# Date 2008-01-16 Time 05:19:46 PST -0800 (1200489586.69 s)
#phil __OFF__

Command line arguments: "../692.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32469
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 692

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.3993, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00073
Completeness in resolution range: 0.953514
Completeness with d_max=infinity: 0.950553

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   2.0007

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 2.00073
Completeness in resolution range: 0.953514
Completeness with d_max=infinity: 0.950553

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2807 [2161/2188]  1942   219  10.1%
  bin  2:  4.2807 -  3.4106 [2068/2084]  1864   204   9.9%
  bin  3:  3.4106 -  2.9833 [2049/2068]  1844   205  10.0%
  bin  4:  2.9833 -  2.7123 [2024/2054]  1820   204  10.1%
  bin  5:  2.7123 -  2.5188 [2003/2022]  1804   199   9.9%
  bin  6:  2.5188 -  2.3709 [2015/2040]  1812   203  10.1%
  bin  7:  2.3709 -  2.2526 [2003/2036]  1809   194   9.7%
  bin  8:  2.2526 -  2.1548 [1975/2006]  1770   205  10.4%
  bin  9:  2.1548 -  2.0721 [1979/2021]  1788   191   9.7%
  bin 10:  2.0721 -  2.0007 [1312/2025]  1177   135  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_692/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.41 -     2.11: 7
        2.11 -     2.81: 748
        2.81 -     3.50: 4372
        3.50 -     4.20: 9158
        4.20 -     4.90: 13535
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.409 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.666 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.666 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.715 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.803 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 27815 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_692/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_692/model_refine_001.geo

CPU time processing inputs: 9.36


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.3993 88.54975 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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4054   r_free= 0.3997   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.206924                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7743 0.99   1401  154 0.3245 0.3219      6.4609      6.3844|
|  2:  4.7743 -  3.8096 0.99   1348  153 0.3262 0.3590      6.6681       6.786|
|  3:  3.8096 -  3.3340 0.99   1321  146 0.3801 0.3250      6.5914       6.491|
|  4:  3.3340 -  3.0318 0.99   1312  140 0.3865 0.3970      6.4265      6.4059|
|  5:  3.0318 -  2.8160 0.99   1313  147 0.4224 0.3657      6.2878      6.2469|
|  6:  2.8160 -  2.6509 0.99   1296  147 0.4259 0.4856      6.1921      6.1849|
|  7:  2.6509 -  2.5188 0.99   1283  144 0.4216 0.4110      6.1594      6.0715|
|  8:  2.5188 -  2.4096 0.98   1292  143 0.4570 0.4409      6.1459      6.1011|
|  9:  2.4096 -  2.3172 0.98   1287  144 0.4480 0.4400      6.0357      6.1072|
| 10:  2.3172 -  2.2375 0.98   1277  138 0.4764 0.4427      6.0806      6.0139|
| 11:  2.2375 -  2.1677 0.99   1283  147 0.4760 0.4795       6.001      6.0266|
| 12:  2.1677 -  2.1060 0.97   1268  138 0.4641 0.4578      5.9211      5.9967|
| 13:  2.1060 -  2.0506 0.99   1272  137 0.4707 0.4881      5.8514      5.8182|
| 14:  2.0506 -  2.0007 0.52    677   81 0.4280 0.4195      5.8225      5.7101|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7743  1401   154  0.77  28.00   0.84     0.79      49582.70|
|  2:  4.7743 -  3.8096  1348   153  0.79  27.57   0.93     0.86      71662.39|
|  3:  3.8096 -  3.3340  1321   146  0.71  34.54   0.91     0.85      73875.86|
|  4:  3.3340 -  3.0318  1312   140  0.65  39.75   0.93     0.79      66441.06|
|  5:  3.0318 -  2.8160  1313   147  0.59  44.48   0.93     0.74      53123.13|
|  6:  2.8160 -  2.6509  1296   147  0.54  48.50   0.92     0.70      50314.50|
|  7:  2.6509 -  2.5188  1283   144  0.55  48.10   0.95     0.70      45284.72|
|  8:  2.5188 -  2.4096  1292   143  0.55  48.25   0.92     0.72      41288.70|
|  9:  2.4096 -  2.3172  1287   144  0.54  48.93   0.94     0.74      37475.83|
| 10:  2.3172 -  2.2375  1277   138  0.53  49.81   0.96     0.72      35600.21|
| 11:  2.2375 -  2.1677  1283   147  0.48  53.53   0.93     0.70      36686.00|
| 12:  2.1677 -  2.1060  1268   138  0.46  55.29   0.95     0.67      35179.23|
| 13:  2.1060 -  2.0506  1272   137  0.44  57.23   0.93     0.64      31303.82|
| 14:  2.0506 -  2.0007   677    81  0.49  53.53   0.99     0.60      24147.22|
|alpha:            min =        0.60 max =            0.86 mean =         0.74|
|beta:             min =    24147.22 max =        73875.86 mean =     47576.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           89.97 mean =        45.03|
|phase err.(test): min =        0.00 max =           89.83 mean =        45.24|
|-----------------------------------------------------------------------------|

============================== 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 = 11.774071             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.507   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.254841              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.508   (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 |  1.409 -  1.758:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.758 -  2.107:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.107 -  2.457:       14 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.457 -  2.806:      734 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.806 -  3.155:     2033 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.155 -  3.504:     2339 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.504 -  3.853:     4491 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.853 -  4.202:     4667 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.202 -  4.551:     6113 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7422 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.409 |       0.269 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.251)------------------------------------------|
|    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: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4054   r_free= 0.3997   ksol= 0.00   Bsol= 0.00   scale= 0.914    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.206924                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3913   r_free= 0.3869   ksol= 0.31   Bsol= 55.40   scale= 0.951   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.63,-0.33,5.51,-0.00,0.00,0.00); trace/3= 0.52                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.189443                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.171332             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.210   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.692491              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.194   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3913      final r-factor (work) = 0.2391          |
| start r-factor (free) = 0.3869      final r-factor (free) = 0.2675          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.6424 = 10.17 * 0.50 * 6.1883 + 1.00 * 0.1709                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4127 = 10.17 * 0.50 * 5.9571 + 1.00 * 0.1168                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2391      final r-factor (work) = 0.2157          |
| start r-factor (free) = 0.2675      final r-factor (free) = 0.2727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1315 = 0.69 * 1.00 * 5.9571 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9619 = 0.69 * 1.00 * 5.7022 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.251)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.72   17.81    None  None   None       |
|    all(noH): 2823   0      0.00    90.72   17.81    None  None   None       |
|    Sol.    : 438    0      3.33    90.72   42.12    None  None   None       |
|    Mac.    : 2385   0      0.00    80.29   13.35    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 -   9.072:  861   |   5:    45.359 -  54.430:  104        |
|      1:     9.072 -  18.144: 1111   |   6:    54.430 -  63.502:   62        |
|      2:    18.144 -  27.215:  337   |   7:    63.502 -  72.574:   37        |
|      3:    27.215 -  36.287:  171   |   8:    72.574 -  81.646:   21        |
|      4:    36.287 -  45.359:  117   |   9:    81.646 -  90.717:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2157 r_free = 0.2727             target_work(ml) = 5.711         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2153 r_free = 0.2730             target_work(ml) = 5.711         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2153   r_free= 0.2730   ksol= 0.31   Bsol= 55.40   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.63,-0.33,5.51,-0.00,0.00,0.00); trace/3= 0.52                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.711122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2113   r_free= 0.2707   ksol= 0.34   Bsol= 84.76   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-1.24,1.42,-0.00,0.00,0.00); trace/3= -0.90                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.700561                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.199636              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.916   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.290709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.044  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2113      final r-factor (work) = 0.1560          |
| start r-factor (free) = 0.2707      final r-factor (free) = 0.2018          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0902 = 4.20 * 0.50 * 5.7021 + 1.00 * 0.1168                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7949 = 4.20 * 0.50 * 5.5834 + 1.00 * 0.0708                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1560      final r-factor (work) = 0.1446          |
| start r-factor (free) = 0.2018      final r-factor (free) = 0.1882          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6364 = 0.29 * 1.00 * 5.5834 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5762 = 0.29 * 1.00 * 5.3878 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.251)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    90.39   17.26    None  None   None       |
|    all(noH): 2823   0      0.91    90.39   17.26    None  None   None       |
|    Sol.    : 438    0      4.69    90.39   41.45    None  None   None       |
|    Mac.    : 2385   0      0.91    78.27   12.81    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:     0.907 -   9.855: 1039   |   5:    45.648 -  54.597:  112        |
|      1:     9.855 -  18.804: 1078   |   6:    54.597 -  63.545:   63        |
|      2:    18.804 -  27.752:  246   |   7:    63.545 -  72.493:   34        |
|      3:    27.752 -  36.700:  124   |   8:    72.493 -  81.442:   12        |
|      4:    36.700 -  45.648:  112   |   9:    81.442 -  90.390:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1446 r_free = 0.1882             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1444 r_free = 0.1880             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1444   r_free= 0.1880   ksol= 0.34   Bsol= 84.76   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-1.24,1.42,-0.00,0.00,0.00); trace/3= -0.90                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.353519                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1442   r_free= 0.1875   ksol= 0.34   Bsol= 80.54   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.51,0.44,-0.00,0.00,0.00); trace/3= -1.21                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.351150                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.727274              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.804  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.386561              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.115  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1442      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.1875      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1115 = 3.73 * 0.50 * 5.3877 + 1.00 * 0.0708                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9300 = 3.73 * 0.50 * 5.2855 + 1.00 * 0.0798                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1195          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0530 = 0.39 * 1.00 * 5.2855 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0246 = 0.39 * 1.00 * 5.2117 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.251)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.18   17.02    None  None   None       |
|    all(noH): 2823   0      0.00    92.18   17.02    None  None   None       |
|    Sol.    : 438    0      1.41    92.18   41.19    None  None   None       |
|    Mac.    : 2385   0      0.00    81.36   12.58    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 -   9.218:  934   |   5:    46.090 -  55.307:   91        |
|      1:     9.218 -  18.436: 1192   |   6:    55.307 -  64.525:   66        |
|      2:    18.436 -  27.654:  244   |   7:    64.525 -  73.743:   38        |
|      3:    27.654 -  36.872:  124   |   8:    73.743 -  82.961:   10        |
|      4:    36.872 -  46.090:  122   |   9:    82.961 -  92.179:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1195 r_free = 0.1658             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1194 r_free = 0.1659             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1659   ksol= 0.34   Bsol= 80.54   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.51,0.44,-0.00,0.00,0.00); trace/3= -1.21                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202925                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1655   ksol= 0.33   Bsol= 69.60   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-1.65,0.04,-0.00,0.00,0.00); trace/3= -1.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.200803                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.909634              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.629  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.571458              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.560  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1655      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0551 = 1.91 * 0.50 * 5.2108 + 1.00 * 0.0798                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0285 = 1.91 * 0.50 * 5.2027 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1194      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9829 = 0.57 * 1.00 * 5.2027 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9801 = 0.57 * 1.00 * 5.1967 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.251)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.93   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    95.93   16.85    None  None   None       |
|    Sol.    : 438    0      1.06    95.93   40.84    None  None   None       |
|    Mac.    : 2385   0      0.00    86.03   12.44    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 -   9.593: 1057   |   5:    47.965 -  57.558:   87        |
|      1:     9.593 -  19.186: 1108   |   6:    57.558 -  67.151:   62        |
|      2:    19.186 -  28.779:  220   |   7:    67.151 -  76.744:   28        |
|      3:    28.779 -  38.372:  130   |   8:    76.744 -  86.337:    6        |
|      4:    38.372 -  47.965:  123   |   9:    86.337 -  95.930:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1186 r_free = 0.1643             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1185 r_free = 0.1642             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1642   ksol= 0.33   Bsol= 69.60   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-1.65,0.04,-0.00,0.00,0.00); trace/3= -1.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.197724                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1641   ksol= 0.33   Bsol= 69.60   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.51,0.07,-0.00,0.00,0.00); trace/3= -1.21                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.197798                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.527274              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.452  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.428156              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.575  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0295 = 1.53 * 0.50 * 5.1970 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0256 = 1.53 * 0.50 * 5.1965 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2352 = 0.43 * 1.00 * 5.1965 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2357 = 0.43 * 1.00 * 5.1983 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.251)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.16   16.53    None  None   None       |
|    all(noH): 2823   0      0.00    96.16   16.53    None  None   None       |
|    Sol.    : 438    0      2.97    96.16   40.01    None  None   None       |
|    Mac.    : 2385   0      0.00    86.88   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 -   9.616: 1112   |   5:    48.081 -  57.697:   84        |
|      1:     9.616 -  19.232: 1064   |   6:    57.697 -  67.313:   57        |
|      2:    19.232 -  28.849:  221   |   7:    67.313 -  76.929:   24        |
|      3:    28.849 -  38.465:  136   |   8:    76.929 -  86.546:    4        |
|      4:    38.465 -  48.081:  118   |   9:    86.546 -  96.162:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1646             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1646             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1646   ksol= 0.33   Bsol= 69.60   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.19,-1.51,0.07,-0.00,0.00,0.00); trace/3= -1.21                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.198010                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7743 0.99   1401  154 0.1011 0.1308      5.4142      5.5478|
|  2:  4.7743 -  3.8096 0.99   1348  153 0.0872 0.1135      5.4574      5.6676|
|  3:  3.8096 -  3.3340 0.99   1321  146 0.1093 0.1556      5.5003      5.8596|
|  4:  3.3340 -  3.0318 0.99   1312  140 0.1257 0.1622      5.4832      5.6294|
|  5:  3.0318 -  2.8160 0.99   1313  147 0.1412 0.1751      5.3808      5.5854|
|  6:  2.8160 -  2.6509 0.99   1296  147 0.1332 0.2108      5.2781      5.5592|
|  7:  2.6509 -  2.5188 0.99   1283  144 0.1353 0.1752      5.2345      5.3941|
|  8:  2.5188 -  2.4096 0.98   1292  143 0.1219 0.1742      5.1383      5.3857|
|  9:  2.4096 -  2.3172 0.98   1287  144 0.1266 0.1977      5.0793      5.3886|
| 10:  2.3172 -  2.2375 0.98   1277  138 0.1223 0.1662      5.0182      5.1842|
| 11:  2.2375 -  2.1677 0.99   1283  147 0.1234 0.1860      4.9905      5.3012|
| 12:  2.1677 -  2.1060 0.97   1268  138 0.1237 0.1781       4.948      5.2563|
| 13:  2.1060 -  2.0506 0.99   1272  137 0.1197 0.1860      4.8478      5.0722|
| 14:  2.0506 -  2.0007 0.52    677   81 0.1036 0.1839      4.7129      5.0003|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7743  1401   154  0.94   9.59   0.96     0.93       7866.09|
|  2:  4.7743 -  3.8096  1348   153  0.95   8.16   1.00     0.98       9405.98|
|  3:  3.8096 -  3.3340  1321   146  0.93  11.57   1.01     1.01      10764.57|
|  4:  3.3340 -  3.0318  1312   140  0.92  14.09   1.00     0.98      10873.60|
|  5:  3.0318 -  2.8160  1313   147  0.90  16.42   0.99     0.96       9024.83|
|  6:  2.8160 -  2.6509  1296   147  0.89  17.64   0.97     0.95       8079.31|
|  7:  2.6509 -  2.5188  1283   144  0.90  16.68   0.98     0.95       7089.77|
|  8:  2.5188 -  2.4096  1292   143  0.90  16.43   0.98     0.95       6202.74|
|  9:  2.4096 -  2.3172  1287   144  0.90  16.52   0.99     0.95       5545.42|
| 10:  2.3172 -  2.2375  1277   138  0.89  16.69   0.98     0.93       4827.80|
| 11:  2.2375 -  2.1677  1283   147  0.89  17.20   0.97     0.93       4777.99|
| 12:  2.1677 -  2.1060  1268   138  0.90  16.71   0.98     0.97       4513.51|
| 13:  2.1060 -  2.0506  1272   137  0.89  17.25   0.97     0.95       3805.50|
| 14:  2.0506 -  2.0007   677    81  0.91  14.87   0.94     0.89       2772.12|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     2772.12 max =        10873.60 mean =      7004.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.92|
|phase err.(test): min =        0.00 max =           88.99 mean =        14.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1644   ksol= 0.33   Bsol= 69.60   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-1.35,0.21,-0.00,0.00,0.00); trace/3= -1.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.198124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1644   ksol= 0.33   Bsol= 69.60   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-1.35,0.21,-0.00,0.00,0.00); trace/3= -1.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.198124                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7743 0.99   1401  154 0.1012 0.1308      5.4148      5.5489|
|  2:  4.7743 -  3.8096 0.99   1348  153 0.0872 0.1135      5.4579      5.6675|
|  3:  3.8096 -  3.3340 0.99   1321  146 0.1093 0.1557      5.5004        5.86|
|  4:  3.3340 -  3.0318 0.99   1312  140 0.1257 0.1622      5.4833      5.6295|
|  5:  3.0318 -  2.8160 0.99   1313  147 0.1412 0.1750      5.3807      5.5851|
|  6:  2.8160 -  2.6509 0.99   1296  147 0.1332 0.2108       5.278      5.5593|
|  7:  2.6509 -  2.5188 0.99   1283  144 0.1353 0.1753      5.2346      5.3942|
|  8:  2.5188 -  2.4096 0.98   1292  143 0.1219 0.1741      5.1385      5.3857|
|  9:  2.4096 -  2.3172 0.98   1287  144 0.1266 0.1976      5.0792      5.3884|
| 10:  2.3172 -  2.2375 0.98   1277  138 0.1223 0.1662      5.0182      5.1843|
| 11:  2.2375 -  2.1677 0.99   1283  147 0.1233 0.1859      4.9904      5.3008|
| 12:  2.1677 -  2.1060 0.97   1268  138 0.1237 0.1779      4.9479      5.2557|
| 13:  2.1060 -  2.0506 0.99   1272  137 0.1196 0.1863      4.8478      5.0729|
| 14:  2.0506 -  2.0007 0.52    677   81 0.1036 0.1838      4.7134           5|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7743  1401   154  0.94   9.60   0.96     0.94       7879.85|
|  2:  4.7743 -  3.8096  1348   153  0.95   8.17   1.00     0.98       9415.71|
|  3:  3.8096 -  3.3340  1321   146  0.93  11.57   1.01     1.01      10770.23|
|  4:  3.3340 -  3.0318  1312   140  0.92  14.09   1.00     0.98      10875.69|
|  5:  3.0318 -  2.8160  1313   147  0.90  16.42   0.99     0.97       9025.28|
|  6:  2.8160 -  2.6509  1296   147  0.89  17.64   0.98     0.95       8077.13|
|  7:  2.6509 -  2.5188  1283   144  0.90  16.69   0.99     0.95       7090.65|
|  8:  2.5188 -  2.4096  1292   143  0.90  16.44   0.99     0.95       6204.42|
|  9:  2.4096 -  2.3172  1287   144  0.90  16.52   0.99     0.96       5546.73|
| 10:  2.3172 -  2.2375  1277   138  0.89  16.69   0.99     0.94       4824.84|
| 11:  2.2375 -  2.1677  1283   147  0.89  17.19   0.98     0.94       4775.07|
| 12:  2.1677 -  2.1060  1268   138  0.90  16.70   0.99     0.98       4512.01|
| 13:  2.1060 -  2.0506  1272   137  0.89  17.25   0.98     0.95       3806.20|
| 14:  2.0506 -  2.0007   677    81  0.91  14.87   0.95     0.90       2773.28|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2773.28 max =        10875.69 mean =      7006.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.93|
|phase err.(test): min =        0.00 max =           88.99 mean =        14.33|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.251)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.16   16.54    None  None   None       |
|    all(noH): 2823   0      0.00    96.16   16.54    None  None   None       |
|    Sol.    : 438    0      2.97    96.16   40.02    None  None   None       |
|    Mac.    : 2385   0      0.00    86.88   12.23    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 -   9.619: 1112   |   5:    48.084 -  57.700:   84        |
|      1:     9.619 -  19.235: 1064   |   6:    57.700 -  67.316:   57        |
|      2:    19.235 -  28.852:  221   |   7:    67.316 -  76.932:   24        |
|      3:    28.852 -  38.468:  136   |   8:    76.932 -  86.548:    4        |
|      4:    38.468 -  48.084:  118   |   9:    86.548 -  96.165:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.515 - 4.919
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 301
   mapped sites are within: 0.713 - 4.919

peak=    5.458 closest distance to " CB  GLN A 223 " =    1.467
peak=    5.167 closest distance to " CZ  PHE A 218 " =    1.129
peak=    5.140 closest distance to " O   HOH Z 113 " =    2.054
peak=    5.008 closest distance to " CG  PRO A  54 " =    1.422
peak=    4.774 closest distance to " CB  ARG A 190 " =    1.631
peak=    4.753 closest distance to " CG  PRO A 198 " =    1.302
peak=    4.513 closest distance to " CA  TYR A  30 " =    0.940
peak=    4.510 closest distance to " O   HOH Z 188 " =    2.897
peak=    4.500 closest distance to " CB  PRO A  54 " =    1.008
peak=    4.494 closest distance to " CB  ARG A 275 " =    0.943
peak=    4.484 closest distance to " O   HOH Z 369 " =    2.113
peak=    4.481 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.460 closest distance to " CB  SER A  63 " =    1.173
peak=    4.414 closest distance to " CG  PRO A 213 " =    1.210
peak=    4.409 closest distance to " O   HOH Z 232 " =    2.329
peak=    4.404 closest distance to " CZ3 TRP A 266 " =    1.098
peak=    4.389 closest distance to " O   HOH Z 298 " =    1.970
peak=    4.326 closest distance to " CG  PRO A 243 " =    1.098
peak=    4.307 closest distance to " ND2 ASN A 187 " =    1.545
peak=    4.269 closest distance to " CB  ASN A 148 " =    1.471
peak=    4.247 closest distance to " CB  ARG A  79 " =    1.282
peak=    4.229 closest distance to " CD  ARG A 269 " =    0.972
peak=    4.223 closest distance to " CB  VAL A 265 " =    1.274
peak=    4.200 closest distance to " O   HOH Z  19 " =    2.117
peak=    4.161 closest distance to " CA  ARG A  36 " =    1.086
peak=    4.147 closest distance to " CZ  PHE A  38 " =    1.227
peak=    4.142 closest distance to " CE  LYS A  76 " =    0.890
peak=    4.126 closest distance to " CB  ASN A  39 " =    0.901
peak=    4.109 closest distance to " CB  TYR A 169 " =    0.800
peak=    4.105 closest distance to " CB  GLU A 277 " =    3.802
peak=    4.100 closest distance to " C   PRO A 198 " =    1.562
peak=    4.100 closest distance to " CB  GLU A 152 " =    1.213
peak=    4.079 closest distance to " CA  ALA A  51 " =    0.918
peak=    4.075 closest distance to " CB  PRO A  90 " =    1.128
peak=    4.063 closest distance to " CB  VAL A 202 " =    1.516
peak=    4.047 closest distance to " ND2 ASN A 249 " =    0.871
peak=    4.039 closest distance to " NE2 GLN A  11 " =    1.127
peak=    4.033 closest distance to " CD2 TRP A 179 " =    1.297
peak=    4.031 closest distance to " O   HOH Z 214 " =    2.367
peak=    4.031 closest distance to " O   HOH Z  43 " =    2.112
peak=    4.022 closest distance to " O   HOH Z 126 " =    1.912
peak=    4.015 closest distance to " O   HOH Z 234 " =    3.870
peak=    3.997 closest distance to " CD1 LEU A  96 " =    0.779
peak=    3.991 closest distance to " O   HOH Z 265 " =    2.116
peak=    3.986 closest distance to " CG2 VAL A 257 " =    0.808
peak=    3.976 closest distance to " O   HOH Z 142 " =    1.658
peak=    3.974 closest distance to " CB  ASP A 124 " =    0.790
peak=    3.958 closest distance to " O   ASN A  74 " =    1.496
peak=    3.957 closest distance to " O   HOH Z 303 " =    2.207
peak=    3.952 closest distance to " O   HOH Z 406 " =    1.677
peak=    3.927 closest distance to " CA  ARG A 195 " =    1.242
peak=    3.926 closest distance to " CG  MET A 185 " =    1.210
peak=    3.910 closest distance to " O   HOH Z 427 " =    3.140
peak=    3.901 closest distance to " OE1 GLN A  55 " =    1.550
peak=    3.889 closest distance to " CB  TRP A 266 " =    1.042
peak=    3.883 closest distance to " CG  ARG A  66 " =    2.572
peak=    3.881 closest distance to " CB  GLU A 128 " =    0.976
peak=    3.871 closest distance to " O   HOH Z  78 " =    1.638
peak=    3.866 closest distance to " CB  ALA A 104 " =    0.756
peak=    3.863 closest distance to " CB  ASN A 142 " =    1.034
peak=    3.855 closest distance to " O   HOH Z  15 " =    2.168
peak=    3.852 closest distance to " O   HOH Z 368 " =    2.192
peak=    3.851 closest distance to " O   HOH Z 412 " =    3.821
peak=    3.849 closest distance to " O   HOH Z 287 " =    1.968
peak=    3.831 closest distance to " NH1AARG A 145 " =    1.364
peak=    3.829 closest distance to " CD  LYS A 166 " =    1.282
peak=    3.823 closest distance to " CG  GLU A  37 " =    0.984
peak=    3.819 closest distance to " O   SER A  87 " =    2.310
peak=    3.819 closest distance to " CA  ALA A 154 " =    1.016
peak=    3.812 closest distance to " O   HOH Z 261 " =    2.106
peak=    3.807 closest distance to " NZ  LYS A 117 " =    3.142
peak=    3.805 closest distance to " CG  LEU A 167 " =    1.200
peak=    3.802 closest distance to " O  BHOH Z 338 " =    2.222
peak=    3.800 closest distance to " CA  ALA A 160 " =    0.984
peak=    3.795 closest distance to " N   ASN A  39 " =    1.280
peak=    3.792 closest distance to " O   HOH Z 248 " =    1.597
peak=    3.790 closest distance to " CB  LEU A 228 " =    1.076
peak=    3.779 closest distance to " O   HOH Z  63 " =    1.962
peak=    3.779 closest distance to " CB  GLU A  46 " =    0.976
peak=    3.778 closest distance to " CB  LEU A  83 " =    0.768
peak=    3.754 closest distance to " CG2 ILE A 120 " =    1.171
peak=    3.754 closest distance to " O   THR A 182 " =    1.392
peak=    3.744 closest distance to " O   HOH Z 158 " =    3.077
peak=    3.739 closest distance to " CG  ARG A 138 " =    1.288
peak=    3.733 closest distance to " O   HOH Z 203 " =    1.727
peak=    3.724 closest distance to " O   HOH Z  40 " =    1.889
peak=    3.698 closest distance to " CH2 TRP A  70 " =    0.879
peak=    3.694 closest distance to " CB  ASP A 140 " =    1.057
peak=    3.693 closest distance to " O   HOH Z 346 " =    1.617
peak=    3.690 closest distance to " O   HOH Z  21 " =    1.825
peak=    3.676 closest distance to " O   HOH Z 353 " =    2.657
peak=    3.669 closest distance to " CD  ARG A 159 " =    0.761
peak=    3.659 closest distance to " O   HOH Z 313 " =    1.882
peak=    3.652 closest distance to " O   HOH Z 133 " =    2.954
peak=    3.650 closest distance to " OG BSER A 134 " =    2.790
peak=    3.644 closest distance to " CB  PHE A 204 " =    0.778
peak=    3.638 closest distance to " CA  ALA A 100 " =    0.962
peak=    3.633 closest distance to " O   HOH Z 126 " =    1.592
peak=    3.628 closest distance to " CA  MET A 105 " =    1.033
peak=    3.625 closest distance to " CA  SER A  87 " =    1.056
peak=    3.623 closest distance to " O   HOH Z 294 " =    1.559
peak=    3.619 closest distance to " CD1 LEU A 300 " =    1.137
peak=    3.607 closest distance to " ND2 ASN A 249 " =    1.921
peak=    3.602 closest distance to " O   HOH Z 361 " =    3.643
peak=    3.598 closest distance to " O   HOH Z 280 " =    2.892
peak=    3.598 closest distance to " CG2AVAL A 121 " =    2.248
peak=    3.592 closest distance to " O   HOH Z 423 " =    1.928
peak=    3.591 closest distance to " OD2 ASP A 298 " =    3.935
peak=    3.585 closest distance to " CA  ASN A 215 " =    1.058
peak=    3.583 closest distance to " O   HOH Z 383 " =    2.054
peak=    3.580 closest distance to " CA  ASP A 162 " =    1.008
peak=    3.580 closest distance to " O   HOH Z 148 " =    3.516
peak=    3.579 closest distance to " CA  THR A 264 " =    0.928
peak=    3.579 closest distance to " O   HOH Z 392 " =    2.505
peak=    3.562 closest distance to " CG  PHE A 204 " =    0.949
peak=    3.560 closest distance to " CB  THR A  31 " =    1.548
peak=    3.558 closest distance to " NE2 GLN A  77 " =    3.427
peak=    3.553 closest distance to " O   HOH Z  62 " =    2.265
peak=    3.553 closest distance to " O   HOH Z  49 " =    0.907
peak=    3.553 closest distance to " O   HOH Z 337 " =    3.614
peak=    3.550 closest distance to " CB  PRO A 198 " =    1.121
peak=    3.545 closest distance to " CA  ILE A 106 " =    0.819
peak=    3.536 closest distance to " O   THR A 220 " =    1.148
peak=    3.533 closest distance to " CG  GLN A  11 " =    1.684
peak=    3.533 closest distance to " CB  ASN A 187 " =    1.357
peak=    3.530 closest distance to " CB  GLN A  89 " =    1.298
peak=    3.527 closest distance to " O   HOH Z  97 " =    2.030
peak=    3.527 closest distance to " CB  ALA A 248 " =    1.331
peak=    3.520 closest distance to " CA  ALA A 295 " =    1.073
peak=    3.520 closest distance to " CG AARG A 275 " =    1.232
peak=    3.519 closest distance to " CB  ASN A 215 " =    1.196
peak=    3.518 closest distance to " O   HOH Z 285 " =    2.287
peak=    3.517 closest distance to " O   HOH Z  88 " =    1.763
peak=    3.514 closest distance to " CB  SER A  22 " =    0.989
peak=    3.506 closest distance to " O   THR A 251 " =    1.104
peak=    3.502 closest distance to " O   HOH Z 316 " =    3.136
peak=    3.499 closest distance to " O   HOH Z   1 " =    2.253
peak=    3.493 closest distance to " CA  GLU A 152 " =    0.896
peak=    3.489 closest distance to " CA  GLN A  94 " =    0.800
peak=    3.488 closest distance to " NZ  LYS A  48 " =    1.240
peak=    3.486 closest distance to " O   ALA A 165 " =    1.410
peak=    3.483 closest distance to " CG2AVAL A  72 " =    1.810
peak=    3.481 closest distance to " CB  GLN A  88 " =    1.200
peak=    3.477 closest distance to " O   HOH Z 209 " =    2.266
peak=    3.475 closest distance to " O   HOH Z 250 " =    1.401
peak=    3.474 closest distance to " CB  MET A  40 " =    1.011
peak=    3.472 closest distance to " O   HOH Z 402 " =    1.403
peak=    3.472 closest distance to " OG BSER A 164 " =    2.373
peak=    3.471 closest distance to " N   HIS A 108 " =    1.871
peak=    3.467 closest distance to " O   HOH Z 251 " =    1.656
peak=    3.466 closest distance to " O   HOH Z  48 " =    1.631
peak=    3.462 closest distance to " CB  SER A 141 " =    1.074
peak=    3.462 closest distance to " O   HOH Z 180 " =    2.180
peak=    3.451 closest distance to " O   HOH Z 359 " =    1.658
peak=    3.444 closest distance to " O   PRO A 213 " =    1.443
peak=    3.440 closest distance to " CB  ALA A 291 " =    1.082
peak=    3.438 closest distance to " CB  ALA A 114 " =    0.787
peak=    3.431 closest distance to " CB  ASN A 110 " =    1.137
peak=    3.431 closest distance to " CG1 VAL A 153 " =    1.016
peak=    3.430 closest distance to " CA  VAL A 125 " =    1.191
peak=    3.427 closest distance to " O   HOH Z 380 " =    2.062
peak=    3.421 closest distance to " CB  LEU A  96 " =    1.401
peak=    3.418 closest distance to " O   HOH Z 272 " =    1.851
peak=    3.418 closest distance to " CB  SER A   3 " =    1.462
peak=    3.414 closest distance to " CB  TRP A 179 " =    1.459
peak=    3.413 closest distance to " OD1 ASN A  69 " =    2.539
peak=    3.407 closest distance to " NE2 HIS A 207 " =    1.112
peak=    3.406 closest distance to " O  BHOH Z  74 " =    1.272
peak=    3.402 closest distance to " CD  ARG A  66 " =    2.302
peak=    3.400 closest distance to " CB  SER A  62 " =    0.830
peak=    3.399 closest distance to " O   HOH Z 128 " =    2.198
peak=    3.398 closest distance to " O   HOH Z 299 " =    4.418
peak=    3.397 closest distance to " O   HOH Z 290 " =    1.044
peak=    3.395 closest distance to " CA  ASN A 127 " =    1.176
peak=    3.392 closest distance to " CD2 LEU A 297 " =    0.828
peak=    3.386 closest distance to " N   ARG A 156 " =    1.443
peak=    3.384 closest distance to " O   HOH Z 199 " =    1.637
peak=    3.382 closest distance to " O   TYR A 116 " =    1.330
peak=    3.367 closest distance to " CD1 ILE A 199 " =    0.956
peak=    3.361 closest distance to " CG2 ILE A 239 " =    0.742
peak=    3.355 closest distance to " CA  TYR A 116 " =    1.446
peak=    3.355 closest distance to " O   HOH Z 185 " =    1.789
peak=    3.343 closest distance to " CA  ILE A 234 " =    0.967
peak=    3.338 closest distance to " O   HOH Z 291 " =    1.474
peak=    3.337 closest distance to " CG1 ILE A  49 " =    1.610
peak=    3.337 closest distance to " OG  SER A  22 " =    2.698
peak=    3.336 closest distance to " CA  THR A 221 " =    1.041
peak=    3.334 closest distance to " O   HOH Z 419 " =    2.036
peak=    3.330 closest distance to " O   ASP A 124 " =    1.207
peak=    3.329 closest distance to " O   HOH Z  94 " =    2.736
peak=    3.323 closest distance to " CG2 ILE A  49 " =    1.393
peak=    3.322 closest distance to " OG  SER A  28 " =    1.511
peak=    3.321 closest distance to " O   HOH Z 371 " =    2.905
peak=    3.320 closest distance to " CB  GLU A  37 " =    0.892
peak=    3.316 closest distance to " O   HOH Z 213 " =    1.995
peak=    3.314 closest distance to " O   HOH Z 325 " =    2.416
peak=    3.310 closest distance to " CG1 ILE A  20 " =    1.298
peak=    3.309 closest distance to " O   HOH Z 305 " =    3.731
peak=    3.306 closest distance to " O   HOH Z  80 " =    1.770
peak=    3.303 closest distance to " CA  ALA A 233 " =    1.540
peak=    3.302 closest distance to " OE2 GLU A  53 " =    1.219
peak=    3.301 closest distance to " CG2 THR A 220 " =    0.842
peak=    3.294 closest distance to " CB  GLN A 205 " =    1.094
peak=    3.291 closest distance to " O   HOH Z 425 " =    1.288
peak=    3.290 closest distance to " CA  ALA A 248 " =    1.213
peak=    3.285 closest distance to " CB  LYS A 117 " =    1.196
peak=    3.284 closest distance to " O   HOH Z 422 " =    2.661
peak=    3.283 closest distance to " CB  PRO A 243 " =    1.439
peak=    3.282 closest distance to " N   GLY A  98 " =    1.172
peak=    3.280 closest distance to " CD1 LEU A  96 " =    1.329
peak=    3.280 closest distance to " CB  ALA A 299 " =    0.937
peak=    3.278 closest distance to " CB  ASP A 298 " =    1.184
peak=    3.276 closest distance to " OG  SER A 245 " =    1.700
peak=    3.275 closest distance to " O   HOH Z 394 " =    4.038
peak=    3.275 closest distance to " O   HOH Z 298 " =    2.496
peak=    3.275 closest distance to " NH2 ARG A 156 " =    1.080
peak=    3.274 closest distance to " N   VAL A 265 " =    1.404
peak=    3.272 closest distance to " O   HOH Z  10 " =    1.741
peak=    3.271 closest distance to " N   TYR A 116 " =    1.545
peak=    3.270 closest distance to " O   GLY A  91 " =    1.363
peak=    3.267 closest distance to " OG1 THR A  82 " =    0.889
peak=    3.267 closest distance to " CB  SER A 210 " =    0.838
peak=    3.262 closest distance to " O   HOH Z 174 " =    2.465
peak=    3.262 closest distance to " CE1 TYR A 186 " =    1.340
peak=    3.262 closest distance to " CG2 ILE A  20 " =    1.369
peak=    3.261 closest distance to " CB  ILE A 120 " =    1.194
peak=    3.258 closest distance to " CB  ASP A 191 " =    1.249
peak=    3.257 closest distance to " O   HOH Z  97 " =    2.285
peak=    3.248 closest distance to " CA  GLU A  46 " =    0.950
peak=    3.248 closest distance to " CB  MET A  47 " =    0.954
peak=    3.246 closest distance to " O   SER A 164 " =    1.377
peak=    3.244 closest distance to " O   HOH Z 128 " =    2.208
peak=    3.241 closest distance to " CB  ARG A 138 " =    0.976
peak=    3.228 closest distance to " O   HOH Z 271 " =    2.490
peak=    3.226 closest distance to " O   HOH Z 193 " =    1.817
peak=    3.224 closest distance to " N   ALA A 256 " =    1.158
peak=    3.224 closest distance to " CB  ALA A 292 " =    1.094
peak=    3.224 closest distance to " CG2 VAL A 197 " =    1.064
peak=    3.219 closest distance to " OH  TYR A 116 " =    1.055
peak=    3.219 closest distance to " O   HOH Z 227 " =    1.436
peak=    3.218 closest distance to " CA  ASN A 217 " =    1.281
peak=    3.217 closest distance to " CG BARG A 102 " =    1.852
peak=    3.216 closest distance to " OE2 GLU A  53 " =    1.865
peak=    3.215 closest distance to " O   HOH Z 171 " =    4.051
peak=    3.214 closest distance to " CG2 THR A 221 " =    1.088
peak=    3.211 closest distance to " CB  ASN A 173 " =    1.155
peak=    3.209 closest distance to " O   HOH Z 285 " =    2.085
peak=    3.209 closest distance to " CB  ALA A  43 " =    0.849
peak=    3.207 closest distance to " CB  GLN A 103 " =    0.803
peak=    3.207 closest distance to " CA  ASN A 176 " =    1.827
peak=    3.205 closest distance to " CG2 ILE A  20 " =    1.450
peak=    3.201 closest distance to " CB  THR A  52 " =    0.742
peak=    3.197 closest distance to " CA  ARG A 102 " =    1.099
peak=    3.190 closest distance to " O   HOH Z  90 " =    2.226
peak=    3.183 closest distance to " O   ALA A 158 " =    1.177
peak=    3.180 closest distance to " O   HOH Z 116 " =    1.822
peak=    3.179 closest distance to " O   HOH Z 426 " =    1.594
peak=    3.174 closest distance to " O   HOH Z 365 " =    2.780
peak=    3.172 closest distance to " O   HOH Z 345 " =    1.771
peak=    3.169 closest distance to " O   HOH Z  59 " =    2.265
peak=    3.165 closest distance to " CB  TYR A 116 " =    0.744
peak=    3.163 closest distance to " CA  ARG A 139 " =    1.048
peak=    3.159 closest distance to " O   HOH Z 106 " =    4.185
peak=    3.157 closest distance to " N   PHE A 130 " =    1.220
peak=    3.148 closest distance to " CG2 THR A  29 " =    1.291
peak=    3.148 closest distance to " O   HOH Z 340 " =    2.100
peak=    3.140 closest distance to " CB  ALA A 242 " =    0.755
peak=    3.134 closest distance to " O   ASP A 191 " =    1.465
peak=    3.129 closest distance to " O   HOH Z  40 " =    1.559
peak=    3.119 closest distance to " CB  ALA A   1 " =    4.913
peak=    3.114 closest distance to " CA  ALA A 158 " =    1.281
peak=    3.110 closest distance to " N   ASN A 127 " =    1.242
peak=    3.108 closest distance to " CG1 ILE A 151 " =    1.043
peak=    3.108 closest distance to " OG  SER A  62 " =    2.873
peak=    3.107 closest distance to " O   HOH Z 183 " =    1.409
peak=    3.107 closest distance to " CB  ARG A 156 " =    1.109
peak=    3.105 closest distance to " CB  PHE A 283 " =    0.774
peak=    3.102 closest distance to " CG  MET A 185 " =    1.003
peak=    3.100 closest distance to " CE2 PHE A  16 " =    0.881
peak=    3.095 closest distance to " O   HOH Z 327 " =    1.680
peak=    3.090 closest distance to " OG1 THR A 279 " =    1.685
peak=    3.089 closest distance to " O   HOH Z   1 " =    2.436
peak=    3.089 closest distance to " O   HOH Z 430 " =    1.550
peak=    3.085 closest distance to " O   TRP A 274 " =    1.821
peak=    3.077 closest distance to " O   HOH Z 216 " =    4.919
peak=    3.076 closest distance to " CA  GLY A 211 " =    1.307
peak=    3.072 closest distance to " CG2 VAL A 268 " =    0.981
peak=    3.059 closest distance to " CB  LEU A 300 " =    0.916
peak=    3.058 closest distance to " CD1 LEU A 281 " =    1.003
peak=    3.049 closest distance to " CD1 LEU A 261 " =    1.273
peak=    3.049 closest distance to " CE1 TYR A  30 " =    1.038
peak=    3.048 closest distance to " CZ3 TRP A 274 " =    4.487
peak=    3.047 closest distance to " O   HOH Z 421 " =    1.955
peak=    3.018 closest distance to " CB  PHE A 204 " =    0.713
peak=    3.015 closest distance to " OG BSER A  99 " =    2.265

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.671 - 5.949
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.892 - 5.949

peak=   -4.682 closest distance to " CD  ARG A  14 " =    3.370
peak=   -4.566 closest distance to " CG1 VAL A 112 " =    2.591
peak=   -4.390 closest distance to " CD2 TYR A 293 " =    1.975
peak=   -4.349 closest distance to " O   PRO A 198 " =    1.254
peak=   -4.349 closest distance to " CD  ARG A 156 " =    2.088
peak=   -4.305 closest distance to " CE2 PHE A  61 " =    2.673
peak=   -4.292 closest distance to " O   HOH Z 231 " =    2.352
peak=   -4.278 closest distance to " CG1 VAL A 250 " =    2.740
peak=   -4.245 closest distance to " O   HOH Z 267 " =    5.674
peak=   -4.224 closest distance to " O   HOH Z 196 " =    2.157
peak=   -4.175 closest distance to " C   HIS A 108 " =    1.101
peak=   -4.155 closest distance to " CB  PRO A 243 " =    2.749
peak=   -4.149 closest distance to " O   HOH Z  73 " =    2.482
peak=   -4.052 closest distance to " CA  VAL A  67 " =    3.049
peak=   -4.044 closest distance to " O   VAL A  67 " =    2.613
peak=   -4.010 closest distance to " O   HOH Z  10 " =    1.546
peak=   -4.006 closest distance to " O   HOH Z 377 " =    1.997
peak=   -3.989 closest distance to " CH2 TRP A 179 " =    1.237
peak=   -3.982 closest distance to " CA  ASP A 298 " =    1.108
peak=   -3.982 closest distance to " N   ALA A  43 " =    2.593
peak=   -3.955 closest distance to " OD1 ASN A 148 " =    1.392
peak=   -3.932 closest distance to " O   HOH Z 211 " =    1.235
peak=   -3.914 closest distance to " CA  GLY A 241 " =    3.396
peak=   -3.907 closest distance to " CE2 TYR A  30 " =    2.764
peak=   -3.888 closest distance to " O   HOH Z 198 " =    1.935
peak=   -3.871 closest distance to " CG1 VAL A 112 " =    2.836
peak=   -3.857 closest distance to " CG2 ILE A  49 " =    2.809
peak=   -3.826 closest distance to " O   HOH Z 128 " =    2.609
peak=   -3.809 closest distance to " O   HOH Z 290 " =    1.110
peak=   -3.800 closest distance to " CG  GLU A 277 " =    1.288
peak=   -3.786 closest distance to " OG  SER A  97 " =    2.337
peak=   -3.782 closest distance to " CD1 LEU A 101 " =    2.411
peak=   -3.774 closest distance to " O   HOH Z 394 " =    1.547
peak=   -3.765 closest distance to " N   THR A  52 " =    1.618
peak=   -3.738 closest distance to " O   ILE A 109 " =    2.640
peak=   -3.734 closest distance to " O   HOH Z 216 " =    1.017
peak=   -3.732 closest distance to " CB  HIS A  86 " =    1.156
peak=   -3.731 closest distance to " CG  GLN A  11 " =    1.660
peak=   -3.724 closest distance to " CA  GLY A 241 " =    2.401
peak=   -3.719 closest distance to " O   HOH Z 166 " =    1.845
peak=   -3.715 closest distance to " OXT GLY A 302 " =    3.002
peak=   -3.714 closest distance to " OG BSER A 134 " =    1.353
peak=   -3.705 closest distance to " CG  ARG A 269 " =    2.345
peak=   -3.690 closest distance to " CE3 TRP A 150 " =    2.274
peak=   -3.687 closest distance to " O   HOH Z 374 " =    1.916
peak=   -3.682 closest distance to " SD  MET A 105 " =    1.026
peak=   -3.661 closest distance to " O   HOH Z 278 " =    1.163
peak=   -3.649 closest distance to " CZ  PHE A 155 " =    1.188
peak=   -3.625 closest distance to " CD  GLN A 223 " =    1.281
peak=   -3.623 closest distance to " O   HOH Z 193 " =    1.353
peak=   -3.620 closest distance to " O   HOH Z 106 " =    1.953
peak=   -3.619 closest distance to " O   HOH Z   6 " =    2.316
peak=   -3.612 closest distance to " CB  PHE A 192 " =    2.042
peak=   -3.612 closest distance to " O   HOH Z  38 " =    1.550
peak=   -3.609 closest distance to " NH2AARG A 275 " =    5.337
peak=   -3.603 closest distance to " O   SER A 210 " =    2.007
peak=   -3.575 closest distance to " O   HOH Z 174 " =    3.706
peak=   -3.573 closest distance to " O   HOH Z 149 " =    2.167
peak=   -3.565 closest distance to " OE1 GLN A 223 " =    2.147
peak=   -3.565 closest distance to " CD1 ILE A 151 " =    2.476
peak=   -3.552 closest distance to " CE BMET A  47 " =    1.673
peak=   -3.548 closest distance to " ND2 ASN A 249 " =    2.436
peak=   -3.545 closest distance to " O   ALA A  10 " =    1.645
peak=   -3.535 closest distance to " O   ALA A  34 " =    2.534
peak=   -3.534 closest distance to " NH2 ARG A  79 " =    1.597
peak=   -3.532 closest distance to " CA  GLY A 241 " =    3.339
peak=   -3.521 closest distance to " CB  ASN A  39 " =    2.334
peak=   -3.520 closest distance to " O   HOH Z 264 " =    1.766
peak=   -3.509 closest distance to " CB  ALA A  43 " =    2.659
peak=   -3.508 closest distance to " OH  TYR A 247 " =    2.238
peak=   -3.504 closest distance to " O   HOH Z  71 " =    2.597
peak=   -3.498 closest distance to " O   HOH Z 133 " =    1.283
peak=   -3.494 closest distance to " O   VAL A 189 " =    1.759
peak=   -3.492 closest distance to " CB  ALA A 291 " =    2.380
peak=   -3.490 closest distance to " O   HOH Z  64 " =    1.486
peak=   -3.490 closest distance to " O   HOH Z 348 " =    2.279
peak=   -3.486 closest distance to " CG1 VAL A 125 " =    1.887
peak=   -3.484 closest distance to " O   HOH Z 351 " =    1.663
peak=   -3.483 closest distance to " O   HOH Z 421 " =    3.460
peak=   -3.475 closest distance to " O   HOH Z 232 " =    1.742
peak=   -3.474 closest distance to " O   HOH Z  37 " =    1.849
peak=   -3.474 closest distance to " O   HOH Z 174 " =    2.576
peak=   -3.463 closest distance to " O   HOH Z 393 " =    1.263
peak=   -3.458 closest distance to " CD  ARG A  79 " =    1.184
peak=   -3.454 closest distance to " O   HOH Z 102 " =    1.569
peak=   -3.431 closest distance to " O   HOH Z 368 " =    1.834
peak=   -3.429 closest distance to " CG  GLU A  53 " =    1.590
peak=   -3.425 closest distance to " CB  ALA A  10 " =    2.242
peak=   -3.421 closest distance to " CG  LYS A 193 " =    2.696
peak=   -3.412 closest distance to " CG  PRO A 243 " =    1.710
peak=   -3.408 closest distance to " CG  ARG A  66 " =    2.403
peak=   -3.407 closest distance to " CG1AVAL A  41 " =    2.658
peak=   -3.399 closest distance to " CB  PHE A  16 " =    2.461
peak=   -3.385 closest distance to " O   HOH Z 429 " =    2.166
peak=   -3.383 closest distance to " ND2 ASN A  45 " =    1.214
peak=   -3.381 closest distance to " O   SER A 276 " =    1.728
peak=   -3.381 closest distance to " O   HOH Z 326 " =    4.998
peak=   -3.374 closest distance to " C   SER A 206 " =    1.426
peak=   -3.373 closest distance to " CZ3 TRP A 274 " =    2.486
peak=   -3.366 closest distance to " CB  ASP A 132 " =    2.353
peak=   -3.363 closest distance to " OD1 ASP A 171 " =    1.556
peak=   -3.362 closest distance to " CG  LEU A  83 " =    2.075
peak=   -3.358 closest distance to " C   MET A 188 " =    1.297
peak=   -3.354 closest distance to " CD  PRO A 243 " =    2.064
peak=   -3.344 closest distance to " O   HOH Z 275 " =    1.551
peak=   -3.344 closest distance to " CG2 ILE A 263 " =    2.363
peak=   -3.344 closest distance to " O   HOH Z 177 " =    1.837
peak=   -3.335 closest distance to " O   ILE A 106 " =    1.886
peak=   -3.329 closest distance to " CB  TRP A  85 " =    2.542
peak=   -3.328 closest distance to " CE  MET A 105 " =    2.305
peak=   -3.328 closest distance to " O   HOH Z 357 " =    2.136
peak=   -3.327 closest distance to " NE2 GLN A  88 " =    1.065
peak=   -3.326 closest distance to " CG  TRP A 266 " =    1.857
peak=   -3.326 closest distance to " O   HOH Z 407 " =    3.121
peak=   -3.325 closest distance to " O   HOH Z 359 " =    2.980
peak=   -3.324 closest distance to " O   HOH Z 185 " =    2.357
peak=   -3.322 closest distance to " O   HOH Z 171 " =    2.142
peak=   -3.322 closest distance to " OD1 ASN A 173 " =    1.344
peak=   -3.321 closest distance to " C   GLY A 262 " =    2.112
peak=   -3.319 closest distance to " O   HOH Z 111 " =    1.630
peak=   -3.317 closest distance to " O   HOH Z 285 " =    1.744
peak=   -3.316 closest distance to " CB  ALA A 248 " =    2.358
peak=   -3.314 closest distance to " CZ  PHE A  38 " =    2.051
peak=   -3.311 closest distance to " CD2 HIS A 207 " =    2.273
peak=   -3.309 closest distance to " NH2 ARG A 159 " =    2.293
peak=   -3.303 closest distance to " CA  GLY A 133 " =    2.336
peak=   -3.302 closest distance to " NE  ARG A  66 " =    4.249
peak=   -3.297 closest distance to " CB  ALA A 291 " =    2.122
peak=   -3.294 closest distance to " OH  TYR A 172 " =    1.870
peak=   -3.292 closest distance to " CE3 TRP A  70 " =    1.894
peak=   -3.283 closest distance to " ND2 ASN A  45 " =    1.955
peak=   -3.279 closest distance to " O   HOH Z 252 " =    3.879
peak=   -3.278 closest distance to " O   PHE A 218 " =    1.445
peak=   -3.268 closest distance to " O   PRO A 163 " =    2.006
peak=   -3.259 closest distance to " O   HOH Z 156 " =    3.525
peak=   -3.257 closest distance to " CD  GLU A 236 " =    1.127
peak=   -3.254 closest distance to " O   TYR A 186 " =    1.767
peak=   -3.253 closest distance to " O   HOH Z 179 " =    2.233
peak=   -3.250 closest distance to " CZ  ARG A 259 " =    0.945
peak=   -3.246 closest distance to " CA  GLY A 203 " =    2.435
peak=   -3.246 closest distance to " O   TRP A  70 " =    1.643
peak=   -3.245 closest distance to " ND2 ASN A  60 " =    4.130
peak=   -3.245 closest distance to " CD1 LEU A   5 " =    2.477
peak=   -3.244 closest distance to " N   THR A 264 " =    1.413
peak=   -3.240 closest distance to " O   HOH Z  19 " =    2.344
peak=   -3.240 closest distance to " ND2 ASN A  60 " =    1.294
peak=   -3.239 closest distance to " O   HOH Z 191 " =    5.949
peak=   -3.237 closest distance to " CG2 VAL A 189 " =    2.192
peak=   -3.236 closest distance to " CD1 TRP A  70 " =    1.098
peak=   -3.235 closest distance to " OD2 ASP A 191 " =    1.467
peak=   -3.233 closest distance to " C   LEU A 143 " =    1.094
peak=   -3.232 closest distance to " O   GLN A  94 " =    2.201
peak=   -3.231 closest distance to " O   HOH Z 396 " =    1.916
peak=   -3.226 closest distance to " O   SER A  62 " =    2.212
peak=   -3.224 closest distance to " CD  ARG A 139 " =    1.613
peak=   -3.222 closest distance to " C   ASN A 285 " =    2.346
peak=   -3.221 closest distance to " CH2 TRP A 150 " =    1.178
peak=   -3.221 closest distance to " O   HOH Z   6 " =    1.377
peak=   -3.217 closest distance to " CG1BVAL A  41 " =    2.675
peak=   -3.216 closest distance to " CG  GLN A  58 " =    1.107
peak=   -3.213 closest distance to " OE1 GLN A  88 " =    1.008
peak=   -3.205 closest distance to " O   ALA A 292 " =    2.149
peak=   -3.202 closest distance to " OG BSER A 210 " =    2.114
peak=   -3.200 closest distance to " CG  GLN A 103 " =    2.487
peak=   -3.196 closest distance to " CG  PHE A 283 " =    2.587
peak=   -3.193 closest distance to " O   TYR A 247 " =    2.833
peak=   -3.186 closest distance to " CB  ALA A 100 " =    2.220
peak=   -3.186 closest distance to " OE1 GLU A  44 " =    0.892
peak=   -3.176 closest distance to " O   HOH Z 139 " =    5.009
peak=   -3.175 closest distance to " ND2 ASN A 187 " =    1.669
peak=   -3.175 closest distance to " O   HOH Z 372 " =    2.382
peak=   -3.174 closest distance to " OG1 THR A  82 " =    1.306
peak=   -3.167 closest distance to " O   SER A 135 " =    1.454
peak=   -3.157 closest distance to " OD2 ASP A 171 " =    1.884
peak=   -3.154 closest distance to " O   GLN A 240 " =    2.631
peak=   -3.151 closest distance to " CD2 LEU A 222 " =    2.180
peak=   -3.142 closest distance to " CZ  TYR A 169 " =    1.815
peak=   -3.139 closest distance to " O   HOH Z 435 " =    2.858
peak=   -3.131 closest distance to " O   HOH Z 234 " =    4.403
peak=   -3.126 closest distance to " O   HOH Z  52 " =    1.666
peak=   -3.120 closest distance to " SG BCYS A 201 " =    1.129
peak=   -3.116 closest distance to " O   HOH Z 166 " =    1.779
peak=   -3.104 closest distance to " O   GLY A 211 " =    1.298
peak=   -3.100 closest distance to " N   ALA A 226 " =    2.051
peak=   -3.089 closest distance to " O   ALA A 227 " =    1.495
peak=   -3.088 closest distance to " CD1 PHE A  59 " =    2.063
peak=   -3.085 closest distance to " C   LEU A 222 " =    1.020
peak=   -3.078 closest distance to " C   PHE A  59 " =    1.290
peak=   -3.078 closest distance to " O   ARG A  24 " =    1.653
peak=   -3.072 closest distance to " ND2 ASN A  45 " =    1.316
peak=   -3.064 closest distance to " O   HOH Z 236 " =    1.515
peak=   -3.029 closest distance to " OG BSER A 134 " =    2.037
peak=   -3.019 closest distance to " N   SER A 276 " =    1.347

================= 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    :  0.4054 0.3997   6.206924e+00   6.188159e+00
   1_bss:  0.3913 0.3869   6.189443e+00   6.169934e+00
   1_xyz:  0.2391 0.2675   5.767239e+00   5.861602e+00
   1_adp:  0.2157 0.2727   5.710517e+00   5.879422e+00
   1_occ:  0.2153 0.2730   5.711122e+00   5.881337e+00
   2_bss:  0.2113 0.2707   5.700561e+00   5.874583e+00
   2_xyz:  0.1560 0.2018   5.421194e+00   5.625604e+00
   2_adp:  0.1446 0.1882   5.354339e+00   5.558741e+00
   2_occ:  0.1444 0.1880   5.353519e+00   5.558380e+00
   3_bss:  0.1442 0.1875   5.351150e+00   5.555008e+00
   3_xyz:  0.1234 0.1683   5.225220e+00   5.452726e+00
   3_adp:  0.1195 0.1658   5.203112e+00   5.436194e+00
   3_occ:  0.1194 0.1659   5.202925e+00   5.436267e+00
   4_bss:  0.1193 0.1655   5.200803e+00   5.434202e+00
   4_xyz:  0.1194 0.1642   5.201254e+00   5.430940e+00
   4_adp:  0.1186 0.1643   5.197954e+00   5.431030e+00
   4_occ:  0.1185 0.1642   5.197724e+00   5.430976e+00
   5_bss:  0.1184 0.1641   5.197798e+00   5.431115e+00
   5_xyz:  0.1180 0.1650   5.199252e+00   5.436409e+00
   5_adp:  0.1180 0.1646   5.197987e+00   5.434318e+00
   5_occ:  0.1179 0.1646   5.198010e+00   5.434516e+00
   5_bss:  0.1179 0.1644   5.198124e+00   5.434592e+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:  0.308  55.399  -3.631  -0.333   5.511  -0.000   0.000   0.000
   1_xyz:  0.308  55.399  -3.631  -0.333   5.511  -0.000   0.000   0.000
   1_adp:  0.308  55.399  -3.631  -0.333   5.511  -0.000   0.000   0.000
   1_occ:  0.308  55.399  -3.631  -0.333   5.511  -0.000   0.000   0.000
   2_bss:  0.343  84.756  -2.871  -1.236   1.417  -0.000   0.000   0.000
   2_xyz:  0.343  84.756  -2.871  -1.236   1.417  -0.000   0.000   0.000
   2_adp:  0.343  84.756  -2.871  -1.236   1.417  -0.000   0.000   0.000
   2_occ:  0.343  84.756  -2.871  -1.236   1.417  -0.000   0.000   0.000
   3_bss:  0.340  80.538  -2.553  -1.505   0.440  -0.000   0.000   0.000
   3_xyz:  0.340  80.538  -2.553  -1.505   0.440  -0.000   0.000   0.000
   3_adp:  0.340  80.538  -2.553  -1.505   0.440  -0.000   0.000   0.000
   3_occ:  0.340  80.538  -2.553  -1.505   0.440  -0.000   0.000   0.000
   4_bss:  0.329  69.601  -2.425  -1.653   0.036  -0.000   0.000   0.000
   4_xyz:  0.329  69.601  -2.425  -1.653   0.036  -0.000   0.000   0.000
   4_adp:  0.329  69.601  -2.425  -1.653   0.036  -0.000   0.000   0.000
   4_occ:  0.329  69.601  -2.425  -1.653   0.036  -0.000   0.000   0.000
   5_bss:  0.329  69.601  -2.189  -1.512   0.074  -0.000   0.000   0.000
   5_xyz:  0.329  69.601  -2.189  -1.512   0.074  -0.000   0.000   0.000
   5_adp:  0.329  69.601  -2.189  -1.512   0.074  -0.000   0.000   0.000
   5_occ:  0.329  69.601  -2.189  -1.512   0.074  -0.000   0.000   0.000
   5_bss:  0.329  69.604  -1.984  -1.346   0.209  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.053 0.5831  0.7350    47571.836
   1_bss:  43.751 0.5976  0.7693    44372.171
   1_xyz:  26.978 0.7912  0.9670    18624.359
   1_adp:  27.789 0.7816  0.9571    19507.354
   1_occ:  27.890 0.7806  0.9555    19620.312
   2_bss:  27.227 0.7881  0.9214    19165.153
   2_xyz:  19.726 0.8637  0.9714    10576.803
   2_adp:  17.907 0.8814  0.9699     9267.731
   2_occ:  17.893 0.8815  0.9700     9257.130
   3_bss:  17.772 0.8826  0.9610     9176.633
   3_xyz:  15.497 0.9024  0.9740     7338.158
   3_adp:  15.043 0.9067  0.9680     7103.911
   3_occ:  15.038 0.9067  0.9680     7101.186
   4_bss:  15.000 0.9070  0.9635     7056.181
   4_xyz:  14.835 0.9086  0.9635     6951.493
   4_adp:  14.817 0.9089  0.9556     6957.054
   4_occ:  14.815 0.9089  0.9556     6955.382
   5_bss:  14.816 0.9089  0.9603     6958.068
   5_xyz:  14.904 0.9082  0.9605     7030.232
   5_adp:  14.861 0.9085  0.9533     7002.881
   5_occ:  14.863 0.9085  0.9531     7003.500
   5_bss:  14.866 0.9085  0.9589     7005.632
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.7093e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.7093e-01
   1_xyz:   1.470  0.012  0.090 15.775  0.006  4.118   1.1684e-01
   1_adp:   1.470  0.012  0.090 15.775  0.006  4.118   1.1684e-01
   1_occ:   1.470  0.012  0.090 15.775  0.006  4.118   1.1684e-01
   2_bss:   1.470  0.012  0.090 15.775  0.006  4.118   1.1684e-01
   2_xyz:   1.109  0.008  0.079 15.166  0.005  4.112   7.0753e-02
   2_adp:   1.109  0.008  0.079 15.166  0.005  4.112   7.0753e-02
   2_occ:   1.109  0.008  0.079 15.166  0.005  4.112   7.0753e-02
   3_bss:   1.109  0.008  0.079 15.166  0.005  4.112   7.0753e-02
   3_xyz:   1.144  0.011  0.085 15.074  0.004  4.125   7.9768e-02
   3_adp:   1.144  0.011  0.085 15.074  0.004  4.125   7.9768e-02
   3_occ:   1.144  0.011  0.085 15.074  0.004  4.125   7.9768e-02
   4_bss:   1.144  0.011  0.085 15.074  0.004  4.125   7.9768e-02
   4_xyz:   0.997  0.008  0.076 14.732  0.003  4.127   6.0898e-02
   4_adp:   0.997  0.008  0.076 14.732  0.003  4.127   6.0898e-02
   4_occ:   0.997  0.008  0.076 14.732  0.003  4.127   6.0898e-02
   5_bss:   0.997  0.008  0.076 14.732  0.003  4.127   6.0898e-02
   5_xyz:   0.982  0.008  0.075 14.595  0.003  4.130   5.7336e-02
   5_adp:   0.982  0.008  0.075 14.595  0.003  4.130   5.7336e-02
   5_occ:   0.982  0.008  0.075 14.595  0.003  4.130   5.7336e-02
   5_bss:   0.982  0.008  0.075 14.595  0.003  4.130   5.7336e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.409   2.4461e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.409   2.4461e-01
   1_xyz:   9.420  0.106  0.326 82.682  0.050  2.019   1.2591e-01
   1_adp:   9.420  0.106  0.326 82.682  0.050  2.019   1.2591e-01
   1_occ:   9.420  0.106  0.326 82.682  0.050  2.019   1.2591e-01
   2_bss:   9.420  0.106  0.326 82.682  0.050  2.019   1.2591e-01
   2_xyz:   7.428  0.039  0.245 84.797  0.058  2.288   5.5631e-02
   2_adp:   7.428  0.039  0.245 84.797  0.058  2.288   5.5631e-02
   2_occ:   7.428  0.039  0.245 84.797  0.058  2.288   5.5631e-02
   3_bss:   7.428  0.039  0.245 84.797  0.058  2.288   5.5631e-02
   3_xyz:   7.969  0.077  0.282 84.027  0.042  2.319   6.4716e-02
   3_adp:   7.969  0.077  0.282 84.027  0.042  2.319   6.4716e-02
   3_occ:   7.969  0.077  0.282 84.027  0.042  2.319   6.4716e-02
   4_bss:   7.969  0.077  0.282 84.027  0.042  2.319   6.4716e-02
   4_xyz:   6.967  0.050  0.239 81.306  0.036  2.420   4.0405e-02
   4_adp:   6.967  0.050  0.239 81.306  0.036  2.420   4.0405e-02
   4_occ:   6.967  0.050  0.239 81.306  0.036  2.420   4.0405e-02
   5_bss:   6.967  0.050  0.239 81.306  0.036  2.420   4.0405e-02
   5_xyz:   7.033  0.043  0.230 82.036  0.034  2.422   3.0761e-02
   5_adp:   7.033  0.043  0.230 82.036  0.034  2.422   3.0761e-02
   5_occ:   7.033  0.043  0.230 82.036  0.034  2.422   3.0761e-02
   5_bss:   7.033  0.043  0.230 82.036  0.034  2.422   3.0761e-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:  90.72   0.00  17.81  80.29   0.00  13.35  90.72   3.33  42.12
   1_occ:  90.72   0.00  17.81  80.29   0.00  13.35  90.72   3.33  42.12
   2_bss:  90.72   0.00  17.81  80.29   0.00  13.35  90.72   3.33  42.12
   2_xyz:  90.72   0.00  17.81  80.29   0.00  13.35  90.72   3.33  42.12
   2_adp:  90.39   0.91  17.26  78.27   0.91  12.81  90.39   4.69  41.45
   2_occ:  90.39   0.91  17.26  78.27   0.91  12.81  90.39   4.69  41.45
   3_bss:  90.39   0.91  17.26  78.27   0.91  12.81  90.39   4.69  41.45
   3_xyz:  90.39   0.91  17.26  78.27   0.91  12.81  90.39   4.69  41.45
   3_adp:  92.18   0.00  17.02  81.36   0.00  12.58  92.18   1.41  41.19
   3_occ:  92.18   0.00  17.02  81.36   0.00  12.58  92.18   1.41  41.19
   4_bss:  92.18   0.00  17.02  81.36   0.00  12.58  92.18   1.41  41.19
   4_xyz:  92.18   0.00  17.02  81.36   0.00  12.58  92.18   1.41  41.19
   4_adp:  95.93   0.00  16.85  86.03   0.00  12.44  95.93   1.06  40.84
   4_occ:  95.93   0.00  16.85  86.03   0.00  12.44  95.93   1.06  40.84
   5_bss:  95.93   0.00  16.85  86.03   0.00  12.44  95.93   1.06  40.84
   5_xyz:  95.93   0.00  16.85  86.03   0.00  12.44  95.93   1.06  40.84
   5_adp:  96.16   0.00  16.53  86.88   0.00  12.22  96.16   2.97  40.01
   5_occ:  96.16   0.00  16.53  86.88   0.00  12.22  96.16   2.97  40.01
   5_bss:  96.16   0.00  16.54  86.88   0.00  12.23  96.16   2.97  40.02
------------------------------------------------------------------------
 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:    1.517    0.028    0.445
   1_adp:    1.517    0.028    0.445
   1_occ:    1.517    0.028    0.445
   2_bss:    1.517    0.028    0.445
   2_xyz:    1.282    0.041    0.524
   2_adp:    1.282    0.041    0.524
   2_occ:    1.282    0.041    0.524
   3_bss:    1.282    0.041    0.524
   3_xyz:    1.151    0.067    0.581
   3_adp:    1.151    0.067    0.581
   3_occ:    1.151    0.067    0.581
   4_bss:    1.151    0.067    0.581
   4_xyz:    1.273    0.051    0.590
   4_adp:    1.273    0.051    0.590
   4_occ:    1.273    0.051    0.590
   5_bss:    1.273    0.051    0.590
   5_xyz:    1.410    0.038    0.599
   5_adp:    1.410    0.038    0.599
   5_occ:    1.410    0.038    0.599
   5_bss:    1.410    0.038    0.599
------------------------------------------------------------------------

CPU time actual refinement: 332.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_692/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_692/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_692/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_692/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_692/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.36 
  Macro-tasks:
    bulk solvent and scale       = 49.47  
    individual site refinement   = 135.28 
    weights calculation          = 28.66  
    collect and process          = 6.51   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 220.01 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 100.96 
    alpha_beta                      = 8.01   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 110.94 
    fmodel                         = 7.94   
    r_factors                      = 0.21   
    phase_errors                   = 11.04  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 242.23 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.644 micro seconds
Total CPU time: 5.77 minutes
from_scatterers_fft:    648 calls, 100.61 s
gradients_fft:          593 calls,  96.97 s

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

# Date 2008-01-16 Time 05:25:31 PST -0800 (1200489931.31 s)
Start R-work = 0.4054, R-free = 0.3997 (no bulk solvent and anisotropic scale)
Final R-work = 0.1375, R-free = 0.1804 (no bulk solvent and anisotropic scale)

Start R-work = 0.3913, R-free = 0.3869
Final R-work = 0.1179, R-free = 0.1644