# Date 2008-01-16 Time 06:17:29 PST -0800 (1200493049.26 s)
#phil __OFF__

Command line arguments: "../1086.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30243
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1086

-------------------------------------------------------------------------------
  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: (71.3037, 48.1033, 87.6859, 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: 3.24, per 1000 atoms: 1.15


================================== 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: (71.3037, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.03046
Completeness in resolution range: 0.976959
Completeness with d_max=infinity: 0.97385

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2189
                             d_min =   2.0305

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: (71.3037, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.03046
Completeness in resolution range: 0.976959
Completeness with d_max=infinity: 0.97385

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2193 -  4.3438 [2103/2130]  1893   210  10.0%
  bin  2:  4.3438 -  3.4611 [2027/2043]  1824   203  10.0%
  bin  3:  3.4611 -  3.0275 [1992/2011]  1791   201  10.1%
  bin  4:  3.0275 -  2.7525 [1976/2006]  1783   193   9.8%
  bin  5:  2.7525 -  2.5562 [1963/1982]  1764   199  10.1%
  bin  6:  2.5562 -  2.4061 [1954/1979]  1756   198  10.1%
  bin  7:  2.4061 -  2.2860 [1952/1985]  1764   188   9.6%
  bin  8:  2.2860 -  2.1868 [1939/1970]  1742   197  10.2%
  bin  9:  2.1868 -  2.1029 [1923/1965]  1728   195  10.1%
  bin 10:  2.1029 -  2.0305 [1760/1980]  1585   175   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1086/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:
        1.48 -     2.17: 4
        2.17 -     2.85: 1050
        2.85 -     3.53: 4287
        3.53 -     4.22: 9035
        4.22 -     4.90: 13187
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.484 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.728 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.073 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A 245 " - " O   HOH Z 202 "  2.178 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27558 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_1086/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1086/model_refine_001.geo

CPU time processing inputs: 8.97


============================ 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 = 71.30375 48.10325 87.68585 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: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4734   r_free= 0.4559   ksol= 0.00   Bsol= 0.00   scale= 0.865    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.282266                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8444 0.99   1373  153 0.3736 0.3820      6.5569      6.5252|
|  2:  4.8444 -  3.8659 0.99   1308  145 0.4190 0.4338      6.8671      6.8747|
|  3:  3.8659 -  3.3833 0.99   1294  144 0.4546 0.3957      6.7234      6.6307|
|  4:  3.3833 -  3.0768 0.99   1286  139 0.4691 0.4590      6.5575      6.4907|
|  5:  3.0768 -  2.8578 0.99   1262  142 0.4991 0.4444      6.3816      6.3642|
|  6:  2.8578 -  2.6903 0.99   1273  144 0.4988 0.4937      6.2844       6.255|
|  7:  2.6903 -  2.5562 0.99   1259  139 0.5086 0.4411      6.2447      6.1448|
|  8:  2.5562 -  2.4454 0.98   1257  142 0.5055 0.4634       6.189      6.1833|
|  9:  2.4454 -  2.3516 0.98   1253  136 0.5141 0.5091      6.1182      6.1704|
| 10:  2.3516 -  2.2707 0.99   1246  138 0.5154 0.4836      6.1161      6.0733|
| 11:  2.2707 -  2.2000 0.99   1258  143 0.5201 0.5141      6.0462      6.0965|
| 12:  2.2000 -  2.1372 0.97   1244  132 0.5273 0.5239      5.9942      6.0193|
| 13:  2.1372 -  2.0811 0.99   1233  137 0.5088 0.5008      5.8915      5.8712|
| 14:  2.0811 -  2.0305 0.85   1084  125 0.5120 0.5273      5.8389      5.7684|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8444  1373   153  0.70  34.38   0.81     0.74      72949.64|
|  2:  4.8444 -  3.8659  1308   145  0.71  34.23   0.88     0.79     100970.38|
|  3:  3.8659 -  3.3833  1294   144  0.63  41.62   0.86     0.76     106357.31|
|  4:  3.3833 -  3.0768  1286   139  0.54  49.06   0.87     0.68      97403.64|
|  5:  3.0768 -  2.8578  1262   142  0.46  55.46   0.86     0.61      76610.10|
|  6:  2.8578 -  2.6903  1273   144  0.44  56.91   0.86     0.57      65644.50|
|  7:  2.6903 -  2.5562  1259   139  0.43  57.71   0.89     0.56      57102.03|
|  8:  2.5562 -  2.4454  1257   142  0.42  58.31   0.88     0.56      54733.11|
|  9:  2.4454 -  2.3516  1253   136  0.40  59.91   0.88     0.56      50804.49|
| 10:  2.3516 -  2.2707  1246   138  0.41  59.51   0.90     0.56      46997.72|
| 11:  2.2707 -  2.2000  1258   143  0.37  62.03   0.90     0.54      44861.84|
| 12:  2.2000 -  2.1372  1244   132  0.35  63.97   0.90     0.51      42822.02|
| 13:  2.1372 -  2.0811  1233   137  0.31  66.52   0.89     0.45      38206.16|
| 14:  2.0811 -  2.0305  1084   125  0.30  67.34   0.89     0.40      30886.58|
|alpha:            min =        0.40 max =            0.79 mean =         0.60|
|beta:             min =    30886.58 max =       106357.31 mean =     64014.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.40|
|phase err.(test): min =        0.00 max =           89.77 mean =        54.50|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.976110             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.082   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.608831              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.616   (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 |  1.484 -  1.825:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.825 -  2.167:        1 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.167 -  2.509:       15 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.509 -  2.850:     1035 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.850 -  3.192:     1921 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.192 -  3.533:     2366 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.533 -  3.875:     4538 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.875 -  4.217:     4497 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.217 -  4.558:     5960 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.558 -  4.900:     7227 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.484 |       0.204 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.529)------------------------------------------|
|    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: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4734   r_free= 0.4559   ksol= 0.00   Bsol= 0.00   scale= 0.865    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.282266                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4671   r_free= 0.4482   ksol= 0.28   Bsol= 57.40   scale= 0.905   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,3.90,0.74,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.277995                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.523556              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.767   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.210896              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.356   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4671      final r-factor (work) = 0.3738          |
| start r-factor (free) = 0.4482      final r-factor (free) = 0.4052          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.0473 = 9.52 * 0.50 * 6.2749 + 1.00 * 0.1677                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.4999 = 9.52 * 0.50 * 6.1682 + 1.00 * 0.1284                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3738      final r-factor (work) = 0.3418          |
| start r-factor (free) = 0.4052      final r-factor (free) = 0.4133          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4750 = 1.21 * 1.00 * 6.1682 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3981 = 1.21 * 1.00 * 6.0916 + 1.00 * 0.0218                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.26  19.00    None  None   None       |
|    all(noH): 2823   0      0.00    114.26  19.00    None  None   None       |
|    Sol.    : 438    0      0.00    114.26  37.59    None  None   None       |
|    Mac.    : 2385   0      0.00    92.09   15.58    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 -  11.426: 1081   |   5:    57.129 -  68.555:   59        |
|      1:    11.426 -  22.852:  892   |   6:    68.555 -  79.980:   26        |
|      2:    22.852 -  34.277:  447   |   7:    79.980 -  91.406:    6        |
|      3:    34.277 -  45.703:  207   |   8:    91.406 - 102.832:    5        |
|      4:    45.703 -  57.129:   99   |   9:   102.832 - 114.258:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3418 r_free = 0.4133             target_work(ml) = 6.097         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3414 r_free = 0.4127             target_work(ml) = 6.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3414   r_free= 0.4127   ksol= 0.28   Bsol= 57.40   scale= 0.976   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,3.90,0.74,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.096513                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3414   r_free= 0.4115   ksol= 0.31   Bsol= 66.98   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,2.71,0.92,0.00,0.00,0.00); trace/3= 0.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.098293                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.545229              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.965   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.642636              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.704  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3414      final r-factor (work) = 0.2977          |
| start r-factor (free) = 0.4115      final r-factor (free) = 0.3611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0712 = 6.55 * 0.50 * 6.0938 + 1.00 * 0.1284                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8594 = 6.55 * 0.50 * 6.0442 + 1.00 * 0.0789                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2977      final r-factor (work) = 0.2930          |
| start r-factor (free) = 0.3611      final r-factor (free) = 0.3582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9061 = 0.64 * 1.00 * 6.0442 + 1.00 * 0.0218                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8849 = 0.64 * 1.00 * 5.9876 + 1.00 * 0.0371                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.25  18.96    None  None   None       |
|    all(noH): 2823   0      0.00    114.25  18.96    None  None   None       |
|    Sol.    : 438    0      0.00    114.25  37.44    None  None   None       |
|    Mac.    : 2385   0      0.00    91.94   15.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.425: 1060   |   5:    57.124 -  68.549:   53        |
|      1:    11.425 -  22.850:  942   |   6:    68.549 -  79.973:   26        |
|      2:    22.850 -  34.274:  442   |   7:    79.973 -  91.398:    7        |
|      3:    34.274 -  45.699:  191   |   8:    91.398 - 102.823:    5        |
|      4:    45.699 -  57.124:   96   |   9:   102.823 - 114.248:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2930 r_free = 0.3582             target_work(ml) = 5.987         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2930 r_free = 0.3580             target_work(ml) = 5.986         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2930   r_free= 0.3580   ksol= 0.31   Bsol= 66.98   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,2.71,0.92,0.00,0.00,0.00); trace/3= 0.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.986125                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2933   r_free= 0.3581   ksol= 0.32   Bsol= 66.98   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,2.29,0.74,0.00,0.00,0.00); trace/3= 0.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.987431                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.065457             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.433  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.206494              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.169   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2933      final r-factor (work) = 0.2289          |
| start r-factor (free) = 0.3581      final r-factor (free) = 0.2842          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2014 = 12.07 * 0.50 * 5.9877 + 1.00 * 0.0794                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.6379 = 12.07 * 0.50 * 5.8864 + 1.00 * 0.1268                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2289      final r-factor (work) = 0.1957          |
| start r-factor (free) = 0.2842      final r-factor (free) = 0.2519          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2014 = 1.21 * 1.00 * 5.8864 + 1.00 * 0.0995                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8675 = 1.21 * 1.00 * 5.6788 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.91  17.97    None  None   None       |
|    all(noH): 2823   0      0.00    113.91  17.97    None  None   None       |
|    Sol.    : 438    0      2.62    113.91  42.71    None  None   None       |
|    Mac.    : 2385   0      0.00    92.91   13.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.391: 1341   |   5:    56.953 -  68.344:   74        |
|      1:    11.391 -  22.781:  791   |   6:    68.344 -  79.735:   28        |
|      2:    22.781 -  34.172:  261   |   7:    79.735 -  91.126:    9        |
|      3:    34.172 -  45.563:  193   |   8:    91.126 - 102.516:    5        |
|      4:    45.563 -  56.953:  120   |   9:   102.516 - 113.907:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1957 r_free = 0.2519             target_work(ml) = 5.624         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1955 r_free = 0.2518             target_work(ml) = 5.623         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1955   r_free= 0.2518   ksol= 0.32   Bsol= 66.98   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,2.29,0.74,0.00,0.00,0.00); trace/3= 0.82                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.623322                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1951   r_free= 0.2511   ksol= 0.33   Bsol= 78.72   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.81,0.45,0.00,0.00,0.00); trace/3= 0.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.621513                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.423576              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.838   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.067057              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.931  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1951      final r-factor (work) = 0.1621          |
| start r-factor (free) = 0.2511      final r-factor (free) = 0.2112          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6896 = 4.42 * 0.50 * 5.6799 + 1.00 * 0.1268                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3487 = 4.42 * 0.50 * 5.5464 + 1.00 * 0.0811                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1621      final r-factor (work) = 0.1481          |
| start r-factor (free) = 0.2112      final r-factor (free) = 0.2026          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.0272 = 3.07 * 1.00 * 5.5464 + 1.00 * 0.0159                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.6372 = 3.07 * 1.00 * 5.4187 + 1.00 * 0.0179                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.70  17.91    None  None   None       |
|    all(noH): 2823   0      0.00    114.70  17.91    None  None   None       |
|    Sol.    : 438    0      3.71    114.70  47.55    None  None   None       |
|    Mac.    : 2385   0      0.00    105.59  12.47    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.470: 1491   |   5:    57.349 -  68.818:   86        |
|      1:    11.470 -  22.939:  740   |   6:    68.818 -  80.288:   70        |
|      2:    22.939 -  34.409:  185   |   7:    80.288 -  91.758:   24        |
|      3:    34.409 -  45.879:  122   |   8:    91.758 - 103.227:    8        |
|      4:    45.879 -  57.349:   91   |   9:   103.227 - 114.697:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1481 r_free = 0.2026             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1481 r_free = 0.2025             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1481   r_free= 0.2025   ksol= 0.33   Bsol= 78.72   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.81,0.45,0.00,0.00,0.00); trace/3= 0.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.390817                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1485   r_free= 0.2031   ksol= 0.34   Bsol= 87.35   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,0.46,0.65,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.392364                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.424570              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.171  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.319496              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.080  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1485      final r-factor (work) = 0.1373          |
| start r-factor (free) = 0.2031      final r-factor (free) = 0.1903          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6506 = 2.42 * 0.50 * 5.4191 + 1.00 * 0.0811                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5650 = 2.42 * 0.50 * 5.3606 + 1.00 * 0.0665                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1373      final r-factor (work) = 0.1354          |
| start r-factor (free) = 0.1903      final r-factor (free) = 0.1833          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7303 = 0.32 * 1.00 * 5.3606 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7139 = 0.32 * 1.00 * 5.3243 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.74  16.64    None  None   None       |
|    all(noH): 2823   0      0.00    111.74  16.64    None  None   None       |
|    Sol.    : 438    0      3.90    111.74  43.93    None  None   None       |
|    Mac.    : 2385   0      0.00    101.64  11.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.174: 1544   |   5:    55.868 -  67.041:   68        |
|      1:    11.174 -  22.347:  747   |   6:    67.041 -  78.215:   50        |
|      2:    22.347 -  33.521:  164   |   7:    78.215 -  89.389:   26        |
|      3:    33.521 -  44.694:  112   |   8:    89.389 - 100.562:    5        |
|      4:    44.694 -  55.868:  102   |   9:   100.562 - 111.736:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1354 r_free = 0.1833             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1352 r_free = 0.1834             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1834   ksol= 0.34   Bsol= 87.35   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,0.46,0.65,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.304521                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8444 0.99   1373  153 0.1064 0.1403      5.4609      5.5957|
|  2:  4.8444 -  3.8659 0.99   1308  145 0.0926 0.1103      5.5094      5.6663|
|  3:  3.8659 -  3.3833 0.99   1294  144 0.1179 0.1679      5.5794        5.97|
|  4:  3.3833 -  3.0768 0.99   1286  139 0.1432 0.1915      5.6022      5.7684|
|  5:  3.0768 -  2.8578 0.99   1262  142 0.1653 0.1995      5.5309      5.6796|
|  6:  2.8578 -  2.6903 0.99   1273  144 0.1599 0.2269      5.4252       5.662|
|  7:  2.6903 -  2.5562 0.99   1259  139 0.1567 0.1961      5.3605      5.5407|
|  8:  2.5562 -  2.4454 0.98   1257  142 0.1488 0.2105      5.2753      5.5385|
|  9:  2.4454 -  2.3516 0.98   1253  136 0.1516 0.2028      5.2254      5.4292|
| 10:  2.3516 -  2.2707 0.99   1246  138 0.1456 0.2160      5.1745      5.4114|
| 11:  2.2707 -  2.2000 0.99   1258  143 0.1439 0.2073      5.1253      5.3807|
| 12:  2.2000 -  2.1372 0.97   1244  132 0.1371 0.1988       5.055      5.3868|
| 13:  2.1372 -  2.0811 0.99   1233  137 0.1438 0.2023      4.9802      5.1841|
| 14:  2.0811 -  2.0305 0.85   1084  125 0.1364 0.2062      4.8456      5.1134|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8444  1373   153  0.93  10.42   0.95     0.92       8584.09|
|  2:  4.8444 -  3.8659  1308   145  0.94   9.22   0.99     0.98      10544.88|
|  3:  3.8659 -  3.3833  1294   144  0.92  12.94   1.01     1.00      12771.09|
|  4:  3.3833 -  3.0768  1286   139  0.90  15.92   1.00     0.97      13386.51|
|  5:  3.0768 -  2.8578  1262   142  0.87  19.49   1.00     0.98      12429.47|
|  6:  2.8578 -  2.6903  1273   144  0.87  19.60   0.98     0.94      10131.38|
|  7:  2.6903 -  2.5562  1259   139  0.87  19.47   0.99     0.96       9203.62|
|  8:  2.5562 -  2.4454  1257   142  0.88  18.62   0.98     0.94       7826.92|
|  9:  2.4454 -  2.3516  1253   136  0.87  19.19   0.98     0.93       7009.75|
| 10:  2.3516 -  2.2707  1246   138  0.87  19.47   0.98     0.93       6470.11|
| 11:  2.2707 -  2.2000  1258   143  0.87  19.81   0.98     0.92       6109.82|
| 12:  2.2000 -  2.1372  1244   132  0.88  18.66   0.98     0.96       5641.00|
| 13:  2.1372 -  2.0811  1233   137  0.88  18.52   0.97     0.95       4619.57|
| 14:  2.0811 -  2.0305  1084   125  0.89  17.90   0.94     0.90       3443.65|
|alpha:            min =        0.90 max =            1.00 mean =         0.95|
|beta:             min =     3443.65 max =        13386.51 mean =      8525.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.94 mean =        17.00|
|phase err.(test): min =        0.00 max =           89.73 mean =        16.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1351   r_free= 0.1834   ksol= 0.33   Bsol= 80.14   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.15,0.67,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.304321                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1351   r_free= 0.1834   ksol= 0.33   Bsol= 80.14   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,0.15,0.67,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.304321                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8444 0.99   1373  153 0.1060 0.1405      5.4597      5.5956|
|  2:  4.8444 -  3.8659 0.99   1308  145 0.0924 0.1095      5.5072      5.6618|
|  3:  3.8659 -  3.3833 0.99   1294  144 0.1179 0.1679      5.5785      5.9702|
|  4:  3.3833 -  3.0768 0.99   1286  139 0.1434 0.1916      5.6031      5.7689|
|  5:  3.0768 -  2.8578 0.99   1262  142 0.1655 0.2001      5.5321       5.681|
|  6:  2.8578 -  2.6903 0.99   1273  144 0.1599 0.2263      5.4255      5.6605|
|  7:  2.6903 -  2.5562 0.99   1259  139 0.1567 0.1963      5.3607      5.5414|
|  8:  2.5562 -  2.4454 0.98   1257  142 0.1488 0.2110      5.2756      5.5391|
|  9:  2.4454 -  2.3516 0.98   1253  136 0.1514 0.2025      5.2253       5.429|
| 10:  2.3516 -  2.2707 0.99   1246  138 0.1455 0.2167      5.1747      5.4119|
| 11:  2.2707 -  2.2000 0.99   1258  143 0.1437 0.2076      5.1252      5.3818|
| 12:  2.2000 -  2.1372 0.97   1244  132 0.1368 0.1993       5.055      5.3878|
| 13:  2.1372 -  2.0811 0.99   1233  137 0.1441 0.2019        4.98      5.1833|
| 14:  2.0811 -  2.0305 0.85   1084  125 0.1365 0.2059      4.8446       5.112|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8444  1373   153  0.93  10.43   0.95     0.92       8592.88|
|  2:  4.8444 -  3.8659  1308   145  0.94   9.21   1.00     0.98      10505.59|
|  3:  3.8659 -  3.3833  1294   144  0.92  12.89   1.01     1.00      12715.80|
|  4:  3.3833 -  3.0768  1286   139  0.90  15.93   1.00     0.97      13397.86|
|  5:  3.0768 -  2.8578  1262   142  0.87  19.50   1.00     0.98      12444.21|
|  6:  2.8578 -  2.6903  1273   144  0.87  19.60   0.98     0.94      10142.34|
|  7:  2.6903 -  2.5562  1259   139  0.87  19.46   0.99     0.96       9200.89|
|  8:  2.5562 -  2.4454  1257   142  0.88  18.63   0.98     0.94       7834.75|
|  9:  2.4454 -  2.3516  1253   136  0.87  19.20   0.99     0.93       7011.62|
| 10:  2.3516 -  2.2707  1246   138  0.87  19.49   0.98     0.93       6480.02|
| 11:  2.2707 -  2.2000  1258   143  0.87  19.82   0.98     0.92       6119.21|
| 12:  2.2000 -  2.1372  1244   132  0.88  18.67   0.98     0.96       5648.12|
| 13:  2.1372 -  2.0811  1233   137  0.88  18.50   0.97     0.95       4612.55|
| 14:  2.0811 -  2.0305  1084   125  0.89  17.87   0.94     0.90       3430.60|
|alpha:            min =        0.90 max =            1.00 mean =         0.95|
|beta:             min =     3430.60 max =        13397.86 mean =      8523.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.00|
|phase err.(test): min =        0.00 max =           89.64 mean =        16.19|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.529)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.14    111.87  16.78    None  None   None       |
|    all(noH): 2823   0      0.14    111.87  16.78    None  None   None       |
|    Sol.    : 438    0      4.03    111.87  44.06    None  None   None       |
|    Mac.    : 2385   0      0.14    101.77  11.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.135 -  11.309: 1544   |   5:    56.003 -  67.177:   68        |
|      1:    11.309 -  22.482:  747   |   6:    67.177 -  78.350:   50        |
|      2:    22.482 -  33.656:  164   |   7:    78.350 -  89.524:   26        |
|      3:    33.656 -  44.829:  112   |   8:    89.524 - 100.697:    5        |
|      4:    44.829 -  56.003:  102   |   9:   100.697 - 111.871:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.604 - 5.966
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 339
   mapped sites are within: 0.739 - 5.966

peak=    8.212 closest distance to " O   HOH Z 400 " =    1.043
peak=    5.956 closest distance to " O   HOH Z 210 " =    1.470
peak=    5.537 closest distance to " O   GLN A  11 " =    1.003
peak=    5.242 closest distance to " O   HOH Z 111 " =    2.094
peak=    5.214 closest distance to " CB  SER A  63 " =    1.308
peak=    5.173 closest distance to " CB  GLN A 223 " =    1.455
peak=    4.980 closest distance to " O   HOH Z  54 " =    1.394
peak=    4.975 closest distance to " CG  PRO A  54 " =    1.420
peak=    4.793 closest distance to " O   HOH Z 117 " =    1.359
peak=    4.652 closest distance to " O   HOH Z 139 " =    1.497
peak=    4.644 closest distance to " O   HOH Z 425 " =    1.781
peak=    4.614 closest distance to " O   HOH Z 412 " =    3.430
peak=    4.552 closest distance to " O   HOH Z  49 " =    1.338
peak=    4.476 closest distance to " CB  GLN A 183 " =    1.206
peak=    4.475 closest distance to " O   HOH Z  82 " =    0.988
peak=    4.468 closest distance to " O   HOH Z 133 " =    2.540
peak=    4.466 closest distance to " CA  TYR A  30 " =    0.967
peak=    4.457 closest distance to " OE1 GLN A  88 " =    0.976
peak=    4.446 closest distance to " CB  ARG A 275 " =    0.827
peak=    4.400 closest distance to " CG  PRO A 280 " =    0.887
peak=    4.371 closest distance to " O   HOH Z 418 " =    2.313
peak=    4.359 closest distance to " CZ  PHE A 218 " =    1.133
peak=    4.358 closest distance to " O   HOH Z 214 " =    1.771
peak=    4.345 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.324 closest distance to " O   HOH Z 232 " =    2.332
peak=    4.313 closest distance to " O   HOH Z  41 " =    1.068
peak=    4.296 closest distance to " O   HOH Z 234 " =    3.897
peak=    4.293 closest distance to " CB  GLU A 128 " =    1.029
peak=    4.284 closest distance to " CB  VAL A 202 " =    1.474
peak=    4.273 closest distance to " N   SER A 164 " =    0.948
peak=    4.261 closest distance to " O   PRO A 198 " =    1.666
peak=    4.226 closest distance to " O   HOH Z 422 " =    1.082
peak=    4.225 closest distance to " NH2 ARG A 156 " =    1.209
peak=    4.225 closest distance to " CB  PRO A  54 " =    0.965
peak=    4.217 closest distance to " OD1 ASN A 301 " =    1.061
peak=    4.202 closest distance to " O   HOH Z 196 " =    2.167
peak=    4.196 closest distance to " O   HOH Z 134 " =    2.051
peak=    4.185 closest distance to " CA  ALA A  51 " =    0.998
peak=    4.168 closest distance to " O   HOH Z 357 " =    2.288
peak=    4.164 closest distance to " NH1AARG A 145 " =    1.254
peak=    4.159 closest distance to " CG2BVAL A  41 " =    0.900
peak=    4.156 closest distance to " CB  TRP A 266 " =    1.038
peak=    4.152 closest distance to " CB  ASP A 124 " =    0.902
peak=    4.127 closest distance to " CA  ILE A 106 " =    0.833
peak=    4.124 closest distance to " O   HOH Z 433 " =    1.841
peak=    4.104 closest distance to " O   ALA A 165 " =    1.373
peak=    4.084 closest distance to " O   HOH Z 176 " =    2.058
peak=    4.066 closest distance to " O   HOH Z 404 " =    1.525
peak=    4.052 closest distance to " CA  ARG A 195 " =    1.100
peak=    4.034 closest distance to " CD  ARG A 269 " =    0.806
peak=    4.032 closest distance to " CG1 VAL A 153 " =    1.146
peak=    4.027 closest distance to " O   HOH Z 394 " =    1.705
peak=    4.008 closest distance to " CG  PRO A 213 " =    1.324
peak=    4.000 closest distance to " CG  PRO A 243 " =    1.185
peak=    3.999 closest distance to " O   HOH Z 120 " =    1.081
peak=    3.994 closest distance to " CB  GLU A 152 " =    1.125
peak=    3.984 closest distance to " O   HOH Z   7 " =    1.469
peak=    3.972 closest distance to " NE2 HIS A 115 " =    1.138
peak=    3.965 closest distance to " CB  ASN A 148 " =    1.484
peak=    3.954 closest distance to " CD2 TRP A 179 " =    1.285
peak=    3.953 closest distance to " O   HOH Z 403 " =    2.111
peak=    3.947 closest distance to " O   HOH Z 389 " =    2.111
peak=    3.943 closest distance to " O   HOH Z 369 " =    1.575
peak=    3.936 closest distance to " CA  ALA A 160 " =    1.086
peak=    3.932 closest distance to " O   HOH Z 377 " =    1.543
peak=    3.917 closest distance to " CG1 ILE A 120 " =    1.148
peak=    3.892 closest distance to " O   HOH Z  95 " =    1.981
peak=    3.885 closest distance to " O   HOH Z 437 " =    1.746
peak=    3.884 closest distance to " CB  ARG A 190 " =    1.821
peak=    3.884 closest distance to " O  BHOH Z 338 " =    0.859
peak=    3.872 closest distance to " O   HOH Z 341 " =    1.221
peak=    3.870 closest distance to " CG AARG A 275 " =    1.118
peak=    3.857 closest distance to " CB  TRP A 179 " =    1.401
peak=    3.853 closest distance to " CG  ARG A 138 " =    1.263
peak=    3.834 closest distance to " CD ALYS A 290 " =    1.079
peak=    3.823 closest distance to " O   HOH Z  80 " =    2.130
peak=    3.803 closest distance to " CA  ARG A  36 " =    1.109
peak=    3.801 closest distance to " O   THR A 251 " =    1.163
peak=    3.792 closest distance to " CD  LYS A 166 " =    1.494
peak=    3.786 closest distance to " O   TYR A 116 " =    1.388
peak=    3.786 closest distance to " O   HOH Z  44 " =    1.911
peak=    3.782 closest distance to " ND2 ASN A 187 " =    1.484
peak=    3.781 closest distance to " NE2 GLN A 278 " =    2.363
peak=    3.779 closest distance to " CD  ARG A  66 " =    2.651
peak=    3.774 closest distance to " CD1 LEU A 300 " =    1.097
peak=    3.772 closest distance to " O   HOH Z 418 " =    1.306
peak=    3.771 closest distance to " CA  SER A  12 " =    1.633
peak=    3.756 closest distance to " O   HOH Z 174 " =    2.050
peak=    3.749 closest distance to " CA  GLU A 152 " =    0.968
peak=    3.749 closest distance to " CG1 ILE A  33 " =    1.248
peak=    3.748 closest distance to " O   HOH Z  78 " =    2.302
peak=    3.748 closest distance to " NE2 GLN A  77 " =    3.208
peak=    3.742 closest distance to " O   HOH Z 316 " =    3.150
peak=    3.740 closest distance to " O   HOH Z 298 " =    1.978
peak=    3.740 closest distance to " O   HOH Z 126 " =    1.656
peak=    3.739 closest distance to " O   HOH Z 343 " =    2.318
peak=    3.725 closest distance to " CB  SER A  62 " =    0.871
peak=    3.723 closest distance to " OE1 GLN A  11 " =    2.262
peak=    3.717 closest distance to " CB  ASN A  39 " =    0.813
peak=    3.714 closest distance to " O   HOH Z 200 " =    1.640
peak=    3.706 closest distance to " CB  LEU A 228 " =    1.112
peak=    3.697 closest distance to " CA  GLN A  11 " =    1.146
peak=    3.693 closest distance to " O   ASP A 200 " =    1.580
peak=    3.685 closest distance to " O   HOH Z 141 " =    1.745
peak=    3.684 closest distance to " CG  LEU A 167 " =    0.997
peak=    3.682 closest distance to " O   HOH Z 301 " =    1.542
peak=    3.671 closest distance to " OE1 GLN A  58 " =    0.793
peak=    3.662 closest distance to " O   HOH Z 403 " =    1.330
peak=    3.658 closest distance to " CB  MET A  47 " =    0.948
peak=    3.643 closest distance to " CB  GLU A 277 " =    3.858
peak=    3.641 closest distance to " O   HOH Z 346 " =    1.566
peak=    3.635 closest distance to " CA  ASP A 162 " =    1.050
peak=    3.631 closest distance to " CA  GLY A 241 " =    0.739
peak=    3.626 closest distance to " O   HOH Z  54 " =    1.335
peak=    3.626 closest distance to " CA  ASP A 191 " =    0.897
peak=    3.621 closest distance to " CB  ASP A 140 " =    0.840
peak=    3.618 closest distance to " O   HOH Z 406 " =    1.712
peak=    3.617 closest distance to " CA  GLN A 223 " =    0.793
peak=    3.616 closest distance to " CA  ASN A 217 " =    1.401
peak=    3.613 closest distance to " NE2 GLN A  11 " =    1.159
peak=    3.610 closest distance to " CB  ALA A 248 " =    1.332
peak=    3.609 closest distance to " CB  PRO A 198 " =    0.895
peak=    3.607 closest distance to " CB  ASN A 142 " =    1.105
peak=    3.607 closest distance to " O   HOH Z 431 " =    1.214
peak=    3.607 closest distance to " O   HOH Z 261 " =    2.182
peak=    3.606 closest distance to " O   HOH Z 395 " =    1.473
peak=    3.604 closest distance to " CG2 VAL A 126 " =    0.911
peak=    3.602 closest distance to " CB  ALA A 256 " =    1.565
peak=    3.599 closest distance to " O   HOH Z  65 " =    1.042
peak=    3.586 closest distance to " O   HOH Z 265 " =    1.950
peak=    3.578 closest distance to " O   GLY A  91 " =    1.095
peak=    3.574 closest distance to " CB  SER A 141 " =    1.154
peak=    3.561 closest distance to " OE1 GLN A  58 " =    3.424
peak=    3.550 closest distance to " NH1 ARG A  14 " =    1.238
peak=    3.539 closest distance to " O   HOH Z 146 " =    1.742
peak=    3.536 closest distance to " CD2 LEU A 255 " =    1.703
peak=    3.529 closest distance to " O   HOH Z 369 " =    2.364
peak=    3.521 closest distance to " O   HOH Z  27 " =    1.136
peak=    3.513 closest distance to " CB  GLU A  37 " =    0.930
peak=    3.507 closest distance to " CB  GLN A 103 " =    0.908
peak=    3.505 closest distance to " CA  ALA A 100 " =    1.082
peak=    3.505 closest distance to " CG  GLN A  11 " =    1.039
peak=    3.504 closest distance to " CA  TRP A 274 " =    0.995
peak=    3.503 closest distance to " CD  PRO A  54 " =    1.004
peak=    3.496 closest distance to " O   HOH Z 139 " =    5.006
peak=    3.495 closest distance to " O   HOH Z 432 " =    1.756
peak=    3.491 closest distance to " CB  MET A  40 " =    0.930
peak=    3.490 closest distance to " CG2 THR A 221 " =    0.998
peak=    3.487 closest distance to " CA  VAL A 125 " =    1.252
peak=    3.486 closest distance to " CB  ALA A 137 " =    1.029
peak=    3.485 closest distance to " CZ  PHE A  38 " =    1.325
peak=    3.481 closest distance to " CE3 TRP A  85 " =    1.232
peak=    3.481 closest distance to " CG2 ILE A  20 " =    1.471
peak=    3.479 closest distance to " O   HOH Z  47 " =    1.350
peak=    3.479 closest distance to " O   HOH Z 335 " =    1.102
peak=    3.478 closest distance to " O   HOH Z  48 " =    1.863
peak=    3.478 closest distance to " CA  VAL A  41 " =    0.825
peak=    3.476 closest distance to " O   HOH Z 126 " =    2.324
peak=    3.472 closest distance to " O   HOH Z 234 " =    1.886
peak=    3.471 closest distance to " CE  LYS A  76 " =    0.857
peak=    3.469 closest distance to " CA  TRP A  92 " =    0.938
peak=    3.466 closest distance to " C   VAL A 265 " =    1.036
peak=    3.466 closest distance to " CG2 VAL A  78 " =    0.992
peak=    3.458 closest distance to " CG  GLU A  37 " =    0.956
peak=    3.458 closest distance to " CB  GLN A  88 " =    1.199
peak=    3.453 closest distance to " CA  GLY A 196 " =    0.973
peak=    3.453 closest distance to " N   TYR A 116 " =    1.675
peak=    3.452 closest distance to " O   HOH Z 128 " =    2.327
peak=    3.452 closest distance to " O   HOH Z  15 " =    2.167
peak=    3.447 closest distance to " O   ASN A  74 " =    1.505
peak=    3.447 closest distance to " N   TYR A  15 " =    0.801
peak=    3.447 closest distance to " O   HOH Z  76 " =    1.280
peak=    3.445 closest distance to " CB  ALA A 291 " =    1.161
peak=    3.443 closest distance to " CB  ASN A 285 " =    0.769
peak=    3.440 closest distance to " CB  GLN A 194 " =    0.956
peak=    3.439 closest distance to " O   HOH Z 423 " =    1.775
peak=    3.438 closest distance to " CB  ALA A  43 " =    1.153
peak=    3.438 closest distance to " O   HOH Z 368 " =    2.235
peak=    3.433 closest distance to " OD2 ASP A 298 " =    3.447
peak=    3.432 closest distance to " CD  ARG A 159 " =    0.827
peak=    3.426 closest distance to " CE1 TYR A 186 " =    1.388
peak=    3.424 closest distance to " CG2 VAL A 197 " =    1.250
peak=    3.412 closest distance to " O   HOH Z 189 " =    2.794
peak=    3.410 closest distance to " O   HOH Z 246 " =    1.796
peak=    3.410 closest distance to " CB  PHE A 283 " =    0.865
peak=    3.409 closest distance to " CD1 LEU A   5 " =    1.338
peak=    3.408 closest distance to " O   HOH Z 132 " =    3.044
peak=    3.407 closest distance to " N   ASN A  39 " =    1.214
peak=    3.403 closest distance to " CG  GLN A  77 " =    0.904
peak=    3.403 closest distance to " O   HOH Z 374 " =    2.764
peak=    3.398 closest distance to " O   HOH Z 104 " =    2.618
peak=    3.396 closest distance to " CA  GLU A  46 " =    1.019
peak=    3.396 closest distance to " O   HOH Z 362 " =    3.339
peak=    3.395 closest distance to " CB  ARG A  79 " =    0.906
peak=    3.394 closest distance to " CA  GLY A  98 " =    1.048
peak=    3.393 closest distance to " O   HOH Z 421 " =    1.772
peak=    3.392 closest distance to " CA  LEU A  83 " =    1.457
peak=    3.391 closest distance to " O   HOH Z 393 " =    3.973
peak=    3.385 closest distance to " O   HOH Z 147 " =    1.514
peak=    3.384 closest distance to " C   ILE A 106 " =    1.838
peak=    3.382 closest distance to " CA  ALA A 154 " =    1.034
peak=    3.381 closest distance to " O   HOH Z  30 " =    1.753
peak=    3.379 closest distance to " OE1 GLU A   2 " =    1.508
peak=    3.379 closest distance to " OG  SER A 245 " =    1.649
peak=    3.378 closest distance to " CB  ARG A  79 " =    1.209
peak=    3.370 closest distance to " O   HOH Z 258 " =    2.234
peak=    3.364 closest distance to " O   HOH Z 285 " =    3.237
peak=    3.362 closest distance to " CG  GLN A  89 " =    1.502
peak=    3.359 closest distance to " CA  ALA A   9 " =    1.181
peak=    3.359 closest distance to " O   HOH Z 193 " =    1.849
peak=    3.353 closest distance to " N   THR A  52 " =    1.158
peak=    3.352 closest distance to " CB  SER A  26 " =    0.841
peak=    3.348 closest distance to " CD1 LEU A  96 " =    0.792
peak=    3.347 closest distance to " O   SER A  87 " =    2.323
peak=    3.346 closest distance to " O   HOH Z 394 " =    4.165
peak=    3.339 closest distance to " CB  TYR A 116 " =    1.315
peak=    3.338 closest distance to " O   HOH Z  20 " =    1.901
peak=    3.329 closest distance to " CB  ALA A 104 " =    0.858
peak=    3.329 closest distance to " CB  SER A  62 " =    0.891
peak=    3.327 closest distance to " O   HOH Z 417 " =    3.004
peak=    3.326 closest distance to " CA  ARG A 102 " =    1.218
peak=    3.324 closest distance to " O   HOH Z 344 " =    2.054
peak=    3.322 closest distance to " N   ILE A  33 " =    0.992
peak=    3.321 closest distance to " CB  GLU A 277 " =    0.739
peak=    3.320 closest distance to " CB  TRP A 179 " =    1.548
peak=    3.319 closest distance to " OD1 ASP A 238 " =    0.889
peak=    3.315 closest distance to " O   HOH Z 287 " =    1.910
peak=    3.309 closest distance to " N   ASN A 252 " =    1.262
peak=    3.306 closest distance to " CB  SER A 210 " =    0.975
peak=    3.305 closest distance to " CA  GLN A  88 " =    1.388
peak=    3.303 closest distance to " CZ3 TRP A  85 " =    0.952
peak=    3.303 closest distance to " CG  ASP A 231 " =    1.181
peak=    3.299 closest distance to " CB  ALA A   1 " =    1.181
peak=    3.297 closest distance to " CA  ALA A 295 " =    1.073
peak=    3.295 closest distance to " O   HOH Z 201 " =    2.862
peak=    3.293 closest distance to " CD  ARG A 195 " =    1.008
peak=    3.292 closest distance to " O   PRO A 213 " =    1.552
peak=    3.291 closest distance to " CA  ARG A 156 " =    1.073
peak=    3.288 closest distance to " CA  ALA A  21 " =    1.424
peak=    3.287 closest distance to " OD1 ASN A 217 " =    1.588
peak=    3.286 closest distance to " CA  TYR A 116 " =    1.523
peak=    3.286 closest distance to " CZ3 TRP A 266 " =    1.122
peak=    3.284 closest distance to " OG BSER A 164 " =    2.317
peak=    3.284 closest distance to " CB  ASN A 187 " =    1.143
peak=    3.283 closest distance to " CB  LEU A  83 " =    0.777
peak=    3.283 closest distance to " O   HOH Z  88 " =    3.413
peak=    3.280 closest distance to " O   HOH Z 134 " =    2.433
peak=    3.279 closest distance to " O   HOH Z  32 " =    2.240
peak=    3.276 closest distance to " N   ALA A 292 " =    0.980
peak=    3.274 closest distance to " O   ARG A 275 " =    0.798
peak=    3.273 closest distance to " CB  MET A 105 " =    0.926
peak=    3.271 closest distance to " CA  PRO A  54 " =    1.062
peak=    3.270 closest distance to " O   HOH Z 284 " =    2.956
peak=    3.269 closest distance to " CB  ALA A  71 " =    1.323
peak=    3.262 closest distance to " CA  SER A  87 " =    0.971
peak=    3.261 closest distance to " O   THR A 294 " =    1.733
peak=    3.261 closest distance to " NE AARG A 275 " =    1.344
peak=    3.261 closest distance to " O   HOH Z 271 " =    1.966
peak=    3.260 closest distance to " CB  PRO A  90 " =    1.378
peak=    3.259 closest distance to " CA  ASN A 215 " =    1.085
peak=    3.258 closest distance to " CG2 THR A 220 " =    0.769
peak=    3.255 closest distance to " CG  LEU A 237 " =    1.052
peak=    3.247 closest distance to " CE  LYS A 119 " =    1.146
peak=    3.246 closest distance to " O   HOH Z  57 " =    1.831
peak=    3.243 closest distance to " O   HOH Z 199 " =    1.717
peak=    3.242 closest distance to " CA  THR A 246 " =    0.999
peak=    3.241 closest distance to " CG  LYS A  76 " =    1.184
peak=    3.240 closest distance to " CG  MET A 185 " =    1.038
peak=    3.239 closest distance to " O   HOH Z  49 " =    1.880
peak=    3.238 closest distance to " CZ3 TRP A 274 " =    4.449
peak=    3.236 closest distance to " O   ASP A 124 " =    1.331
peak=    3.235 closest distance to " O   HOH Z  44 " =    1.806
peak=    3.234 closest distance to " O   HOH Z  85 " =    2.059
peak=    3.232 closest distance to " N   GLU A  44 " =    1.301
peak=    3.230 closest distance to " O   HOH Z 290 " =    1.292
peak=    3.221 closest distance to " O   HOH Z 415 " =    1.371
peak=    3.221 closest distance to " CB  ARG A 156 " =    1.026
peak=    3.216 closest distance to " O   HOH Z 203 " =    1.930
peak=    3.213 closest distance to " CA  ASN A 249 " =    1.331
peak=    3.211 closest distance to " N   CYS A 260 " =    0.814
peak=    3.211 closest distance to " O   PHE A  61 " =    1.398
peak=    3.209 closest distance to " O   HOH Z  22 " =    2.704
peak=    3.206 closest distance to " CB  PRO A 243 " =    1.339
peak=    3.201 closest distance to " CD  ARG A  24 " =    1.366
peak=    3.197 closest distance to " CH2 TRP A 274 " =    2.078
peak=    3.195 closest distance to " O   HOH Z 184 " =    1.817
peak=    3.195 closest distance to " O   HOH Z 420 " =    5.966
peak=    3.194 closest distance to " N   ARG A 190 " =    1.030
peak=    3.193 closest distance to " NH2AARG A 145 " =    0.905
peak=    3.191 closest distance to " O   HOH Z  68 " =    2.055
peak=    3.191 closest distance to " CB  PHE A  16 " =    1.373
peak=    3.190 closest distance to " O   HOH Z  63 " =    1.168
peak=    3.184 closest distance to " CB  PHE A  16 " =    1.096
peak=    3.183 closest distance to " CZ  PHE A 192 " =    0.949
peak=    3.180 closest distance to " ND1 HIS A  81 " =    1.443
peak=    3.174 closest distance to " O   HOH Z  88 " =    1.767
peak=    3.173 closest distance to " O   HOH Z 313 " =    2.024
peak=    3.172 closest distance to " NZ  LYS A  48 " =    1.211
peak=    3.172 closest distance to " CB  PRO A 280 " =    1.145
peak=    3.166 closest distance to " CG2 THR A  42 " =    0.937
peak=    3.161 closest distance to " CB  ALA A   1 " =    1.269
peak=    3.160 closest distance to " CB  TRP A 150 " =    1.651
peak=    3.157 closest distance to " N   ASN A 127 " =    1.233
peak=    3.157 closest distance to " CA  ALA A 291 " =    0.909
peak=    3.153 closest distance to " O   HOH Z 215 " =    1.472
peak=    3.152 closest distance to " N   GLN A 278 " =    1.274
peak=    3.150 closest distance to " CA  LYS A 117 " =    1.365
peak=    3.147 closest distance to " O   ALA A  84 " =    1.335
peak=    3.147 closest distance to " O   HOH Z 285 " =    1.778
peak=    3.144 closest distance to " OH  TYR A 169 " =    0.901
peak=    3.140 closest distance to " CD1 LEU A 167 " =    1.313
peak=    3.126 closest distance to " O   HOH Z 175 " =    3.807
peak=    3.122 closest distance to " O   HOH Z 128 " =    1.843
peak=    3.122 closest distance to " CE1 HIS A 108 " =    1.118
peak=    3.120 closest distance to " ND2 ASN A 301 " =    0.988
peak=    3.119 closest distance to " CA  THR A 221 " =    1.663
peak=    3.118 closest distance to " CG2 VAL A 268 " =    1.024
peak=    3.104 closest distance to " O   HOH Z 435 " =    2.967
peak=    3.099 closest distance to " CA  ASP A 124 " =    0.894
peak=    3.098 closest distance to " CB  GLN A  89 " =    1.084
peak=    3.097 closest distance to " O   HOH Z 383 " =    2.151
peak=    3.093 closest distance to " OD2 ASP A 200 " =    1.331
peak=    3.088 closest distance to " O   HOH Z 102 " =    1.700
peak=    3.087 closest distance to " CG1 VAL A 257 " =    1.079
peak=    3.082 closest distance to " CE1 PHE A 225 " =    1.034
peak=    3.077 closest distance to " CA  SER A  32 " =    1.651
peak=    3.074 closest distance to " O   SER A 276 " =    1.216
peak=    3.067 closest distance to " CA  ARG A  66 " =    0.978
peak=    3.063 closest distance to " O   HOH Z 368 " =    4.217
peak=    3.056 closest distance to " O   HOH Z 247 " =    1.466
peak=    3.037 closest distance to " ND2 ASN A 176 " =    0.784
peak=    3.013 closest distance to " NH2AARG A 190 " =    1.279

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.601 - 5.899
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 218
   mapped sites are within: 0.703 - 5.899

peak=   -4.742 closest distance to " CD  GLN A 223 " =    1.431
peak=   -4.515 closest distance to " CD2 LEU A 237 " =    2.639
peak=   -4.368 closest distance to " O   HOH Z 166 " =    1.385
peak=   -4.251 closest distance to " CG  ARG A 269 " =    2.395
peak=   -4.199 closest distance to " O   HOH Z 407 " =    0.846
peak=   -4.188 closest distance to " CD1 PHE A  59 " =    2.029
peak=   -4.165 closest distance to " O   HOH Z 400 " =    1.392
peak=   -4.160 closest distance to " O   HOH Z 418 " =    1.250
peak=   -4.136 closest distance to " OD1 ASN A 148 " =    1.360
peak=   -4.130 closest distance to " O   GLN A  11 " =    1.180
peak=   -4.096 closest distance to " CD2 PHE A  61 " =    2.048
peak=   -4.095 closest distance to " O   PRO A 198 " =    1.366
peak=   -4.085 closest distance to " O   HOH Z   5 " =    1.591
peak=   -4.076 closest distance to " C   ASN A 285 " =    2.385
peak=   -4.073 closest distance to " O   HOH Z 411 " =    5.435
peak=   -4.056 closest distance to " O   HOH Z 377 " =    0.740
peak=   -4.032 closest distance to " OD2 ASP A 171 " =    1.883
peak=   -4.023 closest distance to " O   HOH Z  19 " =    2.147
peak=   -4.008 closest distance to " O   HOH Z 438 " =    3.019
peak=   -4.002 closest distance to " O   HOH Z 166 " =    2.366
peak=   -4.001 closest distance to " OE1 GLN A  88 " =    0.914
peak=   -3.982 closest distance to " CD  GLN A  58 " =    0.875
peak=   -3.972 closest distance to " CG1 VAL A 112 " =    2.616
peak=   -3.970 closest distance to " CD1 PHE A 130 " =    2.327
peak=   -3.915 closest distance to " N   ARG A 275 " =    1.102
peak=   -3.914 closest distance to " CA  GLY A 241 " =    2.338
peak=   -3.873 closest distance to " N   ALA A  43 " =    2.778
peak=   -3.865 closest distance to " CG2 VAL A 189 " =    2.229
peak=   -3.835 closest distance to " O   HOH Z   6 " =    1.285
peak=   -3.825 closest distance to " CD1 LEU A 167 " =    2.047
peak=   -3.817 closest distance to " N   ASP A 272 " =    1.370
peak=   -3.810 closest distance to " O   HOH Z 155 " =    1.639
peak=   -3.798 closest distance to " O   HOH Z 221 " =    1.143
peak=   -3.797 closest distance to " NH2 ARG A  66 " =    1.690
peak=   -3.795 closest distance to " CD  ARG A  14 " =    3.320
peak=   -3.793 closest distance to " CA  GLY A 203 " =    2.493
peak=   -3.757 closest distance to " CG2 ILE A  49 " =    2.749
peak=   -3.749 closest distance to " CG  PRO A 243 " =    1.726
peak=   -3.746 closest distance to " CA  GLU A 277 " =    1.185
peak=   -3.741 closest distance to " O   HOH Z 183 " =    1.498
peak=   -3.731 closest distance to " O   HOH Z 331 " =    0.993
peak=   -3.720 closest distance to " O   HOH Z 150 " =    0.703
peak=   -3.720 closest distance to " CB  PRO A 243 " =    2.855
peak=   -3.713 closest distance to " O   HOH Z 185 " =    2.504
peak=   -3.712 closest distance to " O   HOH Z  60 " =    1.470
peak=   -3.702 closest distance to " O   HOH Z  52 " =    1.678
peak=   -3.697 closest distance to " CG  MET A  93 " =    2.560
peak=   -3.690 closest distance to " O   HOH Z  38 " =    1.006
peak=   -3.686 closest distance to " O   HOH Z 400 " =    1.046
peak=   -3.685 closest distance to " O   HOH Z  37 " =    2.278
peak=   -3.674 closest distance to " O   HOH Z 308 " =    1.265
peak=   -3.666 closest distance to " CB  ALA A 291 " =    2.469
peak=   -3.664 closest distance to " CB  SER A 146 " =    2.174
peak=   -3.656 closest distance to " O   HOH Z 394 " =    1.736
peak=   -3.639 closest distance to " O   SER A 206 " =    1.316
peak=   -3.636 closest distance to " O   HOH Z 243 " =    2.235
peak=   -3.636 closest distance to " OG  SER A  63 " =    1.092
peak=   -3.627 closest distance to " O   ASP A 171 " =    1.047
peak=   -3.619 closest distance to " CD  GLN A  88 " =    1.064
peak=   -3.602 closest distance to " O   HOH Z 105 " =    2.012
peak=   -3.598 closest distance to " O   HOH Z 283 " =    2.284
peak=   -3.587 closest distance to " O   HOH Z  70 " =    2.323
peak=   -3.585 closest distance to " O   HOH Z 184 " =    1.540
peak=   -3.582 closest distance to " O   SER A 276 " =    1.776
peak=   -3.579 closest distance to " CD  ARG A 156 " =    2.085
peak=   -3.576 closest distance to " CB  ASN A  45 " =    2.265
peak=   -3.572 closest distance to " O   HOH Z 388 " =    1.891
peak=   -3.565 closest distance to " CG  GLN A  11 " =    1.339
peak=   -3.553 closest distance to " O   HOH Z  37 " =    1.487
peak=   -3.546 closest distance to " O   VAL A  67 " =    2.663
peak=   -3.546 closest distance to " NE2 GLN A 223 " =    1.071
peak=   -3.545 closest distance to " O   SER A 135 " =    1.727
peak=   -3.544 closest distance to " CE2 PHE A  61 " =    2.770
peak=   -3.540 closest distance to " SD  MET A 105 " =    2.461
peak=   -3.540 closest distance to " ND2 ASN A  45 " =    1.922
peak=   -3.538 closest distance to " O   HOH Z 200 " =    1.130
peak=   -3.526 closest distance to " O   HOH Z 423 " =    2.372
peak=   -3.512 closest distance to " N   ALA A 226 " =    2.107
peak=   -3.494 closest distance to " O   HOH Z 128 " =    2.680
peak=   -3.493 closest distance to " O   HOH Z 348 " =    2.271
peak=   -3.486 closest distance to " C   THR A 264 " =    1.397
peak=   -3.484 closest distance to " O   HOH Z 414 " =    1.766
peak=   -3.477 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -3.477 closest distance to " CE3 TRP A 150 " =    2.135
peak=   -3.470 closest distance to " O   HOH Z 114 " =    3.957
peak=   -3.457 closest distance to " O   GLN A 240 " =    3.200
peak=   -3.456 closest distance to " NH2 ARG A 159 " =    2.374
peak=   -3.453 closest distance to " O   HOH Z 369 " =    2.465
peak=   -3.453 closest distance to " O   HOH Z 234 " =    4.359
peak=   -3.445 closest distance to " CE3 TRP A 274 " =    2.329
peak=   -3.441 closest distance to " N   THR A  18 " =    1.347
peak=   -3.441 closest distance to " CZ  PHE A 155 " =    1.288
peak=   -3.434 closest distance to " OG1 THR A  82 " =    1.546
peak=   -3.433 closest distance to " O   HOH Z 216 " =    1.606
peak=   -3.428 closest distance to " CG  MET A 105 " =    0.929
peak=   -3.423 closest distance to " ND2 ASN A  69 " =    1.654
peak=   -3.419 closest distance to " CG2BVAL A  41 " =    1.475
peak=   -3.414 closest distance to " SD  MET A  93 " =    1.867
peak=   -3.412 closest distance to " CG  ARG A 259 " =    2.466
peak=   -3.409 closest distance to " NE  ARG A  79 " =    1.245
peak=   -3.407 closest distance to " CD1 LEU A   5 " =    2.498
peak=   -3.406 closest distance to " O   HOH Z 156 " =    3.594
peak=   -3.404 closest distance to " CG  ASP A 231 " =    0.802
peak=   -3.403 closest distance to " O   HOH Z 191 " =    5.899
peak=   -3.402 closest distance to " NH2 ARG A  79 " =    1.882
peak=   -3.398 closest distance to " CD1 ILE A 263 " =    2.079
peak=   -3.397 closest distance to " OG  SER A  97 " =    2.275
peak=   -3.395 closest distance to " O   HOH Z 150 " =    1.950
peak=   -3.392 closest distance to " CB  ALA A  10 " =    2.209
peak=   -3.378 closest distance to " C   ILE A 239 " =    2.239
peak=   -3.377 closest distance to " O   HOH Z 368 " =    1.969
peak=   -3.377 closest distance to " N   ILE A 120 " =    1.235
peak=   -3.372 closest distance to " O   HOH Z 403 " =    0.873
peak=   -3.372 closest distance to " O   HOH Z 205 " =    0.800
peak=   -3.371 closest distance to " CD2 PHE A  59 " =    2.380
peak=   -3.363 closest distance to " O   HOH Z 401 " =    1.329
peak=   -3.361 closest distance to " O   HOH Z 128 " =    4.418
peak=   -3.357 closest distance to " OE1 GLN A 223 " =    2.347
peak=   -3.354 closest distance to " O   HOH Z 137 " =    1.441
peak=   -3.348 closest distance to " O   HOH Z 275 " =    1.656
peak=   -3.346 closest distance to " OD1 ASN A 301 " =    0.909
peak=   -3.344 closest distance to " O   HOH Z 400 " =    0.936
peak=   -3.343 closest distance to " O   HOH Z 109 " =    3.336
peak=   -3.340 closest distance to " O   ALA A   7 " =    1.485
peak=   -3.338 closest distance to " O   HOH Z 198 " =    1.609
peak=   -3.337 closest distance to " O   HOH Z 290 " =    1.225
peak=   -3.336 closest distance to " O   HOH Z 120 " =    1.092
peak=   -3.336 closest distance to " O   HOH Z  54 " =    1.321
peak=   -3.333 closest distance to " CE  MET A  93 " =    1.829
peak=   -3.333 closest distance to " CA  VAL A 232 " =    2.453
peak=   -3.330 closest distance to " O   HOH Z   7 " =    0.792
peak=   -3.328 closest distance to " O   HOH Z 251 " =    4.806
peak=   -3.327 closest distance to " O   HOH Z   7 " =    1.520
peak=   -3.327 closest distance to " OG  SER A  62 " =    4.767
peak=   -3.326 closest distance to " OD1 ASP A 191 " =    1.341
peak=   -3.324 closest distance to " CA  VAL A 197 " =    0.985
peak=   -3.320 closest distance to " CG2 THR A 221 " =    2.300
peak=   -3.319 closest distance to " O   VAL A 174 " =    2.098
peak=   -3.317 closest distance to " CG1 VAL A 189 " =    2.470
peak=   -3.316 closest distance to " O   HOH Z 109 " =    3.572
peak=   -3.315 closest distance to " CG  LEU A 281 " =    1.886
peak=   -3.315 closest distance to " O   HOH Z 151 " =    1.653
peak=   -3.314 closest distance to " NE2 GLN A 194 " =    2.108
peak=   -3.314 closest distance to " CG  LEU A 101 " =    2.446
peak=   -3.311 closest distance to " O   HOH Z 400 " =    0.716
peak=   -3.308 closest distance to " O   HOH Z 111 " =    2.174
peak=   -3.306 closest distance to " O   ARG A 275 " =    2.038
peak=   -3.306 closest distance to " O   HOH Z 288 " =    1.675
peak=   -3.301 closest distance to " C   ALA A 158 " =    1.467
peak=   -3.298 closest distance to " O   HOH Z 252 " =    3.776
peak=   -3.280 closest distance to " CA  SER A 276 " =    1.444
peak=   -3.280 closest distance to " O   HOH Z 231 " =    1.346
peak=   -3.278 closest distance to " SD  MET A  40 " =    2.057
peak=   -3.272 closest distance to " O   HOH Z 211 " =    1.280
peak=   -3.265 closest distance to " O   GLY A 262 " =    2.453
peak=   -3.265 closest distance to " CD2 TYR A 293 " =    1.700
peak=   -3.259 closest distance to " CA  ASP A 298 " =    1.120
peak=   -3.252 closest distance to " CB  PHE A 130 " =    1.218
peak=   -3.251 closest distance to " O   HOH Z 424 " =    2.911
peak=   -3.249 closest distance to " SD  MET A  40 " =    2.019
peak=   -3.243 closest distance to " OH  TYR A 247 " =    2.408
peak=   -3.242 closest distance to " OH  TYR A 169 " =    0.927
peak=   -3.239 closest distance to " C   VAL A 265 " =    0.905
peak=   -3.237 closest distance to " CB  ALA A   9 " =    2.692
peak=   -3.234 closest distance to " CB  ALA A  43 " =    2.716
peak=   -3.230 closest distance to " NE1 TRP A 177 " =    2.100
peak=   -3.227 closest distance to " CG2 VAL A 202 " =    2.640
peak=   -3.227 closest distance to " O   HOH Z 207 " =    1.557
peak=   -3.221 closest distance to " O   HOH Z 396 " =    1.462
peak=   -3.219 closest distance to " CG2BVAL A  41 " =    2.154
peak=   -3.216 closest distance to " ND2 ASN A  60 " =    1.502
peak=   -3.210 closest distance to " O   HOH Z 113 " =    2.328
peak=   -3.209 closest distance to " O   SER A 271 " =    2.191
peak=   -3.207 closest distance to " O   HOH Z  91 " =    2.292
peak=   -3.207 closest distance to " CZ  TYR A 169 " =    1.928
peak=   -3.205 closest distance to " O   HOH Z  53 " =    1.952
peak=   -3.202 closest distance to " CD2 HIS A 115 " =    1.167
peak=   -3.200 closest distance to " O   ALA A  34 " =    2.651
peak=   -3.197 closest distance to " O   HOH Z  90 " =    3.382
peak=   -3.197 closest distance to " CA  ASN A 127 " =    1.075
peak=   -3.191 closest distance to " O   HOH Z 378 " =    1.309
peak=   -3.189 closest distance to " O   ALA A  34 " =    1.967
peak=   -3.186 closest distance to " N   ASP A 191 " =    1.180
peak=   -3.183 closest distance to " NH2 ARG A  66 " =    1.456
peak=   -3.182 closest distance to " N   TYR A  68 " =    2.960
peak=   -3.179 closest distance to " O   HOH Z 111 " =    1.434
peak=   -3.175 closest distance to " O   HOH Z 134 " =    2.094
peak=   -3.156 closest distance to " O   HOH Z 171 " =    2.381
peak=   -3.155 closest distance to " O   HOH Z 114 " =    1.607
peak=   -3.152 closest distance to " O   HOH Z 413 " =    1.039
peak=   -3.152 closest distance to " C   ASP A 270 " =    1.061
peak=   -3.141 closest distance to " OH  TYR A 172 " =    1.774
peak=   -3.139 closest distance to " OE2 GLU A  53 " =    1.284
peak=   -3.136 closest distance to " N   SER A 134 " =    1.188
peak=   -3.133 closest distance to " CB  ASN A  45 " =    0.863
peak=   -3.130 closest distance to " CH2 TRP A 179 " =    1.164
peak=   -3.127 closest distance to " O   HOH Z 277 " =    1.487
peak=   -3.121 closest distance to " O   HOH Z 113 " =    2.371
peak=   -3.109 closest distance to " O   HOH Z  99 " =    1.107
peak=   -3.103 closest distance to " O   HOH Z 261 " =    1.456
peak=   -3.101 closest distance to " O   HOH Z 384 " =    2.050
peak=   -3.099 closest distance to " O   HOH Z 225 " =    1.354
peak=   -3.098 closest distance to " CH2 TRP A 150 " =    1.142
peak=   -3.097 closest distance to " N   ALA A 242 " =    1.762
peak=   -3.096 closest distance to " OG BSER A 216 " =    2.549
peak=   -3.095 closest distance to " CG  ASP A 124 " =    0.945
peak=   -3.093 closest distance to " C   ALA A  10 " =    1.304
peak=   -3.091 closest distance to " CG  LEU A  83 " =    2.149
peak=   -3.087 closest distance to " CG2 ILE A 263 " =    2.291
peak=   -3.081 closest distance to " NE1 TRP A 150 " =    2.395
peak=   -3.076 closest distance to " O   HOH Z 227 " =    1.219
peak=   -3.073 closest distance to " OD2 ASP A 298 " =    0.999
peak=   -3.072 closest distance to " O   HOH Z 371 " =    1.182
peak=   -3.042 closest distance to " CD1 LEU A 101 " =    2.476
peak=   -3.037 closest distance to " O   HOH Z 318 " =    1.342
peak=   -3.016 closest distance to " CA  GLY A 241 " =    2.916

================= 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    :  0.4734 0.4559   6.282266e+00   6.257193e+00
   1_bss:  0.4671 0.4482   6.277995e+00   6.249106e+00
   1_xyz:  0.3738 0.4052   6.142033e+00   6.180414e+00
   1_adp:  0.3418 0.4133   6.097025e+00   6.190463e+00
   1_occ:  0.3414 0.4127   6.096513e+00   6.190329e+00
   2_bss:  0.3414 0.4115   6.098293e+00   6.190896e+00
   2_xyz:  0.2977 0.3611   5.990817e+00   6.116293e+00
   2_adp:  0.2930 0.3582   5.986699e+00   6.113841e+00
   2_occ:  0.2930 0.3580   5.986125e+00   6.114227e+00
   3_bss:  0.2933 0.3581   5.987431e+00   6.114527e+00
   3_xyz:  0.2289 0.2842   5.752906e+00   5.917264e+00
   3_adp:  0.1957 0.2519   5.624099e+00   5.816571e+00
   3_occ:  0.1955 0.2518   5.623322e+00   5.815873e+00
   4_bss:  0.1951 0.2511   5.621513e+00   5.812723e+00
   4_xyz:  0.1621 0.2112   5.459407e+00   5.668501e+00
   4_adp:  0.1481 0.2026   5.391252e+00   5.616742e+00
   4_occ:  0.1481 0.2025   5.390817e+00   5.616453e+00
   5_bss:  0.1485 0.2031   5.392364e+00   5.618379e+00
   5_xyz:  0.1373 0.1903   5.329034e+00   5.562290e+00
   5_adp:  0.1354 0.1833   5.304720e+00   5.529060e+00
   5_occ:  0.1352 0.1834   5.304521e+00   5.529737e+00
   5_bss:  0.1351 0.1834   5.304321e+00   5.529561e+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:  0.282  57.398  -2.022   3.897   0.743   0.000   0.000   0.000
   1_xyz:  0.282  57.398  -2.022   3.897   0.743   0.000   0.000   0.000
   1_adp:  0.282  57.398  -2.022   3.897   0.743   0.000   0.000   0.000
   1_occ:  0.282  57.398  -2.022   3.897   0.743   0.000   0.000   0.000
   2_bss:  0.306  66.976  -0.797   2.712   0.917   0.000   0.000   0.000
   2_xyz:  0.306  66.976  -0.797   2.712   0.917   0.000   0.000   0.000
   2_adp:  0.306  66.976  -0.797   2.712   0.917   0.000   0.000   0.000
   2_occ:  0.306  66.976  -0.797   2.712   0.917   0.000   0.000   0.000
   3_bss:  0.315  66.976  -0.575   2.288   0.742   0.000   0.000   0.000
   3_xyz:  0.315  66.976  -0.575   2.288   0.742   0.000   0.000   0.000
   3_adp:  0.315  66.976  -0.575   2.288   0.742   0.000   0.000   0.000
   3_occ:  0.315  66.976  -0.575   2.288   0.742   0.000   0.000   0.000
   4_bss:  0.330  78.718  -0.848   0.815   0.454   0.000   0.000   0.000
   4_xyz:  0.330  78.718  -0.848   0.815   0.454   0.000   0.000   0.000
   4_adp:  0.330  78.718  -0.848   0.815   0.454   0.000   0.000   0.000
   4_occ:  0.330  78.718  -0.848   0.815   0.454   0.000   0.000   0.000
   5_bss:  0.335  87.347  -0.769   0.463   0.649   0.000   0.000   0.000
   5_xyz:  0.335  87.347  -0.769   0.463   0.649   0.000   0.000   0.000
   5_adp:  0.335  87.347  -0.769   0.463   0.649   0.000   0.000   0.000
   5_occ:  0.335  87.347  -0.769   0.463   0.649   0.000   0.000   0.000
   5_bss:  0.328  80.135  -0.827   0.153   0.673   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.413 0.4659  0.5965    64006.502
   1_bss:  53.619 0.4749  0.6295    61700.614
   1_xyz:  46.242 0.5665  0.7366    47524.231
   1_adp:  47.059 0.5562  0.7189    49119.480
   1_occ:  47.073 0.5560  0.7182    49149.624
   2_bss:  46.995 0.5570  0.7231    49071.775
   2_xyz:  40.018 0.6422  0.8258    37677.688
   2_adp:  39.738 0.6456  0.8274    37273.916
   2_occ:  39.708 0.6460  0.8269    37241.826
   3_bss:  39.712 0.6460  0.8238    37305.839
   3_xyz:  29.509 0.7623  0.9461    21127.881
   3_adp:  25.361 0.8075  0.9522    16426.779
   3_occ:  25.334 0.8078  0.9523    16391.925
   4_bss:  25.212 0.8090  0.9321    16215.085
   4_xyz:  20.773 0.8538  0.9582    11450.704
   4_adp:  19.146 0.8699  0.9470    10222.612
   4_occ:  19.136 0.8699  0.9470    10215.299
   5_bss:  19.159 0.8698  0.9460    10265.704
   5_xyz:  17.819 0.8822  0.9546     9085.955
   5_adp:  16.911 0.8907  0.9488     8518.119
   5_occ:  16.918 0.8906  0.9488     8524.709
   5_bss:  16.917 0.8906  0.9497     8522.168
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6767e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6767e-01
   1_xyz:   1.563  0.012  0.095 15.797  0.006  4.115   1.2840e-01
   1_adp:   1.563  0.012  0.095 15.797  0.006  4.115   1.2840e-01
   1_occ:   1.563  0.012  0.095 15.797  0.006  4.115   1.2840e-01
   2_bss:   1.563  0.012  0.095 15.797  0.006  4.115   1.2840e-01
   2_xyz:   1.210  0.009  0.083 14.863  0.004  4.136   7.8936e-02
   2_adp:   1.210  0.009  0.083 14.863  0.004  4.136   7.8936e-02
   2_occ:   1.210  0.009  0.083 14.863  0.004  4.136   7.8936e-02
   3_bss:   1.210  0.009  0.083 14.863  0.004  4.136   7.8936e-02
   3_xyz:   1.431  0.014  0.100 15.660  0.006  4.120   1.2682e-01
   3_adp:   1.431  0.014  0.100 15.660  0.006  4.120   1.2682e-01
   3_occ:   1.431  0.014  0.100 15.660  0.006  4.120   1.2682e-01
   4_bss:   1.431  0.014  0.100 15.660  0.006  4.120   1.2682e-01
   4_xyz:   1.142  0.010  0.082 14.924  0.004  4.137   8.1141e-02
   4_adp:   1.142  0.010  0.082 14.924  0.004  4.137   8.1141e-02
   4_occ:   1.142  0.010  0.082 14.924  0.004  4.137   8.1141e-02
   5_bss:   1.142  0.010  0.082 14.924  0.004  4.137   8.1141e-02
   5_xyz:   1.059  0.009  0.076 14.708  0.003  4.120   6.6497e-02
   5_adp:   1.059  0.009  0.076 14.708  0.003  4.120   6.6497e-02
   5_occ:   1.059  0.009  0.076 14.708  0.003  4.120   6.6497e-02
   5_bss:   1.059  0.009  0.076 14.708  0.003  4.120   6.6497e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.484   2.4620e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.484   2.4620e-01
   1_xyz:   9.575  0.057  0.315 84.008  0.046  1.984   9.7011e-02
   1_adp:   9.575  0.057  0.315 84.008  0.046  1.984   9.7011e-02
   1_occ:   9.575  0.057  0.315 84.008  0.046  1.984   9.7011e-02
   2_bss:   9.575  0.057  0.315 84.008  0.046  1.984   9.7011e-02
   2_xyz:   6.800  0.059  0.251 84.642  0.026  2.321   6.8970e-02
   2_adp:   6.800  0.059  0.251 84.642  0.026  2.321   6.8970e-02
   2_occ:   6.800  0.059  0.251 84.642  0.026  2.321   6.8970e-02
   3_bss:   6.800  0.059  0.251 84.642  0.026  2.321   6.8970e-02
   3_xyz:   9.409  0.079  0.284 82.184  0.060  2.087   1.7752e-01
   3_adp:   9.409  0.079  0.284 82.184  0.060  2.087   1.7752e-01
   3_occ:   9.409  0.079  0.284 82.184  0.060  2.087   1.7752e-01
   4_bss:   9.409  0.079  0.284 82.184  0.060  2.087   1.7752e-01
   4_xyz:   7.625  0.069  0.230 85.548  0.045  2.170   1.3194e-01
   4_adp:   7.625  0.069  0.230 85.548  0.045  2.170   1.3194e-01
   4_occ:   7.625  0.069  0.230 85.548  0.045  2.170   1.3194e-01
   5_bss:   7.625  0.069  0.230 85.548  0.045  2.170   1.3194e-01
   5_xyz:   7.852  0.039  0.237 82.285  0.038  2.323   4.2394e-02
   5_adp:   7.852  0.039  0.237 82.285  0.038  2.323   4.2394e-02
   5_occ:   7.852  0.039  0.237 82.285  0.038  2.323   4.2394e-02
   5_bss:   7.852  0.039  0.237 82.285  0.038  2.323   4.2394e-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: 114.26   0.00  19.00  92.09   0.00  15.58 114.26   0.00  37.59
   1_occ: 114.26   0.00  19.00  92.09   0.00  15.58 114.26   0.00  37.59
   2_bss: 114.26   0.00  19.00  92.09   0.00  15.58 114.26   0.00  37.59
   2_xyz: 114.26   0.00  19.00  92.09   0.00  15.58 114.26   0.00  37.59
   2_adp: 114.25   0.00  18.96  91.94   0.00  15.57 114.25   0.00  37.44
   2_occ: 114.25   0.00  18.96  91.94   0.00  15.57 114.25   0.00  37.44
   3_bss: 114.25   0.00  18.96  91.94   0.00  15.57 114.25   0.00  37.44
   3_xyz: 114.25   0.00  18.96  91.94   0.00  15.57 114.25   0.00  37.44
   3_adp: 113.91   0.00  17.97  92.91   0.00  13.43 113.91   2.62  42.71
   3_occ: 113.91   0.00  17.97  92.91   0.00  13.43 113.91   2.62  42.71
   4_bss: 113.91   0.00  17.97  92.91   0.00  13.43 113.91   2.62  42.71
   4_xyz: 113.91   0.00  17.97  92.91   0.00  13.43 113.91   2.62  42.71
   4_adp: 114.70   0.00  17.91 105.59   0.00  12.47 114.70   3.71  47.55
   4_occ: 114.70   0.00  17.91 105.59   0.00  12.47 114.70   3.71  47.55
   5_bss: 114.70   0.00  17.91 105.59   0.00  12.47 114.70   3.71  47.55
   5_xyz: 114.70   0.00  17.91 105.59   0.00  12.47 114.70   3.71  47.55
   5_adp: 111.74   0.00  16.64 101.64   0.00  11.63 111.74   3.90  43.93
   5_occ: 111.74   0.00  16.64 101.64   0.00  11.63 111.74   3.90  43.93
   5_bss: 111.87   0.14  16.78 101.77   0.14  11.76 111.87   4.03  44.06
------------------------------------------------------------------------
 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:    1.560    0.023    0.345
   1_adp:    1.560    0.023    0.345
   1_occ:    1.560    0.023    0.345
   2_bss:    1.560    0.023    0.345
   2_xyz:    1.344    0.021    0.465
   2_adp:    1.344    0.021    0.465
   2_occ:    1.344    0.021    0.465
   3_bss:    1.344    0.021    0.465
   3_xyz:    1.906    0.067    0.758
   3_adp:    1.906    0.067    0.758
   3_occ:    1.906    0.067    0.758
   4_bss:    1.906    0.067    0.758
   4_xyz:    1.707    0.086    0.812
   4_adp:    1.707    0.086    0.812
   4_occ:    1.707    0.086    0.812
   5_bss:    1.707    0.086    0.812
   5_xyz:    1.663    0.102    0.850
   5_adp:    1.663    0.102    0.850
   5_occ:    1.663    0.102    0.850
   5_bss:    1.663    0.102    0.850
------------------------------------------------------------------------

CPU time actual refinement: 331.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1086/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_1086/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1086/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1086/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1086/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.00 
  Macro-tasks:
    bulk solvent and scale       = 47.07  
    individual site refinement   = 128.90 
    weights calculation          = 28.75  
    collect and process          = 6.37   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 211.20 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 102.55 
    alpha_beta                      = 8.28   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 110.55 
    fmodel                         = 7.66   
    r_factors                      = 0.26   
    phase_errors                   = 10.57  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 243.64 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.746 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    636 calls, 102.13 s
gradients_fft:          583 calls,  98.00 s

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

# Date 2008-01-16 Time 06:23:13 PST -0800 (1200493393.88 s)
Start R-work = 0.4734, R-free = 0.4559 (no bulk solvent and anisotropic scale)
Final R-work = 0.1501, R-free = 0.1970 (no bulk solvent and anisotropic scale)

Start R-work = 0.4671, R-free = 0.4482
Final R-work = 0.1351, R-free = 0.1834