# Date 2008-01-16 Time 05:36:57 PST -0800 (1200490617.17 s)
#phil __OFF__

Command line arguments: "../809.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24501
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 809

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.3993, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   2.0104

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.3009 [2092/2117]  1883   209  10.0%
  bin  2:  4.3009 -  3.4270 [2025/2043]  1823   202  10.0%
  bin  3:  3.4270 -  2.9977 [1983/2002]  1784   199  10.0%
  bin  4:  2.9977 -  2.7254 [1955/1985]  1760   195  10.0%
  bin  5:  2.7254 -  2.5310 [1960/1979]  1764   196  10.0%
  bin  6:  2.5310 -  2.3824 [1950/1975]  1752   198  10.2%
  bin  7:  2.3824 -  2.2635 [1944/1972]  1755   189   9.7%
  bin  8:  2.2635 -  2.1653 [1938/1974]  1741   197  10.2%
  bin  9:  2.1653 -  2.0821 [1905/1947]  1714   191  10.0%
  bin 10:  2.0821 -  2.0104 [1837/1961]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_809/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: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2167
        3.04 -     3.66: 4617
        3.66 -     4.28: 8920
        4.28 -     4.90: 12280
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.944 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.337 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27988 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_809/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_809/model_refine_001.geo

CPU time processing inputs: 8.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.3993 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2884   r_free= 0.2792   ksol= 0.00   Bsol= 0.00   scale= 0.977    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.948814                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1370  153 0.2675 0.2666      6.2897      6.2385|
|  2:  4.7966 -  3.8277 0.99   1303  145 0.2187 0.2055       6.299       6.281|
|  3:  3.8277 -  3.3500 0.99   1280  142 0.2365 0.2390      6.2115       6.248|
|  4:  3.3500 -  3.0464 0.99   1281  140 0.2739 0.2534      6.1659      6.0826|
|  5:  3.0464 -  2.8296 0.99   1257  142 0.2864 0.2457      5.9952       5.895|
|  6:  2.8296 -  2.6637 0.99   1273  140 0.3017 0.3000      5.9541      5.9345|
|  7:  2.6637 -  2.5310 0.99   1250  139 0.3007 0.2811      5.8928      5.8276|
|  8:  2.5310 -  2.4213 0.98   1255  140 0.3140 0.2956      5.8922      5.9125|
|  9:  2.4213 -  2.3284 0.98   1240  140 0.3138 0.3046      5.8241      5.8128|
| 10:  2.3284 -  2.2483 0.99   1236  137 0.3327 0.3324      5.8667      5.7747|
| 11:  2.2483 -  2.1783 0.98   1254  137 0.3207 0.2901      5.7713      5.7007|
| 12:  2.1783 -  2.1162 0.97   1234  138 0.3371 0.3356      5.7579      5.8394|
| 13:  2.1162 -  2.0606 1.00   1231  134 0.3363 0.3338      5.6698      5.6649|
| 14:  2.0606 -  2.0104 0.91   1166  132 0.3420 0.3656      5.6026      5.6018|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7966  1370   153  0.80  25.03   0.87     0.82      38780.55|
|  2:  4.7966 -  3.8277  1303   145  0.86  19.65   0.98     0.92      35975.21|
|  3:  3.8277 -  3.3500  1280   142  0.86  21.01   0.99     0.95      31876.95|
|  4:  3.3500 -  3.0464  1281   140  0.83  23.27   0.99     0.94      27098.86|
|  5:  3.0464 -  2.8296  1257   142  0.79  27.65   1.00     0.93      23381.46|
|  6:  2.8296 -  2.6637  1273   140  0.78  28.86   1.00     0.92      21488.75|
|  7:  2.6637 -  2.5310  1250   139  0.77  29.90   1.02     0.92      20132.43|
|  8:  2.5310 -  2.4213  1255   140  0.76  30.09   1.02     0.94      19149.21|
|  9:  2.4213 -  2.3284  1240   140  0.76  30.42   1.03     0.95      17211.24|
| 10:  2.3284 -  2.2483  1236   137  0.76  30.33   1.05     0.96      16127.37|
| 11:  2.2483 -  2.1783  1254   137  0.75  31.21   1.05     0.98      15550.57|
| 12:  2.1783 -  2.1162  1234   138  0.75  31.90   1.04     0.98      15421.86|
| 13:  2.1162 -  2.0606  1231   134  0.73  33.60   1.04     0.97      14538.40|
| 14:  2.0606 -  2.0104  1166   132  0.70  35.84   1.04     0.93      13111.96|
|alpha:            min =        0.82 max =            0.98 mean =         0.93|
|beta:             min =    13111.96 max =        38780.55 mean =     22374.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.78|
|phase err.(work): min =        0.00 max =           89.99 mean =        28.37|
|phase err.(test): min =        0.00 max =           89.87 mean =        28.35|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.426949              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.804   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.499243              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.793   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      177 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1990 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1840 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2777 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4581 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4339 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5594 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6686 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.138 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    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: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2884   r_free= 0.2792   ksol= 0.00   Bsol= 0.00   scale= 0.977    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.948814                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2741   r_free= 0.2657   ksol= 0.32   Bsol= 54.87   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,0.81,-0.95,0.00,-0.00,-0.00); trace/3= -0.96                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.919595                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.262592              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.874   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.289616              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.763   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2741      final r-factor (work) = 0.1782          |
| start r-factor (free) = 0.2657      final r-factor (free) = 0.1947          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8764 = 2.26 * 0.50 * 5.9359 + 1.00 * 0.1611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4485 = 2.26 * 0.50 * 5.6490 + 1.00 * 0.0578                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1782      final r-factor (work) = 0.1684          |
| start r-factor (free) = 0.1947      final r-factor (free) = 0.1944          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6439 = 0.29 * 1.00 * 5.6490 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7858 = 0.29 * 1.00 * 5.4651 + 1.00 * 0.2030                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.74   16.13    None  None   None       |
|    all(noH): 2823   0      0.00    80.74   16.13    None  None   None       |
|    Sol.    : 438    0      6.90    63.05   36.96    None  None   None       |
|    Mac.    : 2385   0      0.00    80.74   12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.074:  484   |   5:    40.372 -  48.446:   99        |
|      1:     8.074 -  16.149: 1528   |   6:    48.446 -  56.521:   72        |
|      2:    16.149 -  24.223:  339   |   7:    56.521 -  64.595:   27        |
|      3:    24.223 -  32.298:  146   |   8:    64.595 -  72.669:    0        |
|      4:    32.298 -  40.372:  127   |   9:    72.669 -  80.744:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1684 r_free = 0.1944             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1679 r_free = 0.1937             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1679   r_free= 0.1937   ksol= 0.32   Bsol= 54.87   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,0.81,-0.95,0.00,-0.00,-0.00); trace/3= -0.96                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.462306                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1672   r_free= 0.1916   ksol= 0.33   Bsol= 64.19   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.39,-1.36,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459033                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.831901              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.864  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.439620              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.504   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1672      final r-factor (work) = 0.1298          |
| start r-factor (free) = 0.1916      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0696 = 1.83 * 0.50 * 5.4716 + 1.00 * 0.0578                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9341 = 1.83 * 0.50 * 5.3260 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1298      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6839 = 1.44 * 1.00 * 5.3260 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4717 = 1.44 * 1.00 * 5.1829 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.41   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    85.41   17.18    None  None   None       |
|    Sol.    : 438    0      0.00    77.89   40.75    None  None   None       |
|    Mac.    : 2385   0      0.00    85.41   12.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.541:  712   |   5:    42.703 -  51.243:  106        |
|      1:     8.541 -  17.081: 1329   |   6:    51.243 -  59.784:   82        |
|      2:    17.081 -  25.622:  290   |   7:    59.784 -  68.325:   52        |
|      3:    25.622 -  34.162:  131   |   8:    68.325 -  76.865:   17        |
|      4:    34.162 -  42.703:   99   |   9:    76.865 -  85.406:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1581             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1214 r_free = 0.1579             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1579   ksol= 0.33   Bsol= 64.19   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-1.39,-1.36,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1581   ksol= 0.33   Bsol= 64.19   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.60,-1.01,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.187619                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.099102              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.770  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.164794              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.656  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1213      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4961 = 2.10 * 0.50 * 5.1836 + 1.00 * 0.0557                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4693 = 2.10 * 0.50 * 5.1521 + 1.00 * 0.0620                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8592 = 0.16 * 1.00 * 5.1521 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8559 = 0.16 * 1.00 * 5.1454 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.81   16.48    None  None   None       |
|    all(noH): 2823   0      0.00    84.81   16.48    None  None   None       |
|    Sol.    : 438    0      0.00    72.90   38.03    None  None   None       |
|    Mac.    : 2385   0      1.31    84.81   12.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.481:  719   |   5:    42.406 -  50.888:   92        |
|      1:     8.481 -  16.963: 1335   |   6:    50.888 -  59.369:   72        |
|      2:    16.963 -  25.444:  295   |   7:    59.369 -  67.850:   33        |
|      3:    25.444 -  33.925:  133   |   8:    67.850 -  76.331:    8        |
|      4:    33.925 -  42.406:  133   |   9:    76.331 -  84.813:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1540             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1540             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1540   ksol= 0.33   Bsol= 64.19   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.60,-1.01,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.138777                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1540   ksol= 0.32   Bsol= 56.53   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.59,-0.79,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.138681                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.445997              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.246  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.557320              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.098  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7821 = 1.45 * 0.50 * 5.1454 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7718 = 1.45 * 0.50 * 5.1425 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8740 = 0.56 * 1.00 * 5.1425 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8746 = 0.56 * 1.00 * 5.1420 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.43   16.37    None  None   None       |
|    all(noH): 2823   0      0.00    85.43   16.37    None  None   None       |
|    Sol.    : 438    0      1.48    73.01   38.30    None  None   None       |
|    Mac.    : 2385   0      0.00    85.43   12.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.543:  805   |   5:    42.715 -  51.258:   91        |
|      1:     8.543 -  17.086: 1254   |   6:    51.258 -  59.801:   73        |
|      2:    17.086 -  25.629:  288   |   7:    59.801 -  68.344:   33        |
|      3:    25.629 -  34.172:  136   |   8:    68.344 -  76.887:    8        |
|      4:    34.172 -  42.715:  132   |   9:    76.887 -  85.430:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1563             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1563             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1563   ksol= 0.32   Bsol= 56.53   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-1.59,-0.79,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.148021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1563   ksol= 0.32   Bsol= 56.53   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.48,-0.61,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.148026                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.088254              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.622  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.833420              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.557  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9945 = 3.09 * 0.50 * 5.1425 + 1.00 * 0.0539                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9909 = 3.09 * 0.50 * 5.1272 + 1.00 * 0.0738                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4092 = 1.83 * 1.00 * 5.1272 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3947 = 1.83 * 1.00 * 5.1186 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.32   16.42    None  None   None       |
|    all(noH): 2823   0      0.00    90.32   16.42    None  None   None       |
|    Sol.    : 438    0      3.19    75.55   39.31    None  None   None       |
|    Mac.    : 2385   0      0.00    90.32   12.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.032:  990   |   5:    45.161 -  54.193:   95        |
|      1:     9.032 -  18.065: 1133   |   6:    54.193 -  63.226:   73        |
|      2:    18.065 -  27.097:  248   |   7:    63.226 -  72.258:   24        |
|      3:    27.097 -  36.129:  125   |   8:    72.258 -  81.290:    7        |
|      4:    36.129 -  45.161:  124   |   9:    81.290 -  90.322:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1077 r_free = 0.1572             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1077 r_free = 0.1572             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1572   ksol= 0.32   Bsol= 56.53   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.48,-0.61,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121903                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1370  153 0.0983 0.1310      5.3881      5.5158|
|  2:  4.7966 -  3.8277 0.99   1303  145 0.0816 0.1085      5.4079      5.6051|
|  3:  3.8277 -  3.3500 0.99   1280  142 0.1005 0.1462      5.4468      5.8487|
|  4:  3.3500 -  3.0464 0.99   1281  140 0.1164 0.1494      5.4318      5.5772|
|  5:  3.0464 -  2.8296 0.99   1257  142 0.1270 0.1760      5.3132      5.5252|
|  6:  2.8296 -  2.6637 0.99   1273  140 0.1176 0.1775       5.202      5.4573|
|  7:  2.6637 -  2.5310 0.99   1250  139 0.1202 0.1706      5.1357       5.372|
|  8:  2.5310 -  2.4213 0.98   1255  140 0.1099 0.1711       5.052      5.3527|
|  9:  2.4213 -  2.3284 0.98   1240  140 0.1127 0.1674      5.0122      5.2533|
| 10:  2.3284 -  2.2483 0.99   1236  137 0.1083 0.1911       4.973      5.2723|
| 11:  2.2483 -  2.1783 0.98   1254  137 0.1101 0.1743      4.9321       5.226|
| 12:  2.1783 -  2.1162 0.97   1234  138 0.1099 0.1713      4.8895      5.2376|
| 13:  2.1162 -  2.0606 1.00   1231  134 0.1064 0.1692      4.7824      5.0621|
| 14:  2.0606 -  2.0104 0.91   1166  132 0.0997 0.1768      4.6422      4.9567|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7966  1370   153  0.94   9.47   0.97     0.94       7478.33|
|  2:  4.7966 -  3.8277  1303   145  0.95   7.86   1.00     0.99       8792.12|
|  3:  3.8277 -  3.3500  1280   142  0.94  10.57   1.02     1.01       9801.59|
|  4:  3.3500 -  3.0464  1281   140  0.92  13.04   1.00     0.99       9892.14|
|  5:  3.0464 -  2.8296  1257   142  0.90  15.44   0.99     0.96       8208.01|
|  6:  2.8296 -  2.6637  1273   140  0.90  15.59   0.98     0.95       6969.95|
|  7:  2.6637 -  2.5310  1250   139  0.91  15.25   0.98     0.95       5937.26|
|  8:  2.5310 -  2.4213  1255   140  0.92  14.37   0.98     0.96       5168.25|
|  9:  2.4213 -  2.3284  1240   140  0.91  15.20   0.98     0.95       4869.73|
| 10:  2.3284 -  2.2483  1236   137  0.90  15.53   0.98     0.93       4526.66|
| 11:  2.2483 -  2.1783  1254   137  0.90  16.16   0.98     0.94       4424.25|
| 12:  2.1783 -  2.1162  1234   138  0.91  15.22   0.98     0.97       4053.92|
| 13:  2.1162 -  2.0606  1231   134  0.91  15.22   0.98     0.96       3344.12|
| 14:  2.0606 -  2.0104  1166   132  0.92  14.29   0.95     0.91       2467.45|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2467.45 max =         9892.14 mean =      6193.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.72 mean =        13.74|
|phase err.(test): min =        0.00 max =           88.75 mean =        13.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1570   ksol= 0.32   Bsol= 56.40   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-1.16,-0.28,-0.00,-0.00,-0.00); trace/3= -1.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.121977                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1570   ksol= 0.32   Bsol= 56.40   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-1.16,-0.28,-0.00,-0.00,-0.00); trace/3= -1.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.121977                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7966 0.99   1370  153 0.0983 0.1313      5.3887      5.5173|
|  2:  4.7966 -  3.8277 0.99   1303  145 0.0817 0.1085      5.4088       5.605|
|  3:  3.8277 -  3.3500 0.99   1280  142 0.1005 0.1463       5.447      5.8492|
|  4:  3.3500 -  3.0464 0.99   1281  140 0.1164 0.1494      5.4317      5.5774|
|  5:  3.0464 -  2.8296 0.99   1257  142 0.1270 0.1759       5.313      5.5247|
|  6:  2.8296 -  2.6637 0.99   1273  140 0.1176 0.1775      5.2019       5.457|
|  7:  2.6637 -  2.5310 0.99   1250  139 0.1202 0.1706      5.1358      5.3722|
|  8:  2.5310 -  2.4213 0.98   1255  140 0.1100 0.1711       5.052      5.3525|
|  9:  2.4213 -  2.3284 0.98   1240  140 0.1126 0.1673      5.0122      5.2532|
| 10:  2.3284 -  2.2483 0.99   1236  137 0.1083 0.1911       4.973      5.2724|
| 11:  2.2483 -  2.1783 0.98   1254  137 0.1101 0.1742       4.932      5.2257|
| 12:  2.1783 -  2.1162 0.97   1234  138 0.1099 0.1712      4.8893      5.2374|
| 13:  2.1162 -  2.0606 1.00   1231  134 0.1064 0.1691      4.7822       5.062|
| 14:  2.0606 -  2.0104 0.91   1166  132 0.0997 0.1767      4.6422      4.9567|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7966  1370   153  0.94   9.49   0.97     0.94       7501.06|
|  2:  4.7966 -  3.8277  1303   145  0.95   7.87   1.01     0.99       8808.57|
|  3:  3.8277 -  3.3500  1280   142  0.94  10.58   1.02     1.01       9807.41|
|  4:  3.3500 -  3.0464  1281   140  0.92  13.04   1.01     0.99       9889.83|
|  5:  3.0464 -  2.8296  1257   142  0.90  15.44   1.00     0.97       8203.67|
|  6:  2.8296 -  2.6637  1273   140  0.90  15.59   0.99     0.96       6966.28|
|  7:  2.6637 -  2.5310  1250   139  0.91  15.25   0.99     0.96       5936.53|
|  8:  2.5310 -  2.4213  1255   140  0.92  14.37   0.99     0.97       5166.95|
|  9:  2.4213 -  2.3284  1240   140  0.91  15.21   1.00     0.96       4870.80|
| 10:  2.3284 -  2.2483  1236   137  0.90  15.53   0.99     0.95       4525.05|
| 11:  2.2483 -  2.1783  1254   137  0.90  16.16   0.99     0.96       4422.79|
| 12:  2.1783 -  2.1162  1234   138  0.91  15.22   1.00     0.99       4051.62|
| 13:  2.1162 -  2.0606  1231   134  0.91  15.21   1.00     0.98       3342.58|
| 14:  2.0606 -  2.0104  1166   132  0.92  14.29   0.97     0.93       2467.18|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2467.18 max =         9889.83 mean =      6195.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.73 mean =        13.75|
|phase err.(test): min =        0.00 max =           88.74 mean =        13.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.146)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.33   16.43    None  None   None       |
|    all(noH): 2823   0      0.00    90.33   16.43    None  None   None       |
|    Sol.    : 438    0      3.20    75.55   39.32    None  None   None       |
|    Mac.    : 2385   0      0.00    90.33   12.22    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 -   9.035:  990   |   5:    45.164 -  54.196:   95        |
|      1:     9.035 -  18.067: 1133   |   6:    54.196 -  63.229:   73        |
|      2:    18.067 -  27.100:  248   |   7:    63.229 -  72.261:   24        |
|      3:    27.100 -  36.132:  125   |   8:    72.261 -  81.293:    7        |
|      4:    36.132 -  45.164:  124   |   9:    81.293 -  90.325:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.450 - 4.856
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 289 from: 295
   mapped sites are within: 0.721 - 4.856

peak=    5.861 closest distance to " NH2 ARG A  56 " =    2.352
peak=    5.561 closest distance to " CB  GLN A 223 " =    1.418
peak=    5.232 closest distance to " CG  PRO A  54 " =    1.269
peak=    5.011 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.902 closest distance to " CB  SER A  63 " =    1.206
peak=    4.880 closest distance to " CB  ARG A 275 " =    0.935
peak=    4.801 closest distance to " O   HOH Z 126 " =    1.852
peak=    4.720 closest distance to " CB  ARG A 190 " =    1.631
peak=    4.718 closest distance to " CB  GLN A 183 " =    1.261
peak=    4.606 closest distance to " O   HOH Z 298 " =    1.945
peak=    4.605 closest distance to " O   HOH Z 369 " =    2.229
peak=    4.463 closest distance to " C   PRO A 198 " =    1.489
peak=    4.439 closest distance to " CB  TYR A 169 " =    0.770
peak=    4.378 closest distance to " CB  GLU A 152 " =    1.174
peak=    4.366 closest distance to " CG  PRO A 213 " =    1.188
peak=    4.365 closest distance to " CA  TYR A  30 " =    0.956
peak=    4.356 closest distance to " CB  ARG A  79 " =    1.367
peak=    4.337 closest distance to " O   HOH Z  78 " =    1.648
peak=    4.301 closest distance to " O   HOH Z 142 " =    1.540
peak=    4.298 closest distance to " O   HOH Z  15 " =    2.136
peak=    4.276 closest distance to " CB  GLU A 277 " =    3.679
peak=    4.229 closest distance to " CB  PRO A  54 " =    0.866
peak=    4.215 closest distance to " O   HOH Z 203 " =    1.707
peak=    4.192 closest distance to " NE2 GLN A  11 " =    1.007
peak=    4.164 closest distance to " CB  ASN A 148 " =    1.522
peak=    4.162 closest distance to " O   HOH Z 392 " =    2.952
peak=    4.160 closest distance to " O   HOH Z 250 " =    1.481
peak=    4.153 closest distance to " O   HOH Z 236 " =    2.096
peak=    4.152 closest distance to " CB  LEU A 228 " =    1.098
peak=    4.150 closest distance to " CG  PRO A 198 " =    1.259
peak=    4.140 closest distance to " O   HOH Z  40 " =    1.875
peak=    4.137 closest distance to " OD1 ASN A  69 " =    2.589
peak=    4.131 closest distance to " CZ  PHE A 218 " =    1.088
peak=    4.128 closest distance to " O   HOH Z 427 " =    3.082
peak=    4.119 closest distance to " O   HOH Z 403 " =    1.677
peak=    4.113 closest distance to " CB  ASP A 140 " =    0.987
peak=    4.090 closest distance to " O   HOH Z 234 " =    3.801
peak=    4.043 closest distance to " O   HOH Z  19 " =    2.273
peak=    4.029 closest distance to " ND2 ASN A 187 " =    1.446
peak=    4.014 closest distance to " O   HOH Z 303 " =    2.193
peak=    3.991 closest distance to " CB  TRP A 266 " =    0.965
peak=    3.979 closest distance to " O   HOH Z  44 " =    2.282
peak=    3.973 closest distance to " O   HOH Z 368 " =    2.151
peak=    3.958 closest distance to " O   HOH Z 158 " =    3.081
peak=    3.922 closest distance to " CA  ARG A  36 " =    1.128
peak=    3.890 closest distance to " O   HOH Z 265 " =    2.296
peak=    3.886 closest distance to " C   ILE A 106 " =    1.896
peak=    3.884 closest distance to " CB  GLU A 128 " =    1.073
peak=    3.879 closest distance to " CD1 LEU A 300 " =    1.208
peak=    3.878 closest distance to " O   HOH Z  61 " =    1.594
peak=    3.877 closest distance to " O   HOH Z 280 " =    2.955
peak=    3.870 closest distance to " O   HOH Z 193 " =    1.844
peak=    3.868 closest distance to " CA  ARG A 195 " =    1.191
peak=    3.866 closest distance to " O   HOH Z 147 " =    1.832
peak=    3.862 closest distance to " NH2 ARG A 156 " =    1.184
peak=    3.860 closest distance to " O   SER A  87 " =    2.269
peak=    3.852 closest distance to " NZ  LYS A 117 " =    3.226
peak=    3.850 closest distance to " O   HOH Z 402 " =    1.440
peak=    3.849 closest distance to " O   HOH Z 346 " =    1.632
peak=    3.843 closest distance to " O   HOH Z 423 " =    1.938
peak=    3.842 closest distance to " CE  LYS A  76 " =    0.843
peak=    3.838 closest distance to " O   HOH Z  43 " =    1.918
peak=    3.832 closest distance to " O   HOH Z 389 " =    1.914
peak=    3.823 closest distance to " CB  VAL A 202 " =    1.545
peak=    3.809 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.802 closest distance to " CA  ALA A  51 " =    0.916
peak=    3.793 closest distance to " O   HOH Z 272 " =    1.861
peak=    3.793 closest distance to " CD2 TRP A 179 " =    1.354
peak=    3.777 closest distance to " CD2 LEU A 297 " =    0.885
peak=    3.775 closest distance to " O   HOH Z 189 " =    2.547
peak=    3.774 closest distance to " CD  ARG A 269 " =    0.907
peak=    3.771 closest distance to " OG BSER A 164 " =    2.334
peak=    3.769 closest distance to " CA  ASN A 215 " =    1.171
peak=    3.763 closest distance to " O   HOH Z 133 " =    2.487
peak=    3.755 closest distance to " O   HOH Z 108 " =    2.853
peak=    3.748 closest distance to " CD  LYS A 166 " =    1.286
peak=    3.744 closest distance to " CA  TYR A  30 " =    1.029
peak=    3.742 closest distance to " CG  PRO A  90 " =    1.135
peak=    3.735 closest distance to " CG1 ILE A  33 " =    1.195
peak=    3.732 closest distance to " O   HOH Z 126 " =    2.028
peak=    3.721 closest distance to " O   HOH Z 316 " =    3.148
peak=    3.718 closest distance to " O   HOH Z 214 " =    2.114
peak=    3.711 closest distance to " CB  VAL A 265 " =    1.275
peak=    3.710 closest distance to " O   HOH Z 261 " =    2.016
peak=    3.709 closest distance to " O   HOH Z 371 " =    3.285
peak=    3.696 closest distance to " O   HOH Z   1 " =    2.168
peak=    3.695 closest distance to " NH1AARG A 145 " =    1.235
peak=    3.695 closest distance to " CG  ARG A  66 " =    2.500
peak=    3.676 closest distance to " CA  THR A 221 " =    0.975
peak=    3.671 closest distance to " CB  ARG A 139 " =    0.932
peak=    3.668 closest distance to " CB  SER A   3 " =    1.277
peak=    3.660 closest distance to " CA  ALA A  21 " =    1.222
peak=    3.650 closest distance to " NE2 GLN A  77 " =    3.275
peak=    3.649 closest distance to " CB  ASN A  39 " =    0.878
peak=    3.642 closest distance to " O   HOH Z 128 " =    2.073
peak=    3.637 closest distance to " O   HOH Z 383 " =    2.161
peak=    3.625 closest distance to " CG2 VAL A 257 " =    0.870
peak=    3.606 closest distance to " OD2 ASP A 298 " =    3.896
peak=    3.606 closest distance to " CA  PRO A  54 " =    1.350
peak=    3.606 closest distance to " OG1 THR A 294 " =    2.409
peak=    3.606 closest distance to " O   HOH Z 403 " =    1.361
peak=    3.604 closest distance to " CB  TRP A 179 " =    1.406
peak=    3.601 closest distance to " CG  PRO A 243 " =    1.050
peak=    3.593 closest distance to " CB  TYR A 169 " =    0.796
peak=    3.590 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.589 closest distance to " CG2 ILE A  20 " =    1.374
peak=    3.587 closest distance to " CB  ASN A 187 " =    1.080
peak=    3.587 closest distance to " CB  GLU A  46 " =    0.992
peak=    3.579 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.575 closest distance to " O   HOH Z  97 " =    1.951
peak=    3.564 closest distance to " O   HOH Z  66 " =    2.094
peak=    3.558 closest distance to " O   HOH Z 291 " =    1.560
peak=    3.557 closest distance to " O   HOH Z 126 " =    1.684
peak=    3.556 closest distance to " O   HOH Z 245 " =    1.283
peak=    3.556 closest distance to " OD2 ASP A 286 " =    2.884
peak=    3.555 closest distance to " CD BLYS A 290 " =    0.955
peak=    3.554 closest distance to " CA  MET A 105 " =    1.049
peak=    3.554 closest distance to " O   HOH Z 426 " =    1.566
peak=    3.553 closest distance to " CD1 LEU A  96 " =    0.721
peak=    3.549 closest distance to " N   ARG A 156 " =    1.426
peak=    3.542 closest distance to " NH2BARG A 145 " =    2.128
peak=    3.539 closest distance to " O   HOH Z 425 " =    2.035
peak=    3.532 closest distance to " CB  SER A 212 " =    1.066
peak=    3.527 closest distance to " O   HOH Z 411 " =    3.751
peak=    3.520 closest distance to " CZ2 TRP A 179 " =    1.727
peak=    3.519 closest distance to " O  BHOH Z 338 " =    2.260
peak=    3.517 closest distance to " CG2AVAL A  72 " =    1.781
peak=    3.513 closest distance to " O   HOH Z 406 " =    1.521
peak=    3.512 closest distance to " CD1 ILE A 106 " =    0.833
peak=    3.509 closest distance to " O   HOH Z 193 " =    1.678
peak=    3.509 closest distance to " CG2 ILE A 120 " =    1.020
peak=    3.504 closest distance to " O   HOH Z  80 " =    1.579
peak=    3.499 closest distance to " O   HOH Z 135 " =    1.745
peak=    3.493 closest distance to " CG1 VAL A 153 " =    0.960
peak=    3.491 closest distance to " CA  ASN A 176 " =    1.638
peak=    3.489 closest distance to " O   HOH Z  97 " =    2.531
peak=    3.487 closest distance to " O   HOH Z 421 " =    1.736
peak=    3.486 closest distance to " CB  SER A 141 " =    1.009
peak=    3.484 closest distance to " O   HOH Z 299 " =    4.522
peak=    3.484 closest distance to " O   HOH Z  21 " =    1.798
peak=    3.483 closest distance to " CB  ALA A 291 " =    1.329
peak=    3.478 closest distance to " CB  ILE A 120 " =    1.296
peak=    3.474 closest distance to " O   HOH Z 305 " =    3.621
peak=    3.469 closest distance to " O   HOH Z 185 " =    1.806
peak=    3.456 closest distance to " CB  ASN A 142 " =    1.129
peak=    3.455 closest distance to " O   HOH Z 148 " =    3.262
peak=    3.453 closest distance to " O   HOH Z 261 " =    1.593
peak=    3.447 closest distance to " O   HOH Z 132 " =    2.567
peak=    3.444 closest distance to " O   HOH Z 361 " =    3.370
peak=    3.441 closest distance to " CE1 TYR A 186 " =    1.296
peak=    3.433 closest distance to " O   HOH Z 344 " =    3.208
peak=    3.432 closest distance to " O   HOH Z 279 " =    2.207
peak=    3.429 closest distance to " CB  SER A  26 " =    1.721
peak=    3.422 closest distance to " O   HOH Z 313 " =    1.889
peak=    3.421 closest distance to " O   HOH Z 391 " =    2.915
peak=    3.420 closest distance to " N   ASN A 127 " =    1.275
peak=    3.419 closest distance to " O   TRP A 274 " =    1.893
peak=    3.418 closest distance to " ND1 HIS A  81 " =    1.643
peak=    3.414 closest distance to " CB  MET A  47 " =    1.016
peak=    3.414 closest distance to " CA  MET A  40 " =    1.126
peak=    3.399 closest distance to " CG2 VAL A 197 " =    1.107
peak=    3.397 closest distance to " O   HOH Z  59 " =    2.312
peak=    3.390 closest distance to " CB  THR A  31 " =    1.766
peak=    3.377 closest distance to " O   ALA A 165 " =    1.485
peak=    3.365 closest distance to " CA  ALA A 160 " =    0.897
peak=    3.364 closest distance to " O   HOH Z 285 " =    2.912
peak=    3.363 closest distance to " CA  ASP A 191 " =    0.870
peak=    3.362 closest distance to " CB  ALA A   1 " =    4.856
peak=    3.360 closest distance to " OG  SER A  22 " =    2.714
peak=    3.350 closest distance to " O   HOH Z 134 " =    1.297
peak=    3.348 closest distance to " CG  MET A 185 " =    1.154
peak=    3.346 closest distance to " CA  VAL A 125 " =    1.179
peak=    3.341 closest distance to " O   HOH Z 365 " =    2.921
peak=    3.337 closest distance to " O   HOH Z 213 " =    1.802
peak=    3.336 closest distance to " CB  ARG A  79 " =    0.833
peak=    3.329 closest distance to " CA  THR A 264 " =    0.912
peak=    3.328 closest distance to " O   HOH Z 422 " =    2.709
peak=    3.324 closest distance to " N   VAL A 126 " =    1.401
peak=    3.324 closest distance to " O   HOH Z 359 " =    1.441
peak=    3.322 closest distance to " O   HOH Z 163 " =    1.501
peak=    3.319 closest distance to " CA  ASN A 217 " =    1.152
peak=    3.319 closest distance to " O   THR A 251 " =    1.124
peak=    3.313 closest distance to " CA  ALA A 158 " =    1.211
peak=    3.312 closest distance to " CA  ALA A  84 " =    1.305
peak=    3.311 closest distance to " O   HOH Z 227 " =    1.672
peak=    3.310 closest distance to " O   HOH Z 417 " =    3.192
peak=    3.309 closest distance to " CB  ALA A 248 " =    0.960
peak=    3.306 closest distance to " CD  LYS A  76 " =    2.054
peak=    3.304 closest distance to " CB  TYR A 116 " =    0.763
peak=    3.302 closest distance to " CB  GLN A  89 " =    1.282
peak=    3.301 closest distance to " CB  ASN A 215 " =    1.161
peak=    3.296 closest distance to " O   ALA A 158 " =    1.221
peak=    3.296 closest distance to " CB  GLN A 103 " =    0.862
peak=    3.290 closest distance to " O   HOH Z  66 " =    2.152
peak=    3.290 closest distance to " O   HOH Z 171 " =    2.048
peak=    3.286 closest distance to " O   HOH Z  10 " =    1.746
peak=    3.283 closest distance to " O   HOH Z 353 " =    2.757
peak=    3.281 closest distance to " O   HOH Z 193 " =    2.146
peak=    3.279 closest distance to " CA  LYS A 117 " =    1.250
peak=    3.278 closest distance to " O   THR A 220 " =    1.252
peak=    3.273 closest distance to " O   HOH Z  88 " =    3.544
peak=    3.269 closest distance to " CA  ALA A 295 " =    1.094
peak=    3.268 closest distance to " CB  ASN A 110 " =    1.184
peak=    3.266 closest distance to " O   HOH Z 248 " =    1.603
peak=    3.265 closest distance to " O   HOH Z 250 " =    1.422
peak=    3.265 closest distance to " CA  ALA A 233 " =    1.536
peak=    3.265 closest distance to " O   ASP A 124 " =    1.169
peak=    3.259 closest distance to " O   HOH Z  44 " =    1.703
peak=    3.256 closest distance to " CG BARG A 275 " =    1.424
peak=    3.254 closest distance to " NH2AARG A 275 " =    3.589
peak=    3.248 closest distance to " CB  GLN A  88 " =    1.199
peak=    3.242 closest distance to " CB  ALA A   9 " =    1.561
peak=    3.241 closest distance to " O   HOH Z 173 " =    1.980
peak=    3.238 closest distance to " CA  ASP A 162 " =    1.053
peak=    3.236 closest distance to " O   HOH Z 295 " =    1.494
peak=    3.231 closest distance to " CA  ALA A 291 " =    0.823
peak=    3.231 closest distance to " CB  SER A  62 " =    0.824
peak=    3.230 closest distance to " O   HOH Z 374 " =    2.740
peak=    3.229 closest distance to " CG1 ILE A 151 " =    0.981
peak=    3.228 closest distance to " CD  ARG A  66 " =    2.459
peak=    3.227 closest distance to " O   HOH Z 411 " =    1.770
peak=    3.223 closest distance to " NZ  LYS A  48 " =    1.312
peak=    3.221 closest distance to " CB  MET A  40 " =    0.799
peak=    3.221 closest distance to " O   HOH Z 102 " =    1.259
peak=    3.218 closest distance to " O   HOH Z 425 " =    1.277
peak=    3.216 closest distance to " O   HOH Z 281 " =    4.133
peak=    3.214 closest distance to " O   HOH Z 298 " =    2.601
peak=    3.213 closest distance to " O   HOH Z  88 " =    1.922
peak=    3.212 closest distance to " O   HOH Z 294 " =    1.521
peak=    3.212 closest distance to " CG  GLN A  11 " =    1.586
peak=    3.211 closest distance to " O   HOH Z  20 " =    1.520
peak=    3.209 closest distance to " CA  ALA A 154 " =    0.977
peak=    3.208 closest distance to " N   ASN A  39 " =    1.349
peak=    3.206 closest distance to " CB  ASP A 298 " =    1.205
peak=    3.205 closest distance to " N   GLY A  98 " =    1.101
peak=    3.202 closest distance to " CA  SER A  87 " =    1.081
peak=    3.199 closest distance to " CB  THR A  52 " =    0.870
peak=    3.199 closest distance to " CA  ASN A  74 " =    1.312
peak=    3.196 closest distance to " CD  LYS A 119 " =    1.386
peak=    3.195 closest distance to " O   HOH Z 285 " =    1.456
peak=    3.187 closest distance to " CG  LEU A 167 " =    1.237
peak=    3.186 closest distance to " C   TYR A 214 " =    1.474
peak=    3.185 closest distance to " CA  ASP A 140 " =    1.165
peak=    3.185 closest distance to " O   HOH Z 325 " =    2.402
peak=    3.185 closest distance to " CA  TYR A 116 " =    1.375
peak=    3.184 closest distance to " CA  LEU A 101 " =    1.560
peak=    3.171 closest distance to " CB  PHE A 204 " =    0.953
peak=    3.170 closest distance to " CE  LYS A  48 " =    1.011
peak=    3.168 closest distance to " O   HOH Z 407 " =    2.703
peak=    3.166 closest distance to " CG2 ILE A 234 " =    0.815
peak=    3.165 closest distance to " O   HOH Z 345 " =    3.198
peak=    3.163 closest distance to " O   HOH Z 234 " =    1.865
peak=    3.162 closest distance to " O   HOH Z 174 " =    2.570
peak=    3.156 closest distance to " O   HOH Z 199 " =    1.580
peak=    3.156 closest distance to " CA  ASN A 252 " =    1.929
peak=    3.151 closest distance to " CA  ALA A 248 " =    1.141
peak=    3.148 closest distance to " CG2BVAL A  41 " =    0.813
peak=    3.146 closest distance to " CG  MET A 185 " =    1.029
peak=    3.144 closest distance to " O   HOH Z 327 " =    1.638
peak=    3.143 closest distance to " CB  ASN A 285 " =    0.918
peak=    3.141 closest distance to " CB  LYS A 117 " =    1.153
peak=    3.140 closest distance to " O   HOH Z 387 " =    3.060
peak=    3.140 closest distance to " CZ3 TRP A  85 " =    0.945
peak=    3.137 closest distance to " CD  ARG A 219 " =    1.091
peak=    3.132 closest distance to " ND2 ASN A 249 " =    0.857
peak=    3.125 closest distance to " CB  GLN A 205 " =    1.095
peak=    3.123 closest distance to " O   HOH Z  49 " =    2.338
peak=    3.123 closest distance to " NE AARG A 190 " =    2.267
peak=    3.122 closest distance to " O   HOH Z  62 " =    2.261
peak=    3.122 closest distance to " CB  ALA A 227 " =    1.115
peak=    3.114 closest distance to " CG1 ILE A  49 " =    1.542
peak=    3.112 closest distance to " OG  SER A 245 " =    1.627
peak=    3.110 closest distance to " CG  LYS A  76 " =    0.982
peak=    3.107 closest distance to " CB  THR A 157 " =    1.136
peak=    3.107 closest distance to " O   HOH Z 116 " =    1.827
peak=    3.104 closest distance to " O   HOH Z 357 " =    2.011
peak=    3.101 closest distance to " O   HOH Z 128 " =    2.384
peak=    3.100 closest distance to " CG BARG A 102 " =    1.837
peak=    3.098 closest distance to " CB  HIS A 108 " =    0.799
peak=    3.098 closest distance to " O   GLU A   2 " =    1.674
peak=    3.091 closest distance to " O   HOH Z 271 " =    2.451
peak=    3.086 closest distance to " O   HOH Z 419 " =    1.902
peak=    3.085 closest distance to " O   ASN A  74 " =    1.639
peak=    3.079 closest distance to " CB  ALA A 100 " =    1.189
peak=    3.079 closest distance to " ND1 HIS A  86 " =    1.818
peak=    3.062 closest distance to " CB  ALA A  43 " =    0.815
peak=    3.050 closest distance to " O   HOH Z 329 " =    3.896
peak=    3.035 closest distance to " ND2 ASN A 110 " =    1.547
peak=    3.026 closest distance to " O   HOH Z  97 " =    2.278

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.799 - 5.330
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.799 - 5.330

peak=   -4.759 closest distance to " O   HOH Z 266 " =    5.165
peak=   -4.558 closest distance to " CD  ARG A 156 " =    2.057
peak=   -4.486 closest distance to " CD  GLN A  58 " =    0.978
peak=   -4.466 closest distance to " CB  PRO A 243 " =    2.643
peak=   -4.430 closest distance to " O   VAL A  67 " =    2.718
peak=   -4.421 closest distance to " C   HIS A 108 " =    1.088
peak=   -4.383 closest distance to " CD  ARG A  14 " =    3.574
peak=   -4.320 closest distance to " N   ALA A  43 " =    2.800
peak=   -4.221 closest distance to " OE1 GLN A 223 " =    2.100
peak=   -4.214 closest distance to " O   HOH Z 196 " =    1.975
peak=   -4.205 closest distance to " O   HOH Z  10 " =    1.565
peak=   -4.159 closest distance to " O   HOH Z 231 " =    2.292
peak=   -4.148 closest distance to " CB  ALA A 161 " =    2.600
peak=   -4.084 closest distance to " O   HOH Z 377 " =    2.121
peak=   -4.009 closest distance to " OG  SER A  97 " =    2.239
peak=   -3.983 closest distance to " CG1 VAL A 112 " =    2.596
peak=   -3.968 closest distance to " CZ3 TRP A 179 " =    1.203
peak=   -3.961 closest distance to " OG BSER A 134 " =    1.234
peak=   -3.925 closest distance to " CB  ASP A 132 " =    2.344
peak=   -3.918 closest distance to " ND2 ASN A  45 " =    1.845
peak=   -3.917 closest distance to " O   HOH Z  73 " =    2.280
peak=   -3.910 closest distance to " CE2 TYR A  30 " =    2.716
peak=   -3.903 closest distance to " CB  ALA A 291 " =    2.266
peak=   -3.892 closest distance to " CD1 PHE A  59 " =    2.006
peak=   -3.888 closest distance to " OXT GLY A 302 " =    2.932
peak=   -3.878 closest distance to " CG1 VAL A 250 " =    2.662
peak=   -3.861 closest distance to " O   HOH Z 114 " =    3.252
peak=   -3.859 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.842 closest distance to " O   HOH Z 198 " =    2.105
peak=   -3.809 closest distance to " CG2 ILE A 263 " =    2.342
peak=   -3.786 closest distance to " O   HOH Z  52 " =    1.500
peak=   -3.784 closest distance to " O   HOH Z 292 " =    4.575
peak=   -3.775 closest distance to " O   PRO A 198 " =    1.334
peak=   -3.761 closest distance to " O   HOH Z 372 " =    2.379
peak=   -3.745 closest distance to " CG  ARG A  66 " =    2.473
peak=   -3.744 closest distance to " O   VAL A  67 " =    2.830
peak=   -3.711 closest distance to " O   HOH Z 389 " =    1.849
peak=   -3.709 closest distance to " CD1 LEU A 101 " =    2.444
peak=   -3.708 closest distance to " O   HOH Z 211 " =    1.577
peak=   -3.701 closest distance to " O   HOH Z 311 " =    3.728
peak=   -3.700 closest distance to " CE2 PHE A  61 " =    2.543
peak=   -3.693 closest distance to " O   HOH Z 290 " =    1.217
peak=   -3.692 closest distance to " O   SER A 210 " =    1.915
peak=   -3.683 closest distance to " CB  ALA A 291 " =    2.379
peak=   -3.683 closest distance to " O   HOH Z  13 " =    1.698
peak=   -3.680 closest distance to " CG1 VAL A 112 " =    2.811
peak=   -3.676 closest distance to " CB  ASN A  39 " =    2.392
peak=   -3.675 closest distance to " O   HOH Z 353 " =    2.170
peak=   -3.673 closest distance to " O   HOH Z 126 " =    1.924
peak=   -3.668 closest distance to " CD2 PHE A 192 " =    2.039
peak=   -3.668 closest distance to " CE  MET A 105 " =    2.460
peak=   -3.666 closest distance to " O   PRO A 163 " =    2.103
peak=   -3.663 closest distance to " ND2 ASN A  45 " =    1.126
peak=   -3.659 closest distance to " NE2 GLN A  88 " =    1.881
peak=   -3.652 closest distance to " OD1 ASN A 148 " =    1.515
peak=   -3.650 closest distance to " O   HOH Z 166 " =    1.807
peak=   -3.636 closest distance to " O   HOH Z 394 " =    1.509
peak=   -3.628 closest distance to " OD1 ASP A 171 " =    1.608
peak=   -3.612 closest distance to " O   HOH Z 253 " =    4.038
peak=   -3.611 closest distance to " NH2AARG A 275 " =    5.330
peak=   -3.582 closest distance to " CA  GLY A 241 " =    3.170
peak=   -3.573 closest distance to " CA  GLY A 203 " =    2.354
peak=   -3.569 closest distance to " O   HOH Z  43 " =    1.581
peak=   -3.568 closest distance to " CB  ALA A  43 " =    2.598
peak=   -3.547 closest distance to " O   HOH Z 185 " =    2.369
peak=   -3.526 closest distance to " O   HOH Z  60 " =    1.986
peak=   -3.520 closest distance to " CE BMET A  47 " =    1.777
peak=   -3.514 closest distance to " NH2 ARG A 159 " =    2.403
peak=   -3.509 closest distance to " CD  ARG A 195 " =    5.150
peak=   -3.504 closest distance to " CD2 TYR A 293 " =    2.019
peak=   -3.478 closest distance to " CD1 ILE A 151 " =    2.399
peak=   -3.476 closest distance to " O   ALA A  10 " =    1.720
peak=   -3.473 closest distance to " CG1 VAL A 125 " =    1.990
peak=   -3.465 closest distance to " OD2 ASP A 171 " =    1.833
peak=   -3.464 closest distance to " O   HOH Z 407 " =    3.250
peak=   -3.462 closest distance to " N   ALA A 226 " =    2.088
peak=   -3.453 closest distance to " CD1 LEU A  83 " =    2.624
peak=   -3.452 closest distance to " C   LEU A 143 " =    1.091
peak=   -3.452 closest distance to " O   HOH Z 243 " =    2.034
peak=   -3.442 closest distance to " CG2 VAL A 189 " =    2.191
peak=   -3.434 closest distance to " OE2 GLU A   2 " =    1.744
peak=   -3.430 closest distance to " O   HOH Z  38 " =    1.440
peak=   -3.424 closest distance to " OG  SER A  62 " =    1.742
peak=   -3.423 closest distance to " CZ  TYR A 169 " =    1.802
peak=   -3.420 closest distance to " CZ  PHE A  59 " =    1.695
peak=   -3.419 closest distance to " CD  ARG A 139 " =    1.561
peak=   -3.418 closest distance to " O   HOH Z 166 " =    1.615
peak=   -3.417 closest distance to " NE2 GLN A 194 " =    1.805
peak=   -3.415 closest distance to " O   HOH Z 351 " =    1.488
peak=   -3.414 closest distance to " CG  GLU A 277 " =    1.124
peak=   -3.413 closest distance to " CB  ALA A 248 " =    2.322
peak=   -3.413 closest distance to " O   HOH Z 234 " =    4.281
peak=   -3.412 closest distance to " O   HOH Z 313 " =    2.000
peak=   -3.412 closest distance to " ND2 ASN A 249 " =    2.386
peak=   -3.412 closest distance to " CG  ARG A 269 " =    2.353
peak=   -3.389 closest distance to " CE2 PHE A 218 " =    2.455
peak=   -3.381 closest distance to " O   HOH Z   6 " =    1.488
peak=   -3.379 closest distance to " SG ACYS A 201 " =    1.986
peak=   -3.371 closest distance to " O   HOH Z 128 " =    2.646
peak=   -3.367 closest distance to " NH2 ARG A  79 " =    1.582
peak=   -3.366 closest distance to " O   HOH Z 165 " =    1.872
peak=   -3.365 closest distance to " CD  LYS A 289 " =    2.423
peak=   -3.365 closest distance to " NE2 GLN A 103 " =    1.749
peak=   -3.362 closest distance to " O   HOH Z  37 " =    1.845
peak=   -3.359 closest distance to " O   HOH Z 377 " =    1.638
peak=   -3.358 closest distance to " CE3 TRP A 150 " =    2.236
peak=   -3.357 closest distance to " CG1AVAL A  41 " =    2.902
peak=   -3.357 closest distance to " O   HOH Z 435 " =    2.751
peak=   -3.356 closest distance to " C   ALA A 158 " =    1.259
peak=   -3.354 closest distance to " CB  TRP A  85 " =    2.554
peak=   -3.353 closest distance to " C   ASN A 285 " =    2.461
peak=   -3.351 closest distance to " O   HOH Z 177 " =    1.745
peak=   -3.345 closest distance to " O   HOH Z 295 " =    1.584
peak=   -3.345 closest distance to " CB  PHE A  16 " =    2.599
peak=   -3.338 closest distance to " CB  PHE A 208 " =    2.259
peak=   -3.332 closest distance to " NH1 ARG A 195 " =    2.612
peak=   -3.330 closest distance to " CB  ASP A 286 " =    1.893
peak=   -3.326 closest distance to " O   HOH Z 393 " =    1.372
peak=   -3.325 closest distance to " CB  TYR A  15 " =    2.208
peak=   -3.325 closest distance to " CG  ASP A 231 " =    0.799
peak=   -3.323 closest distance to " O   ALA A  34 " =    2.440
peak=   -3.322 closest distance to " CG  PRO A 163 " =    2.490
peak=   -3.320 closest distance to " SD  MET A 188 " =    2.132
peak=   -3.317 closest distance to " O   PHE A 218 " =    1.583
peak=   -3.314 closest distance to " CD2 TYR A 247 " =    2.373
peak=   -3.314 closest distance to " O   HOH Z 193 " =    1.797
peak=   -3.312 closest distance to " O   HOH Z 265 " =    2.237
peak=   -3.300 closest distance to " O   HOH Z  44 " =    2.152
peak=   -3.298 closest distance to " C   SER A 206 " =    1.503
peak=   -3.290 closest distance to " O   HOH Z   6 " =    2.287
peak=   -3.289 closest distance to " OG BSER A 134 " =    1.879
peak=   -3.288 closest distance to " O   HOH Z 426 " =    1.643
peak=   -3.287 closest distance to " O   HOH Z  51 " =    1.732
peak=   -3.285 closest distance to " O   SER A 135 " =    1.489
peak=   -3.284 closest distance to " O   PRO A 198 " =    1.929
peak=   -3.280 closest distance to " OD2 ASP A 191 " =    1.524
peak=   -3.278 closest distance to " O   VAL A 189 " =    2.583
peak=   -3.278 closest distance to " CB  PRO A 163 " =    2.479
peak=   -3.275 closest distance to " CD1 LEU A 228 " =    2.292
peak=   -3.271 closest distance to " CA  GLY A 133 " =    2.319
peak=   -3.264 closest distance to " CG  HIS A  86 " =    1.056
peak=   -3.263 closest distance to " O   HOH Z  11 " =    1.759
peak=   -3.256 closest distance to " CA  GLY A 241 " =    2.307
peak=   -3.256 closest distance to " OD1 ASN A 187 " =    1.609
peak=   -3.254 closest distance to " CD1 LEU A 101 " =    2.885
peak=   -3.250 closest distance to " CG2 ILE A  49 " =    2.802
peak=   -3.246 closest distance to " O   HOH Z 357 " =    2.065
peak=   -3.243 closest distance to " CD2 PHE A 225 " =    1.159
peak=   -3.235 closest distance to " O   HOH Z 396 " =    1.731
peak=   -3.233 closest distance to " CB  ALA A 248 " =    2.144
peak=   -3.228 closest distance to " ND2BASN A 224 " =    1.752
peak=   -3.225 closest distance to " CZ  PHE A 155 " =    1.262
peak=   -3.219 closest distance to " CG  PHE A 283 " =    2.545
peak=   -3.215 closest distance to " CG  GLU A  53 " =    1.505
peak=   -3.209 closest distance to " OD2 ASP A 171 " =    2.499
peak=   -3.208 closest distance to " CG  GLN A  11 " =    1.761
peak=   -3.203 closest distance to " O   HOH Z 232 " =    1.687
peak=   -3.203 closest distance to " O   HOH Z  76 " =    2.024
peak=   -3.202 closest distance to " O   HOH Z 123 " =    2.260
peak=   -3.197 closest distance to " O   HOH Z 317 " =    2.213
peak=   -3.195 closest distance to " NE1 TRP A 266 " =    2.306
peak=   -3.193 closest distance to " OG BSER A 210 " =    2.102
peak=   -3.192 closest distance to " O   HOH Z  71 " =    1.986
peak=   -3.188 closest distance to " CD1 ILE A 239 " =    2.108
peak=   -3.184 closest distance to " CG1 VAL A 125 " =    2.363
peak=   -3.182 closest distance to " OE1 GLN A  88 " =    1.166
peak=   -3.179 closest distance to " NH2 ARG A  79 " =    2.032
peak=   -3.176 closest distance to " O   ASN A 301 " =    1.415
peak=   -3.169 closest distance to " O   HOH Z 322 " =    1.660
peak=   -3.162 closest distance to " CD2 LEU A 300 " =    2.931
peak=   -3.162 closest distance to " CG1 VAL A  67 " =    3.073
peak=   -3.153 closest distance to " O   HOH Z 414 " =    1.608
peak=   -3.152 closest distance to " CD  PRO A 213 " =    2.189
peak=   -3.150 closest distance to " O   HOH Z 139 " =    3.006
peak=   -3.147 closest distance to " O   ILE A 234 " =    1.311
peak=   -3.147 closest distance to " OH  TYR A 247 " =    1.884
peak=   -3.147 closest distance to " CG  TRP A 266 " =    1.901
peak=   -3.146 closest distance to " O   HOH Z 353 " =    2.154
peak=   -3.145 closest distance to " O   HOH Z 171 " =    1.984
peak=   -3.141 closest distance to " O   HOH Z 275 " =    1.539
peak=   -3.140 closest distance to " C   MET A 188 " =    1.452
peak=   -3.138 closest distance to " N   SER A 276 " =    1.415
peak=   -3.138 closest distance to " O   HOH Z  93 " =    2.401
peak=   -3.131 closest distance to " O   HOH Z 298 " =    2.489
peak=   -3.128 closest distance to " O   ALA A 161 " =    1.758
peak=   -3.124 closest distance to " O   HOH Z 421 " =    3.376
peak=   -3.120 closest distance to " O   HOH Z 236 " =    1.464
peak=   -3.118 closest distance to " CA  GLY A 241 " =    2.843
peak=   -3.110 closest distance to " O   MET A  40 " =    2.826
peak=   -3.104 closest distance to " CG2BVAL A  41 " =    1.907
peak=   -3.101 closest distance to " O   HOH Z 137 " =    2.457
peak=   -3.099 closest distance to " O   HOH Z 244 " =    2.039
peak=   -3.097 closest distance to " ND2 ASN A  60 " =    1.361
peak=   -3.081 closest distance to " O   GLN A 240 " =    2.465
peak=   -3.068 closest distance to " CD2 TYR A 293 " =    2.150
peak=   -3.058 closest distance to " NH2 ARG A  66 " =    2.019
peak=   -3.051 closest distance to " CD2 LEU A 237 " =    2.648
peak=   -3.050 closest distance to " NH2BARG A 275 " =    2.248
peak=   -3.042 closest distance to " CG2 THR A 221 " =    2.224
peak=   -3.024 closest distance to " O   HOH Z 357 " =    2.177
peak=   -3.024 closest distance to " OD1 ASN A 301 " =    2.021
peak=   -3.023 closest distance to " O   PRO A 198 " =    1.338

================= 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    :  0.2884 0.2792   5.948814e+00   5.921392e+00
   1_bss:  0.2741 0.2657   5.919595e+00   5.888205e+00
   1_xyz:  0.1782 0.1947   5.510505e+00   5.589553e+00
   1_adp:  0.1684 0.1944   5.464878e+00   5.590809e+00
   1_occ:  0.1679 0.1937   5.462306e+00   5.588871e+00
   2_bss:  0.1672 0.1916   5.459033e+00   5.582515e+00
   2_xyz:  0.1298 0.1565   5.223295e+00   5.386309e+00
   2_adp:  0.1216 0.1581   5.187259e+00   5.391119e+00
   2_occ:  0.1214 0.1579   5.186832e+00   5.390779e+00
   3_bss:  0.1213 0.1581   5.187619e+00   5.391537e+00
   3_xyz:  0.1128 0.1565   5.143797e+00   5.378492e+00
   3_adp:  0.1132 0.1540   5.139523e+00   5.367790e+00
   3_occ:  0.1130 0.1540   5.138777e+00   5.367731e+00
   4_bss:  0.1129 0.1540   5.138681e+00   5.367892e+00
   4_xyz:  0.1137 0.1550   5.146698e+00   5.376723e+00
   4_adp:  0.1132 0.1563   5.147897e+00   5.384433e+00
   4_occ:  0.1132 0.1563   5.148021e+00   5.384796e+00
   5_bss:  0.1131 0.1563   5.148026e+00   5.384828e+00
   5_xyz:  0.1081 0.1565   5.122451e+00   5.378419e+00
   5_adp:  0.1077 0.1572   5.121779e+00   5.380862e+00
   5_occ:  0.1077 0.1572   5.121903e+00   5.381214e+00
   5_bss:  0.1074 0.1570   5.121977e+00   5.381279e+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:  0.317  54.869  -2.759   0.812  -0.948   0.000  -0.000  -0.000
   1_xyz:  0.317  54.869  -2.759   0.812  -0.948   0.000  -0.000  -0.000
   1_adp:  0.317  54.869  -2.759   0.812  -0.948   0.000  -0.000  -0.000
   1_occ:  0.317  54.869  -2.759   0.812  -0.948   0.000  -0.000  -0.000
   2_bss:  0.331  64.193  -2.942  -1.389  -1.361  -0.000  -0.000  -0.000
   2_xyz:  0.331  64.193  -2.942  -1.389  -1.361  -0.000  -0.000  -0.000
   2_adp:  0.331  64.193  -2.942  -1.389  -1.361  -0.000  -0.000  -0.000
   2_occ:  0.331  64.193  -2.942  -1.389  -1.361  -0.000  -0.000  -0.000
   3_bss:  0.328  64.193  -2.483  -1.598  -1.010  -0.000  -0.000  -0.000
   3_xyz:  0.328  64.193  -2.483  -1.598  -1.010  -0.000  -0.000  -0.000
   3_adp:  0.328  64.193  -2.483  -1.598  -1.010  -0.000  -0.000  -0.000
   3_occ:  0.328  64.193  -2.483  -1.598  -1.010  -0.000  -0.000  -0.000
   4_bss:  0.323  56.535  -2.222  -1.588  -0.785  -0.000  -0.000  -0.000
   4_xyz:  0.323  56.535  -2.222  -1.588  -0.785  -0.000  -0.000  -0.000
   4_adp:  0.323  56.535  -2.222  -1.588  -0.785  -0.000  -0.000  -0.000
   4_occ:  0.323  56.535  -2.222  -1.588  -0.785  -0.000  -0.000  -0.000
   5_bss:  0.323  56.535  -2.017  -1.478  -0.608  -0.000  -0.000  -0.000
   5_xyz:  0.323  56.535  -2.017  -1.478  -0.608  -0.000  -0.000  -0.000
   5_adp:  0.323  56.535  -2.017  -1.478  -0.608  -0.000  -0.000  -0.000
   5_occ:  0.323  56.535  -2.017  -1.478  -0.608  -0.000  -0.000  -0.000
   5_bss:  0.321  56.399  -1.650  -1.159  -0.276  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  28.365 0.7794  0.9345    22374.342
   1_bss:  27.274 0.7894  0.9145    19616.096
   1_xyz:  18.357 0.8785  0.9839     9674.615
   1_adp:  18.455 0.8772  0.9750     9683.811
   1_occ:  18.411 0.8776  0.9749     9617.867
   2_bss:  18.229 0.8792  0.9457     9465.480
   2_xyz:  13.915 0.9158  0.9663     6243.580
   2_adp:  13.987 0.9152  0.9593     6225.522
   2_occ:  13.983 0.9153  0.9591     6221.650
   3_bss:  13.999 0.9152  0.9661     6255.681
   3_xyz:  13.690 0.9177  0.9680     6138.885
   3_adp:  13.457 0.9196  0.9628     6048.517
   3_occ:  13.463 0.9196  0.9626     6049.119
   4_bss:  13.465 0.9195  0.9685     6047.443
   4_xyz:  13.586 0.9187  0.9682     6141.091
   4_adp:  13.739 0.9175  0.9597     6224.271
   4_occ:  13.747 0.9175  0.9596     6229.160
   5_bss:  13.747 0.9175  0.9654     6230.307
   5_xyz:  13.641 0.9182  0.9665     6179.887
   5_adp:  13.691 0.9178  0.9584     6188.448
   5_occ:  13.694 0.9178  0.9583     6193.379
   5_bss:  13.697 0.9178  0.9702     6195.470
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6112e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6112e-01
   1_xyz:   1.002  0.007  0.065 14.966  0.003  4.113   5.7816e-02
   1_adp:   1.002  0.007  0.065 14.966  0.003  4.113   5.7816e-02
   1_occ:   1.002  0.007  0.065 14.966  0.003  4.113   5.7816e-02
   2_bss:   1.002  0.007  0.065 14.966  0.003  4.113   5.7816e-02
   2_xyz:   0.982  0.007  0.073 14.470  0.004  4.124   5.5723e-02
   2_adp:   0.982  0.007  0.073 14.470  0.004  4.124   5.5723e-02
   2_occ:   0.982  0.007  0.073 14.470  0.004  4.124   5.5723e-02
   3_bss:   0.982  0.007  0.073 14.470  0.004  4.124   5.5723e-02
   3_xyz:   1.010  0.008  0.079 14.608  0.004  4.114   6.2006e-02
   3_adp:   1.010  0.008  0.079 14.608  0.004  4.114   6.2006e-02
   3_occ:   1.010  0.008  0.079 14.608  0.004  4.114   6.2006e-02
   4_bss:   1.010  0.008  0.079 14.608  0.004  4.114   6.2006e-02
   4_xyz:   0.933  0.007  0.073 14.381  0.004  4.114   5.3862e-02
   4_adp:   0.933  0.007  0.073 14.381  0.004  4.114   5.3862e-02
   4_occ:   0.933  0.007  0.073 14.381  0.004  4.114   5.3862e-02
   5_bss:   0.933  0.007  0.073 14.381  0.004  4.114   5.3862e-02
   5_xyz:   1.093  0.011  0.085 14.715  0.004  4.117   7.3799e-02
   5_adp:   1.093  0.011  0.085 14.715  0.004  4.117   7.3799e-02
   5_occ:   1.093  0.011  0.085 14.715  0.004  4.117   7.3799e-02
   5_bss:   1.093  0.011  0.085 14.715  0.004  4.117   7.3799e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4295e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4295e-01
   1_xyz:   6.879  0.042  0.290 83.527  0.019  2.270   6.0606e-02
   1_adp:   6.879  0.042  0.290 83.527  0.019  2.270   6.0606e-02
   1_occ:   6.879  0.042  0.290 83.527  0.019  2.270   6.0606e-02
   2_bss:   6.879  0.042  0.290 83.527  0.019  2.270   6.0606e-02
   2_xyz:   6.939  0.047  0.224 82.398  0.038  2.341   3.8914e-02
   2_adp:   6.939  0.047  0.224 82.398  0.038  2.341   3.8914e-02
   2_occ:   6.939  0.047  0.224 82.398  0.038  2.341   3.8914e-02
   3_bss:   6.939  0.047  0.224 82.398  0.038  2.341   3.8914e-02
   3_xyz:   7.295  0.041  0.258 83.431  0.040  2.359   4.4930e-02
   3_adp:   7.295  0.041  0.258 83.431  0.040  2.359   4.4930e-02
   3_occ:   7.295  0.041  0.258 83.431  0.040  2.359   4.4930e-02
   4_bss:   7.295  0.041  0.258 83.431  0.040  2.359   4.4930e-02
   4_xyz:   6.909  0.042  0.229 82.124  0.036  2.415   3.6199e-02
   4_adp:   6.909  0.042  0.229 82.124  0.036  2.415   3.6199e-02
   4_occ:   6.909  0.042  0.229 82.124  0.036  2.415   3.6199e-02
   5_bss:   6.909  0.042  0.229 82.124  0.036  2.415   3.6199e-02
   5_xyz:   7.660  0.053  0.284 82.722  0.037  2.320   5.8809e-02
   5_adp:   7.660  0.053  0.284 82.722  0.037  2.320   5.8809e-02
   5_occ:   7.660  0.053  0.284 82.722  0.037  2.320   5.8809e-02
   5_bss:   7.660  0.053  0.284 82.722  0.037  2.320   5.8809e-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:  80.74   0.00  16.13  80.74   0.00  12.30  63.05   6.90  36.96
   1_occ:  80.74   0.00  16.13  80.74   0.00  12.30  63.05   6.90  36.96
   2_bss:  80.74   0.00  16.13  80.74   0.00  12.30  63.05   6.90  36.96
   2_xyz:  80.74   0.00  16.13  80.74   0.00  12.30  63.05   6.90  36.96
   2_adp:  85.41   0.00  17.18  85.41   0.00  12.86  77.89   0.00  40.75
   2_occ:  85.41   0.00  17.18  85.41   0.00  12.86  77.89   0.00  40.75
   3_bss:  85.41   0.00  17.18  85.41   0.00  12.86  77.89   0.00  40.75
   3_xyz:  85.41   0.00  17.18  85.41   0.00  12.86  77.89   0.00  40.75
   3_adp:  84.81   0.00  16.48  84.81   1.31  12.52  72.90   0.00  38.03
   3_occ:  84.81   0.00  16.48  84.81   1.31  12.52  72.90   0.00  38.03
   4_bss:  84.81   0.00  16.48  84.81   1.31  12.52  72.90   0.00  38.03
   4_xyz:  84.81   0.00  16.48  84.81   1.31  12.52  72.90   0.00  38.03
   4_adp:  85.43   0.00  16.37  85.43   0.00  12.34  73.01   1.48  38.30
   4_occ:  85.43   0.00  16.37  85.43   0.00  12.34  73.01   1.48  38.30
   5_bss:  85.43   0.00  16.37  85.43   0.00  12.34  73.01   1.48  38.30
   5_xyz:  85.43   0.00  16.37  85.43   0.00  12.34  73.01   1.48  38.30
   5_adp:  90.32   0.00  16.42  90.32   0.00  12.22  75.55   3.19  39.31
   5_occ:  90.32   0.00  16.42  90.32   0.00  12.22  75.55   3.19  39.31
   5_bss:  90.33   0.00  16.43  90.33   0.00  12.22  75.55   3.20  39.32
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.193    0.009    0.233
   1_adp:    1.193    0.009    0.233
   1_occ:    1.193    0.009    0.233
   2_bss:    1.193    0.009    0.233
   2_xyz:    0.791    0.024    0.304
   2_adp:    0.791    0.024    0.304
   2_occ:    0.791    0.024    0.304
   3_bss:    0.791    0.024    0.304
   3_xyz:    0.805    0.017    0.334
   3_adp:    0.805    0.017    0.334
   3_occ:    0.805    0.017    0.334
   4_bss:    0.805    0.017    0.334
   4_xyz:    0.935    0.010    0.343
   4_adp:    0.935    0.010    0.343
   4_occ:    0.935    0.010    0.343
   5_bss:    0.935    0.010    0.343
   5_xyz:    0.932    0.014    0.350
   5_adp:    0.932    0.014    0.350
   5_occ:    0.932    0.014    0.350
   5_bss:    0.932    0.014    0.350
------------------------------------------------------------------------

CPU time actual refinement: 276.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_809/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_809/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_809/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_809/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_809/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 276.55 
  Macro-tasks:
    bulk solvent and scale       = 32.88  
    individual site refinement   = 116.60 
    weights calculation          = 24.28  
    collect and process          = 5.51   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 179.35 
  Micro-tasks:
    mask                            = 0.98   
    f_calc                          = 87.36  
    alpha_beta                      = 6.76   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 96.43  
    fmodel                         = 5.60   
    r_factors                      = 0.22   
    phase_errors                   = 9.25   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 207.82 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.885 micro seconds
Total CPU time: 4.80 minutes
from_scatterers_fft:    658 calls, 86.96 s
gradients_fft:          603 calls, 84.41 s

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

# Date 2008-01-16 Time 05:41:44 PST -0800 (1200490904.35 s)
Start R-work = 0.2884, R-free = 0.2792 (no bulk solvent and anisotropic scale)
Final R-work = 0.1276, R-free = 0.1725 (no bulk solvent and anisotropic scale)

Start R-work = 0.2741, R-free = 0.2657
Final R-work = 0.1074, R-free = 0.1570