000  -0.000  -0.000
   4_occ:  0.337  78.829  -1.085  -1.908  -0.418  -0.000  -0.000  -0.000
   5_bss:  0.328  69.813  -1.587  -2.425  -0.784  -0.000  -0.000  -0.000
   5_xyz:  0.328  69.813  -1.587  -2.425  -0.784  -0.000  -0.000  -0.000
   5_adp:  0.328  69.813  -1.587  -2.425  -0.784  -0.000  -0.000  -0.000
   5_occ:  0.328  69.813  -1.587  -2.425  -0.784  -0.000  -0.000  -0.000
   5_bss:  0.319  64.049  -1.928  -2.777  -1.066  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.619 0.4109  0.5612    72867.057
   1_bss:  58.215 0.4151  0.5847    71590.905
   1_xyz:  45.395 0.5769  0.7817    47443.889
   1_adp:  46.689 0.5604  0.7684    49978.843
   1_occ:  46.750 0.5596  0.7664    50014.699
   2_bss:  46.460 0.5631  0.7629    49446.530
   2_xyz:  36.190 0.6859  0.9034    31316.231
   2_adp:  34.389 0.7075  0.9169    29201.927
   2_occ:  34.349 0.7079  0.9169    29118.362
   3_bss:  34.284 0.7086  0.8989    29026.752
   3_xyz:  27.091 0.7880  0.9737    18601.309
   3_adp:  25.268 0.8079  0.9761    16558.526
   3_occ:  25.258 0.8079  0.9758    16535.278
   4_bss:  25.182 0.8086  0.9505    16457.340
   4_xyz:  21.367 0.8470  0.9747    12081.946
   4_adp:  19.213 0.8689  0.9834    10356.847
   4_occ:  19.205 0.8690  0.9832    10341.659
   5_bss:  19.200 0.8690  0.9676    10326.172
   5_xyz:  17.065 0.8886  0.9787     8491.188
   5_adp:  16.377 0.8952  0.9810     8100.673
   5_occ:  16.380 0.8952  0.9809     8099.644
   5_bss:  16.372 0.8952  0.9699     8091.910
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7231e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7231e-01
   1_xyz:   1.559  0.012  0.104 16.240  0.006  4.108   1.3603e-01
   1_adp:   1.559  0.012  0.104 16.240  0.006  4.108   1.3603e-01
   1_occ:   1.559  0.012  0.104 16.240  0.006  4.108   1.3603e-01
   2_bss:   1.559  0.012  0.104 16.240  0.006  4.108   1.3603e-01
   2_xyz:   1.235  0.009  0.084 14.907  0.005  4.109   8.5684e-02
   2_adp:   1.235  0.009  0.084 14.907  0.005  4.109   8.5684e-02
   2_occ:   1.235  0.009  0.084 14.907  0.005  4.109   8.5684e-02
   3_bss:   1.235  0.009  0.084 14.907  0.005  4.109   8.5684e-02
   3_xyz:   0.979  0.007  0.069 14.305  0.004  4.108   6.0385e-02
   3_adp:   0.979  0.007  0.069 14.305  0.004  4.108   6.0385e-02
   3_occ:   0.979  0.007  0.069 14.305  0.004  4.108   6.0385e-02
   4_bss:   0.979  0.007  0.069 14.305  0.004  4.108   6.0385e-02
   4_xyz:   0.993  0.007  0.072 14.018  0.003  4.118   5.6415e-02
   4_adp:   0.993  0.007  0.072 14.018  0.003  4.118   5.6415e-02
   4_occ:   0.993  0.007  0.072 14.018  0.003  4.118   5.6415e-02
   5_bss:   0.993  0.007  0.072 14.018  0.003  4.118   5.6415e-02
   5_xyz:   0.919  0.006  0.068 13.970  0.003  4.124   5.0312e-02
   5_adp:   0.919  0.006  0.068 13.970  0.003  4.124   5.0312e-02
   5_occ:   0.919  0.006  0.068 13.970  0.003  4.124   5.0312e-02
   5_bss:   0.919  0.006  0.068 13.970  0.003  4.124   5.0312e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.792   2.4219e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.792   2.4219e-01
   1_xyz:   9.943  0.063  0.385 85.315  0.034  2.020   1.0783e-01
   1_adp:   9.943  0.063  0.385 85.315  0.034  2.020   1.0783e-01
   1_occ:   9.943  0.063  0.385 85.315  0.034  2.020   1.0783e-01
   2_bss:   9.943  0.063  0.385 85.315  0.034  2.020   1.0783e-01
   2_xyz:   7.062  0.050  0.236 82.442  0.046  2.240   9.0533e-02
   2_adp:   7.062  0.050  0.236 82.442  0.046  2.240   9.0533e-02
   2_occ:   7.062  0.050  0.236 82.442  0.046  2.240   9.0533e-02
   3_bss:   7.062  0.050  0.236 82.442  0.046  2.240   9.0533e-02
   3_xyz:   8.789  0.052  0.336 82.189  0.025  2.283   9.9448e-02
   3_adp:   8.789  0.052  0.336 82.189  0.025  2.283   9.9448e-02
   3_occ:   8.789  0.052  0.336 82.189  0.025  2.283   9.9448e-02
   4_bss:   8.789  0.052  0.336 82.189  0.025  2.283   9.9448e-02
   4_xyz:   8.098  0.046  0.232 81.367  0.030  2.393   4.0534e-02
   4_adp:   8.098  0.046  0.232 81.367  0.030  2.393   4.0534e-02
   4_occ:   8.098  0.046  0.232 81.367  0.030  2.393   4.0534e-02
   5_bss:   8.098  0.046  0.232 81.367  0.030  2.393   4.0534e-02
   5_xyz:   8.758  0.047  0.221 81.864  0.022  2.344   3.5087e-02
   5_adp:   8.758  0.047  0.221 81.864  0.022  2.344   3.5087e-02
   5_occ:   8.758  0.047  0.221 81.864  0.022  2.344   3.5087e-02
   5_bss:   8.758  0.047  0.221 81.864  0.022  2.344   3.5087e-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: 106.49   0.00  19.70  71.23   0.00  16.06 106.49   0.00  39.57
   1_occ: 106.49   0.00  19.70  71.23   0.00  16.06 106.49   0.00  39.57
   2_bss: 106.49   0.00  19.70  71.23   0.00  16.06 106.49   0.00  39.57
   2_xyz: 106.49   0.00  19.70  71.23   0.00  16.06 106.49   0.00  39.57
   2_adp: 106.41   0.00  19.34  74.08   0.00  15.29 106.41   0.00  41.36
   2_occ: 106.41   0.00  19.34  74.08   0.00  15.29 106.41   0.00  41.36
   3_bss: 106.41   0.00  19.34  74.08   0.00  15.29 106.41   0.00  41.36
   3_xyz: 106.41   0.00  19.34  74.08   0.00  15.29 106.41   0.00  41.36
   3_adp: 118.09   0.00  19.90  98.85   0.00  14.43 118.09   4.23  49.67
   3_occ: 118.09   0.00  19.90  98.85   0.00  14.43 118.09   4.23  49.67
   4_bss: 118.09   0.00  19.90  98.85   0.00  14.43 118.09   4.23  49.67
   4_xyz: 118.09   0.00  19.90  98.85   0.00  14.43 118.09   4.23  49.67
   4_adp: 113.32   0.00  18.81  95.78   0.00  13.51 113.32   5.85  47.66
   4_occ: 113.32   0.00  18.81  95.78   0.00  13.51 113.32   5.85  47.66
   5_bss: 113.32   0.00  18.81  95.78   0.00  13.51 113.32   5.85  47.66
   5_xyz: 113.32   0.00  18.81  95.78   0.00  13.51 113.32   5.85  47.66
   5_adp: 111.03   0.00  18.43  93.86   0.00  13.32 111.03   6.02  46.25
   5_occ: 111.03   0.00  18.43  93.86   0.00  13.32 111.03   6.02  46.25
   5_bss: 111.03   0.00  18.43  93.86   0.00  13.32 111.03   6.02  46.25
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.724    0.025    0.365
   1_adp:    1.724    0.025    0.365
   1_occ:    1.724    0.025    0.365
   2_bss:    1.724    0.025    0.365
   2_xyz:    1.341    0.033    0.521
   2_adp:    1.341    0.033    0.521
   2_occ:    1.341    0.033    0.521
   3_bss:    1.341    0.033    0.521
   3_xyz:    1.485    0.032    0.665
   3_adp:    1.485    0.032    0.665
   3_occ:    1.485    0.032    0.665
   4_bss:    1.485    0.032    0.665
   4_xyz:    1.482    0.066    0.734
   4_adp:    1.482    0.066    0.734
   4_occ:    1.482    0.066    0.734
   5_bss:    1.482    0.066    0.734
   5_xyz:    1.611    0.080    0.767
   5_adp:    1.611    0.080    0.767
   5_occ:    1.611    0.080    0.767
   5_bss:    1.611    0.080    0.767
------------------------------------------------------------------------

CPU time actual refinement: 379.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1228/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_1228/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1228/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1228/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1228/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 379.43 
  Macro-tasks:
    bulk solvent and scale       = 50.01  
    individual site refinement   = 160.65 
    weights calculation          = 30.31  
    collect and process          = 6.52   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 247.59 
  Micro-tasks:
    mask                            = 2.53   
    f_calc                          = 123.55 
    alpha_beta                      = 8.31   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 132.37 
    fmodel                         = 8.33   
    r_factors                      = 0.31   
    phase_errors                   = 10.16  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 286.97 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.269 micro seconds
Total CPU time: 6.55 minutes
from_scatterers_fft:    663 calls, 123.19 s
gradients_fft:          608 calls, 118.35 s

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

# Date 2008-01-16 Time 06:44:46 PST -0800 (1200494686.33 s)
Start R-work = 0.4719, R-free = 0.4736 (no bulk solvent and anisotropic scale)
Final R-work = 0.1535, R-free = 0.1969 (no bulk solvent and anisotropic scale)

Start R-work = 0.4646, R-free = 0.4680
Final R-work = 0.1330, R-free = 0.1789