# Date 2008-01-16 Time 06:06:12 PST -0800 (1200492372.93 s)
#phil __OFF__

Command line arguments: "../1008.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1166
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1008

-------------------------------------------------------------------------------
  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, 46.4607, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.98322
Completeness in resolution range: 0.948207
Completeness with d_max=infinity: 0.945415

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   1.9832

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, 46.4607, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.98322
Completeness in resolution range: 0.948207
Completeness with d_max=infinity: 0.945415

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.2446 [2172/2198]  1953   219  10.1%
  bin  2:  4.2446 -  3.3813 [2087/2107]  1880   207   9.9%
  bin  3:  3.3813 -  2.9574 [2064/2083]  1857   207  10.0%
  bin  4:  2.9574 -  2.6887 [2042/2072]  1836   206  10.1%
  bin  5:  2.6887 -  2.4968 [2013/2032]  1820   193   9.6%
  bin  6:  2.4968 -  2.3502 [2020/2045]  1809   211  10.4%
  bin  7:  2.3502 -  2.2329 [2010/2038]  1809   201  10.0%
  bin  8:  2.2329 -  2.1360 [1999/2035]  1801   198   9.9%
  bin  9:  2.1360 -  2.0539 [1989/2031]  1795   194   9.8%
  bin 10:  2.0539 -  1.9832 [1193/2018]  1070   123  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1008/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2171
        3.04 -     3.66: 4671
        3.66 -     4.28: 8964
        4.28 -     4.90: 12276
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.290 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.305 3.040 -x,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  ... (remaining 28094 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_1008/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1008/model_refine_001.geo

CPU time processing inputs: 7.89


============================ 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 46.4607 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3683   r_free= 0.3613   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.131046                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7347 0.99   1408  157 0.3046 0.2820      6.3974      6.3053|
|  2:  4.7347 -  3.7770 0.99   1351  151 0.2949 0.2789      6.5566      6.4749|
|  3:  3.7770 -  3.3052 0.99   1340  144 0.3129 0.2959      6.4122      6.4401|
|  4:  3.3052 -  3.0056 0.99   1327  152 0.3448 0.3757      6.3208       6.349|
|  5:  3.0056 -  2.7915 0.99   1320  147 0.3938 0.3391      6.2056      6.1743|
|  6:  2.7915 -  2.6279 0.99   1302  142 0.3679 0.3887      6.0873      6.0769|
|  7:  2.6279 -  2.4968 0.99   1298  139 0.4050 0.3914      6.1164      6.0995|
|  8:  2.4968 -  2.3886 0.98   1287  147 0.4154 0.3949      6.0549      6.0449|
|  9:  2.3886 -  2.2970 0.98   1276  150 0.4150 0.3986      6.0072      5.9934|
| 10:  2.2970 -  2.2179 1.00   1315  147 0.4251 0.4429      5.9979      5.9655|
| 11:  2.2179 -  2.1488 0.98   1291  134 0.4374 0.4622      5.9654      5.9917|
| 12:  2.1488 -  2.0875 0.98   1262  144 0.4370 0.4395      5.8758      5.9237|
| 13:  2.0875 -  2.0327 0.99   1293  136 0.4370 0.4192      5.7828      5.7154|
| 14:  2.0327 -  1.9832 0.43    560   69 0.4462 0.4682      5.8033       5.796|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7347  1408   157  0.80  25.28   0.85     0.82      40750.74|
|  2:  4.7347 -  3.7770  1351   151  0.84  22.73   0.95     0.91      49773.35|
|  3:  3.7770 -  3.3052  1340   144  0.78  28.66   0.98     0.93      54028.09|
|  4:  3.3052 -  3.0056  1327   152  0.73  32.91   0.96     0.89      49779.63|
|  5:  3.0056 -  2.7915  1320   147  0.66  39.00   0.95     0.85      42918.59|
|  6:  2.7915 -  2.6279  1302   142  0.66  38.96   0.98     0.83      36026.33|
|  7:  2.6279 -  2.4968  1298   139  0.64  40.64   0.97     0.81      34955.38|
|  8:  2.4968 -  2.3886  1287   147  0.62  42.20   0.96     0.81      32619.11|
|  9:  2.3886 -  2.2970  1276   150  0.61  43.00   0.98     0.82      31580.84|
| 10:  2.2970 -  2.2179  1315   147  0.60  44.03   1.00     0.82      29432.29|
| 11:  2.2179 -  2.1488  1291   134  0.58  46.05   1.00     0.81      29935.29|
| 12:  2.1488 -  2.0875  1262   144  0.55  47.94   0.99     0.78      27870.92|
| 13:  2.0875 -  2.0327  1293   136  0.53  49.78   0.98     0.78      24665.44|
| 14:  2.0327 -  1.9832   560    69  0.59  45.38   1.01     0.79      19827.54|
|alpha:            min =        0.78 max =            0.93 mean =         0.83|
|beta:             min =    19827.54 max =        54028.09 mean =     36857.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           89.98 mean =        38.58|
|phase err.(test): min =        0.00 max =           89.90 mean =        38.25|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.560393              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.960   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.978443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.514   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1976 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1844 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2827 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4597 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4367 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5607 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6669 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| 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  1.806 |       0.155 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3683   r_free= 0.3613   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.131046                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3581   r_free= 0.3544   ksol= 0.33   Bsol= 59.33   scale= 0.975   |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.117788                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.834463              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.142   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.505811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.317   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3581      final r-factor (work) = 0.1968          |
| start r-factor (free) = 0.3544      final r-factor (free) = 0.2240          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9476 = 4.83 * 0.50 * 6.1168 + 1.00 * 0.1618                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1919 = 4.83 * 0.50 * 5.8410 + 1.00 * 0.0728                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1968      final r-factor (work) = 0.1784          |
| start r-factor (free) = 0.2240      final r-factor (free) = 0.2325          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9606 = 0.51 * 1.00 * 5.8410 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8065 = 0.51 * 1.00 * 5.5275 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.13    86.09   17.57    None  None   None       |
|    all(noH): 2823   0      1.13    86.09   17.57    None  None   None       |
|    Sol.    : 438    0      3.43    86.09   41.30    None  None   None       |
|    Mac.    : 2385   0      1.13    72.59   13.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.129 -   9.625:  894   |   5:    43.609 -  52.106:   95        |
|      1:     9.625 -  18.121: 1134   |   6:    52.106 -  60.602:   83        |
|      2:    18.121 -  26.617:  306   |   7:    60.602 -  69.098:   38        |
|      3:    26.617 -  35.113:  141   |   8:    69.098 -  77.594:   12        |
|      4:    35.113 -  43.609:  114   |   9:    77.594 -  86.090:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1784 r_free = 0.2325             target_work(ml) = 5.543         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1779 r_free = 0.2320             target_work(ml) = 5.541         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1779   r_free= 0.2320   ksol= 0.33   Bsol= 59.33   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.541374                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1764   r_free= 0.2297   ksol= 0.34   Bsol= 66.56   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.23,-1.14,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.541313                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.019528              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.501   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.153890              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.221  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1764      final r-factor (work) = 0.1386          |
| start r-factor (free) = 0.2297      final r-factor (free) = 0.1858          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6826 = 2.02 * 0.50 * 5.5556 + 1.00 * 0.0728                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5452 = 2.02 * 0.50 * 5.4400 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1386      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.1858      final r-factor (free) = 0.1753          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8478 = 0.15 * 1.00 * 5.4400 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8258 = 0.15 * 1.00 * 5.3146 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    82.74   17.17    None  None   None       |
|    all(noH): 2823   0      1.48    82.74   17.17    None  None   None       |
|    Sol.    : 438    0      6.00    82.74   39.88    None  None   None       |
|    Mac.    : 2385   0      1.48    70.73   13.00    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:     1.478 -   9.604:  881   |   5:    42.107 -  50.233:   90        |
|      1:     9.604 -  17.729: 1172   |   6:    50.233 -  58.359:   83        |
|      2:    17.729 -  25.855:  283   |   7:    58.359 -  66.485:   39        |
|      3:    25.855 -  33.981:  139   |   8:    66.485 -  74.610:   15        |
|      4:    33.981 -  42.107:  116   |   9:    74.610 -  82.736:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1336 r_free = 0.1753             target_work(ml) = 5.286         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1334 r_free = 0.1753             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1753   ksol= 0.34   Bsol= 66.56   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-2.23,-1.14,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.285344                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1749   ksol= 0.33   Bsol= 66.56   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.61,-1.07,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.284366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.393486              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.905  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.019913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.314  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1335      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1749      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4119 = 2.39 * 0.50 * 5.3142 + 1.00 * 0.0521                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3189 = 2.39 * 0.50 * 5.2285 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3404 = 1.02 * 1.00 * 5.2285 + 1.00 * 0.0078                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2802 = 1.02 * 1.00 * 5.1674 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.89   17.49    None  None   None       |
|    all(noH): 2823   0      0.00    87.89   17.49    None  None   None       |
|    Sol.    : 438    0      6.06    87.89   41.71    None  None   None       |
|    Mac.    : 2385   0      0.00    81.91   13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.789:  742   |   5:    43.943 -  52.731:   94        |
|      1:     8.789 -  17.577: 1302   |   6:    52.731 -  61.520:   79        |
|      2:    17.577 -  26.366:  296   |   7:    61.520 -  70.308:   47        |
|      3:    26.366 -  35.154:  133   |   8:    70.308 -  79.097:   22        |
|      4:    35.154 -  43.943:  102   |   9:    79.097 -  87.885:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1594             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1594             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1594   ksol= 0.33   Bsol= 66.56   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.61,-1.07,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163646                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1594   ksol= 0.33   Bsol= 66.56   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.59,-1.02,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163571                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.733031              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.352  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.365203              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.716  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5393 = 1.73 * 0.50 * 5.1673 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5277 = 1.73 * 0.50 * 5.1620 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8949 = 0.37 * 1.00 * 5.1620 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8954 = 0.37 * 1.00 * 5.1640 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.45    88.02   17.31    None  None   None       |
|    all(noH): 2823   0      0.45    88.02   17.31    None  None   None       |
|    Sol.    : 438    0      5.90    88.02   41.26    None  None   None       |
|    Mac.    : 2385   0      0.45    82.43   12.91    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:     0.447 -   9.204:  868   |   5:    44.232 -  52.990:   90        |
|      1:     9.204 -  17.961: 1215   |   6:    52.990 -  61.747:   78        |
|      2:    17.961 -  26.718:  271   |   7:    61.747 -  70.504:   39        |
|      3:    26.718 -  35.475:  129   |   8:    70.504 -  79.261:   21        |
|      4:    35.475 -  44.232:  106   |   9:    79.261 -  88.018:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1589             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1589             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1589   ksol= 0.33   Bsol= 66.56   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.59,-1.02,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161858                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1588   ksol= 0.32   Bsol= 60.06   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.48,-0.86,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161902                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.189077              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.968  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.260840              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.843  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2893 = 3.19 * 0.50 * 5.1642 + 1.00 * 0.0547                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2737 = 3.19 * 0.50 * 5.1425 + 1.00 * 0.0739                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4932 = 1.26 * 1.00 * 5.1425 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4842 = 1.26 * 1.00 * 5.1348 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.26   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    91.26   17.18    None  None   None       |
|    Sol.    : 438    0      5.86    91.26   41.09    None  None   None       |
|    Mac.    : 2385   0      0.00    86.59   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.126:  892   |   5:    45.630 -  54.756:   87        |
|      1:     9.126 -  18.252: 1211   |   6:    54.756 -  63.882:   72        |
|      2:    18.252 -  27.378:  256   |   7:    63.882 -  73.008:   33        |
|      3:    27.378 -  36.504:  138   |   8:    73.008 -  82.134:   17        |
|      4:    36.504 -  45.630:  111   |   9:    82.134 -  91.260:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1588             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1587             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1587   ksol= 0.32   Bsol= 60.06   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.48,-0.86,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136851                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7347 0.99   1408  157 0.0964 0.1311      5.3737      5.5587|
|  2:  4.7347 -  3.7770 0.99   1351  151 0.0823 0.1096      5.4178      5.6089|
|  3:  3.7770 -  3.3052 0.99   1340  144 0.1033 0.1534      5.4587       5.851|
|  4:  3.3052 -  3.0056 0.99   1327  152 0.1184 0.1713      5.4469      5.6122|
|  5:  3.0056 -  2.7915 0.99   1320  147 0.1323 0.1725      5.3163      5.5764|
|  6:  2.7915 -  2.6279 0.99   1302  142 0.1175 0.1951      5.1938      5.4932|
|  7:  2.6279 -  2.4968 0.99   1298  139 0.1226 0.1546       5.155      5.3029|
|  8:  2.4968 -  2.3886 0.98   1287  147 0.1121 0.1635      5.0471      5.3125|
|  9:  2.3886 -  2.2970 0.98   1276  150 0.1146 0.1777      5.0262       5.315|
| 10:  2.2970 -  2.2179 1.00   1315  147 0.1077 0.1743      4.9251      5.2014|
| 11:  2.2179 -  2.1488 0.98   1291  134 0.1058 0.1815      4.9186      5.3139|
| 12:  2.1488 -  2.0875 0.98   1262  144 0.1084 0.1689       4.852      5.1348|
| 13:  2.0875 -  2.0327 0.99   1293  136 0.1115 0.1700      4.7829      5.0169|
| 14:  2.0327 -  1.9832 0.43    560   69 0.0996 0.1596      4.6791      4.9083|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7347  1408   157  0.94   9.31   0.97     0.95       7347.15|
|  2:  4.7347 -  3.7770  1351   151  0.95   7.94   1.01     1.00       9083.98|
|  3:  3.7770 -  3.3052  1340   144  0.94  11.09   1.02     1.02      10129.24|
|  4:  3.3052 -  3.0056  1327   152  0.92  14.12   1.01     0.98      10536.70|
|  5:  3.0056 -  2.7915  1320   147  0.90  16.02   0.99     0.97       8375.25|
|  6:  2.7915 -  2.6279  1302   142  0.90  16.24   0.99     0.96       7109.14|
|  7:  2.6279 -  2.4968  1298   139  0.91  15.41   0.99     0.95       6157.76|
|  8:  2.4968 -  2.3886  1287   147  0.91  15.23   0.98     0.96       5244.55|
|  9:  2.3886 -  2.2970  1276   150  0.91  15.33   0.99     0.95       4964.11|
| 10:  2.2970 -  2.2179  1315   147  0.90  15.67   0.99     0.96       4249.17|
| 11:  2.2179 -  2.1488  1291   134  0.91  15.37   0.97     0.93       4164.27|
| 12:  2.1488 -  2.0875  1262   144  0.91  15.57   1.00     0.99       3912.73|
| 13:  2.0875 -  2.0327  1293   136  0.90  16.78   0.98     0.96       3422.74|
| 14:  2.0327 -  1.9832   560    69  0.92  14.50   0.96     0.93       2744.18|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2744.18 max =        10536.70 mean =      6433.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.11|
|phase err.(test): min =        0.00 max =           89.47 mean =        13.58|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1581   ksol= 0.32   Bsol= 60.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.34,-0.73,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135629                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1581   ksol= 0.32   Bsol= 60.72   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.34,-0.73,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135629                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7347 0.99   1408  157 0.0969 0.1242      5.3659      5.5269|
|  2:  4.7347 -  3.7770 0.99   1351  151 0.0828 0.1081       5.411      5.5949|
|  3:  3.7770 -  3.3052 0.99   1340  144 0.1035 0.1521       5.457      5.8426|
|  4:  3.3052 -  3.0056 0.99   1327  152 0.1181 0.1722      5.4457      5.6158|
|  5:  3.0056 -  2.7915 0.99   1320  147 0.1323 0.1724       5.317      5.5759|
|  6:  2.7915 -  2.6279 0.99   1302  142 0.1174 0.1949      5.1933       5.493|
|  7:  2.6279 -  2.4968 0.99   1298  139 0.1226 0.1549      5.1554      5.3029|
|  8:  2.4968 -  2.3886 0.98   1287  147 0.1121 0.1637      5.0471      5.3137|
|  9:  2.3886 -  2.2970 0.98   1276  150 0.1145 0.1777      5.0263      5.3154|
| 10:  2.2970 -  2.2179 1.00   1315  147 0.1076 0.1745      4.9254      5.2023|
| 11:  2.2179 -  2.1488 0.98   1291  134 0.1060 0.1818      4.9195      5.3151|
| 12:  2.1488 -  2.0875 0.98   1262  144 0.1084 0.1688      4.8521      5.1353|
| 13:  2.0875 -  2.0327 0.99   1293  136 0.1114 0.1700      4.7829      5.0169|
| 14:  2.0327 -  1.9832 0.43    560   69 0.0995 0.1597      4.6788      4.9082|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7347  1408   157  0.94   8.93   0.97     0.94       6765.70|
|  2:  4.7347 -  3.7770  1351   151  0.95   7.65   1.01     1.00       8687.57|
|  3:  3.7770 -  3.3052  1340   144  0.94  11.04   1.02     1.02      10009.61|
|  4:  3.3052 -  3.0056  1327   152  0.92  14.12   1.01     0.98      10526.34|
|  5:  3.0056 -  2.7915  1320   147  0.90  16.02   1.00     0.98       8389.78|
|  6:  2.7915 -  2.6279  1302   142  0.90  16.23   0.99     0.96       7100.58|
|  7:  2.6279 -  2.4968  1298   139  0.91  15.41   0.99     0.96       6163.58|
|  8:  2.4968 -  2.3886  1287   147  0.91  15.25   0.99     0.97       5248.25|
|  9:  2.3886 -  2.2970  1276   150  0.91  15.34   1.00     0.96       4968.34|
| 10:  2.2970 -  2.2179  1315   147  0.90  15.68   1.00     0.97       4256.76|
| 11:  2.2179 -  2.1488  1291   134  0.91  15.40   0.98     0.93       4171.08|
| 12:  2.1488 -  2.0875  1262   144  0.91  15.59   1.01     1.00       3918.80|
| 13:  2.0875 -  2.0327  1293   136  0.90  16.78   0.99     0.97       3423.21|
| 14:  2.0327 -  1.9832   560    69  0.92  14.50   0.97     0.94       2742.45|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2742.45 max =        10526.34 mean =      6349.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.06|
|phase err.(test): min =        0.00 max =           89.40 mean =        13.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.26   17.19    None  None   None       |
|    all(noH): 2823   0      0.00    91.26   17.19    None  None   None       |
|    Sol.    : 438    0      5.86    91.26   41.09    None  None   None       |
|    Mac.    : 2385   0      0.00    86.60   12.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.129:  892   |   5:    45.633 -  54.759:   87        |
|      1:     9.129 -  18.255: 1211   |   6:    54.759 -  63.885:   72        |
|      2:    18.255 -  27.381:  256   |   7:    63.885 -  73.011:   33        |
|      3:    27.381 -  36.507:  138   |   8:    73.011 -  82.137:   17        |
|      4:    36.507 -  45.633:  111   |   9:    82.137 -  91.263:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.546 - 4.722
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 289 from: 294
   mapped sites are within: 0.708 - 4.722

peak=    5.717 closest distance to " NE2 GLN A  11 " =    1.175
peak=    5.605 closest distance to " NH2 ARG A  56 " =    2.162
peak=    5.400 closest distance to " CB  GLN A 223 " =    1.458
peak=    5.272 closest distance to " O   HOH Z 144 " =    1.782
peak=    5.224 closest distance to " O   HOH Z 232 " =    2.277
peak=    5.149 closest distance to " CG  PRO A  54 " =    1.241
peak=    4.892 closest distance to " CB  GLN A 183 " =    1.245
peak=    4.881 closest distance to " O   HOH Z 369 " =    2.138
peak=    4.868 closest distance to " O   HOH Z 126 " =    1.953
peak=    4.858 closest distance to " O   HOH Z 133 " =    2.385
peak=    4.765 closest distance to " CB  SER A  63 " =    1.216
peak=    4.640 closest distance to " O   HOH Z 298 " =    2.063
peak=    4.493 closest distance to " CB  ARG A 190 " =    1.611
peak=    4.480 closest distance to " CG  PRO A 213 " =    1.182
peak=    4.461 closest distance to " CB  ARG A  79 " =    1.495
peak=    4.451 closest distance to " CB  PRO A  54 " =    0.936
peak=    4.436 closest distance to " CB  ASN A 148 " =    1.416
peak=    4.429 closest distance to " C   PRO A 198 " =    1.535
peak=    4.405 closest distance to " O   HOH Z  78 " =    1.762
peak=    4.398 closest distance to " CB  ARG A 275 " =    0.918
peak=    4.374 closest distance to " O   HOH Z   9 " =    2.209
peak=    4.333 closest distance to " O   HOH Z 427 " =    2.923
peak=    4.266 closest distance to " CB  LEU A 228 " =    1.084
peak=    4.263 closest distance to " CD  ARG A 159 " =    0.772
peak=    4.238 closest distance to " O   HOH Z 180 " =    2.093
peak=    4.217 closest distance to " O   HOH Z 287 " =    2.149
peak=    4.208 closest distance to " CA  TYR A  30 " =    0.990
peak=    4.188 closest distance to " CE  LYS A  76 " =    0.874
peak=    4.170 closest distance to " CZ  PHE A 218 " =    1.055
peak=    4.153 closest distance to " O   HOH Z 303 " =    2.240
peak=    4.133 closest distance to " ND2 ASN A 187 " =    1.438
peak=    4.067 closest distance to " O   HOH Z 316 " =    3.075
peak=    4.062 closest distance to " NH1AARG A 145 " =    1.240
peak=    4.058 closest distance to " CB  VAL A 265 " =    1.318
peak=    4.043 closest distance to " O   HOH Z 193 " =    1.749
peak=    4.036 closest distance to " CB  SER A 212 " =    1.120
peak=    4.035 closest distance to " O   HOH Z 158 " =    3.053
peak=    4.031 closest distance to " CG  LEU A 167 " =    1.266
peak=    4.027 closest distance to " CB  TRP A 266 " =    1.020
peak=    4.014 closest distance to " O   HOH Z 423 " =    1.463
peak=    4.012 closest distance to " O   HOH Z 272 " =    1.808
peak=    4.004 closest distance to " ND1 HIS A  86 " =    1.790
peak=    4.001 closest distance to " O   HOH Z 250 " =    1.496
peak=    3.989 closest distance to " CG2 VAL A 257 " =    0.920
peak=    3.981 closest distance to " O   HOH Z 368 " =    2.057
peak=    3.960 closest distance to " O   HOH Z   1 " =    2.039
peak=    3.956 closest distance to " O   HOH Z  68 " =    2.186
peak=    3.952 closest distance to " O   HOH Z  61 " =    1.595
peak=    3.951 closest distance to " O   HOH Z 425 " =    1.332
peak=    3.946 closest distance to " CB  GLU A 152 " =    1.303
peak=    3.944 closest distance to " CG  PRO A 198 " =    1.247
peak=    3.938 closest distance to " O   HOH Z  21 " =    1.744
peak=    3.919 closest distance to " O   HOH Z 261 " =    1.984
peak=    3.906 closest distance to " O   HOH Z  78 " =    2.365
peak=    3.903 closest distance to " CD  ARG A  66 " =    2.248
peak=    3.889 closest distance to " O   HOH Z 285 " =    2.424
peak=    3.881 closest distance to " O   HOH Z 189 " =    2.737
peak=    3.870 closest distance to " CD2 TRP A 179 " =    1.329
peak=    3.868 closest distance to " OD1 ASN A  69 " =    2.684
peak=    3.866 closest distance to " O   HOH Z 346 " =    1.716
peak=    3.862 closest distance to " O   HOH Z 217 " =    3.147
peak=    3.862 closest distance to " CB  GLU A 128 " =    0.983
peak=    3.823 closest distance to " CB  GLU A 277 " =    3.661
peak=    3.807 closest distance to " O   HOH Z 234 " =    3.746
peak=    3.806 closest distance to " O   HOH Z 214 " =    2.102
peak=    3.804 closest distance to " CG  PRO A 243 " =    1.101
peak=    3.803 closest distance to " O   HOH Z 132 " =    2.557
peak=    3.781 closest distance to " CG2 THR A 221 " =    1.058
peak=    3.768 closest distance to " CA  ASN A 215 " =    1.194
peak=    3.753 closest distance to " O   HOH Z 405 " =    1.196
peak=    3.752 closest distance to " O   HOH Z 265 " =    2.383
peak=    3.724 closest distance to " O   HOH Z 419 " =    2.059
peak=    3.723 closest distance to " O   HOH Z 406 " =    1.612
peak=    3.722 closest distance to " O   HOH Z  10 " =    1.827
peak=    3.714 closest distance to " O   HOH Z 391 " =    2.894
peak=    3.709 closest distance to " O   HOH Z 135 " =    1.751
peak=    3.703 closest distance to " O   HOH Z 371 " =    2.802
peak=    3.702 closest distance to " O   HOH Z  53 " =    2.505
peak=    3.679 closest distance to " CB  TYR A 169 " =    0.771
peak=    3.677 closest distance to " CA  PRO A  54 " =    1.355
peak=    3.675 closest distance to " O   HOH Z 193 " =    1.864
peak=    3.674 closest distance to " CB  VAL A 202 " =    1.647
peak=    3.672 closest distance to " CB  ASN A 142 " =    0.960
peak=    3.663 closest distance to " O   HOH Z 368 " =    3.611
peak=    3.662 closest distance to " O   HOH Z   1 " =    1.685
peak=    3.659 closest distance to " O   HOH Z 203 " =    1.880
peak=    3.658 closest distance to " CB  ASP A 140 " =    1.007
peak=    3.658 closest distance to " O   HOH Z 172 " =    3.117
peak=    3.657 closest distance to " O   HOH Z  61 " =    1.512
peak=    3.654 closest distance to " O   HOH Z 213 " =    2.179
peak=    3.653 closest distance to " CB  SER A   3 " =    1.356
peak=    3.653 closest distance to " CB  ASN A 187 " =    1.189
peak=    3.645 closest distance to " O   HOH Z 313 " =    1.961
peak=    3.640 closest distance to " O   HOH Z 128 " =    2.267
peak=    3.639 closest distance to " O   HOH Z 365 " =    2.934
peak=    3.626 closest distance to " CA  MET A  40 " =    1.237
peak=    3.615 closest distance to " O   HOH Z 386 " =    3.068
peak=    3.608 closest distance to " O   HOH Z 209 " =    2.294
peak=    3.597 closest distance to " CD1 LEU A 300 " =    1.189
peak=    3.596 closest distance to " CA  ARG A 195 " =    1.262
peak=    3.595 closest distance to " O   HOH Z 193 " =    2.117
peak=    3.595 closest distance to " CA  ALA A 158 " =    1.177
peak=    3.592 closest distance to " O   HOH Z  88 " =    3.998
peak=    3.592 closest distance to " CB  ASN A  39 " =    0.918
peak=    3.591 closest distance to " O   HOH Z 325 " =    4.000
peak=    3.589 closest distance to " CD  LYS A 166 " =    1.262
peak=    3.588 closest distance to " CA  SER A  87 " =    0.989
peak=    3.584 closest distance to " CA  ALA A 233 " =    1.188
peak=    3.583 closest distance to " O   MET A 105 " =    1.886
peak=    3.580 closest distance to " CD BLYS A 290 " =    0.947
peak=    3.578 closest distance to " O   HOH Z 280 " =    3.080
peak=    3.576 closest distance to " CB  TYR A 116 " =    0.815
peak=    3.576 closest distance to " O   SER A  87 " =    2.316
peak=    3.572 closest distance to " CB  GLU A  46 " =    0.946
peak=    3.565 closest distance to " O   HOH Z 437 " =    1.386
peak=    3.560 closest distance to " CB  ALA A   1 " =    4.722
peak=    3.560 closest distance to " O   TYR A 116 " =    1.303
peak=    3.544 closest distance to " CA  TYR A 116 " =    1.318
peak=    3.541 closest distance to " CB  ASN A 110 " =    1.124
peak=    3.540 closest distance to " CB  LYS A 117 " =    1.215
peak=    3.539 closest distance to " CA  THR A 221 " =    0.974
peak=    3.534 closest distance to " O   HOH Z 353 " =    2.629
peak=    3.527 closest distance to " CB  SER A 216 " =    0.916
peak=    3.527 closest distance to " CB  GLN A  88 " =    1.267
peak=    3.525 closest distance to " NH2 ARG A 156 " =    1.215
peak=    3.522 closest distance to " N   PHE A 130 " =    1.212
peak=    3.519 closest distance to " NE2 HIS A 207 " =    1.336
peak=    3.513 closest distance to " CG1 ILE A  33 " =    1.184
peak=    3.513 closest distance to " O   HOH Z 213 " =    2.772
peak=    3.510 closest distance to " O   HOH Z 329 " =    3.962
peak=    3.503 closest distance to " CD2 LEU A 255 " =    1.707
peak=    3.495 closest distance to " O   HOH Z 183 " =    1.377
peak=    3.487 closest distance to " O   HOH Z 411 " =    3.702
peak=    3.487 closest distance to " O   HOH Z 108 " =    2.624
peak=    3.486 closest distance to " CB  ARG A 139 " =    0.978
peak=    3.485 closest distance to " OG BSER A 164 " =    2.366
peak=    3.481 closest distance to " O   HOH Z 422 " =    2.730
peak=    3.480 closest distance to " CA  THR A 264 " =    0.886
peak=    3.479 closest distance to " CB  ALA A  34 " =    1.050
peak=    3.472 closest distance to " CA  VAL A 125 " =    1.152
peak=    3.467 closest distance to " CA  ALA A  51 " =    0.933
peak=    3.465 closest distance to " O   HOH Z 327 " =    1.866
peak=    3.463 closest distance to " OE1 GLN A  11 " =    2.152
peak=    3.460 closest distance to " ND2 ASN A 249 " =    0.864
peak=    3.448 closest distance to " O   HOH Z 124 " =    1.905
peak=    3.448 closest distance to " O   HOH Z  58 " =    1.512
peak=    3.442 closest distance to " CB  MET A  47 " =    1.072
peak=    3.430 closest distance to " N   ASN A 127 " =    1.311
peak=    3.426 closest distance to " CA  GLY A 267 " =    1.181
peak=    3.425 closest distance to " CD  ARG A 269 " =    0.888
peak=    3.422 closest distance to " O   HOH Z 148 " =    3.403
peak=    3.421 closest distance to " CB  THR A  82 " =    1.319
peak=    3.417 closest distance to " CG BARG A 275 " =    1.487
peak=    3.415 closest distance to " CB  MET A  40 " =    0.780
peak=    3.405 closest distance to " O   HOH Z 425 " =    1.965
peak=    3.403 closest distance to " CB  TRP A 150 " =    1.220
peak=    3.400 closest distance to " CA  ILE A 234 " =    0.994
peak=    3.399 closest distance to " O   HOH Z 426 " =    1.903
peak=    3.398 closest distance to " CA  ALA A 291 " =    0.859
peak=    3.393 closest distance to " O   HOH Z 344 " =    3.167
peak=    3.390 closest distance to " O  BHOH Z 338 " =    2.390
peak=    3.378 closest distance to " CA  MET A 105 " =    0.986
peak=    3.377 closest distance to " O   HOH Z 294 " =    1.514
peak=    3.376 closest distance to " O   HOH Z  59 " =    1.900
peak=    3.374 closest distance to " O   HOH Z 291 " =    1.535
peak=    3.373 closest distance to " O   HOH Z 409 " =    2.509
peak=    3.369 closest distance to " NE2 GLN A  73 " =    3.884
peak=    3.367 closest distance to " N   ARG A 156 " =    1.323
peak=    3.364 closest distance to " O   HOH Z 290 " =    0.884
peak=    3.361 closest distance to " O   THR A 220 " =    1.334
peak=    3.360 closest distance to " CB  TRP A 179 " =    1.553
peak=    3.358 closest distance to " O   HOH Z 147 " =    1.796
peak=    3.356 closest distance to " O   HOH Z   2 " =    1.364
peak=    3.356 closest distance to " CA  GLU A  46 " =    0.845
peak=    3.355 closest distance to " OG  SER A  62 " =    2.978
peak=    3.353 closest distance to " CD2 LEU A 297 " =    0.891
peak=    3.348 closest distance to " NE  ARG A  79 " =    1.157
peak=    3.347 closest distance to " O   HOH Z 116 " =    3.150
peak=    3.346 closest distance to " CB  ILE A 120 " =    1.374
peak=    3.345 closest distance to " CD1 ILE A  33 " =    1.664
peak=    3.343 closest distance to " CA  ARG A 102 " =    1.138
peak=    3.334 closest distance to " CG1 VAL A 189 " =    1.936
peak=    3.332 closest distance to " O   HOH Z 368 " =    4.147
peak=    3.332 closest distance to " CG1 VAL A 153 " =    0.923
peak=    3.332 closest distance to " O   HOH Z 403 " =    1.457
peak=    3.331 closest distance to " OD2 ASP A 286 " =    2.874
peak=    3.328 closest distance to " O   HOH Z 188 " =    1.887
peak=    3.325 closest distance to " O   HOH Z 126 " =    1.509
peak=    3.323 closest distance to " CA  TYR A  30 " =    1.053
peak=    3.319 closest distance to " O   HOH Z 258 " =    2.127
peak=    3.317 closest distance to " O   ALA A 291 " =    1.555
peak=    3.315 closest distance to " O   ASN A 209 " =    1.337
peak=    3.313 closest distance to " CB  TYR A 169 " =    0.822
peak=    3.311 closest distance to " CB  ALA A   9 " =    1.632
peak=    3.310 closest distance to " CG  MET A 113 " =    1.441
peak=    3.309 closest distance to " O   HOH Z  66 " =    2.178
peak=    3.306 closest distance to " CG2 ILE A  20 " =    1.415
peak=    3.304 closest distance to " OD1BASN A 224 " =    2.402
peak=    3.303 closest distance to " CB  THR A 235 " =    1.269
peak=    3.303 closest distance to " NH2 ARG A 219 " =    1.774
peak=    3.293 closest distance to " CB  ARG A 138 " =    0.968
peak=    3.293 closest distance to " CE1 PHE A 218 " =    0.986
peak=    3.291 closest distance to " CA  ARG A 159 " =    1.282
peak=    3.288 closest distance to " O   HOH Z  44 " =    2.873
peak=    3.287 closest distance to " O   HOH Z 175 " =    2.232
peak=    3.286 closest distance to " CG  ARG A 159 " =    0.850
peak=    3.285 closest distance to " O   HOH Z 287 " =    2.246
peak=    3.285 closest distance to " CB  SER A 245 " =    3.153
peak=    3.283 closest distance to " O   HOH Z 380 " =    1.607
peak=    3.279 closest distance to " CB  ALA A 104 " =    0.708
peak=    3.279 closest distance to " O   HOH Z 109 " =    2.608
peak=    3.276 closest distance to " CA  ASN A 217 " =    1.206
peak=    3.275 closest distance to " ND1 HIS A  81 " =    1.643
peak=    3.275 closest distance to " CE1 TYR A 186 " =    1.347
peak=    3.274 closest distance to " ND2 ASN A 110 " =    1.674
peak=    3.271 closest distance to " O   HOH Z 218 " =    4.509
peak=    3.270 closest distance to " CA  ALA A 154 " =    1.048
peak=    3.263 closest distance to " OG BSER A 134 " =    3.127
peak=    3.261 closest distance to " ND2 ASN A 249 " =    1.919
peak=    3.261 closest distance to " O   HOH Z 188 " =    2.311
peak=    3.259 closest distance to " CG  GLN A  89 " =    1.528
peak=    3.259 closest distance to " CB  LEU A 143 " =    1.150
peak=    3.257 closest distance to " O   HOH Z 185 " =    1.912
peak=    3.257 closest distance to " O   HOH Z  63 " =    1.287
peak=    3.256 closest distance to " O   ALA A 165 " =    1.548
peak=    3.253 closest distance to " CA  LYS A 290 " =    1.349
peak=    3.251 closest distance to " O   HOH Z 305 " =    3.562
peak=    3.250 closest distance to " O   HOH Z 326 " =    2.497
peak=    3.248 closest distance to " O   HOH Z 417 " =    3.520
peak=    3.246 closest distance to " CD2 TYR A 186 " =    1.061
peak=    3.245 closest distance to " O   HOH Z 343 " =    3.513
peak=    3.243 closest distance to " CA  ARG A  36 " =    1.101
peak=    3.241 closest distance to " NH1 ARG A 138 " =    1.041
peak=    3.241 closest distance to " OG  SER A  22 " =    2.871
peak=    3.230 closest distance to " CB  ALA A 248 " =    0.939
peak=    3.230 closest distance to " CE  LYS A  48 " =    1.074
peak=    3.230 closest distance to " CD  LYS A  76 " =    1.938
peak=    3.230 closest distance to " N   CYS A 260 " =    0.929
peak=    3.230 closest distance to " O   HOH Z 286 " =    2.350
peak=    3.225 closest distance to " CD  PRO A 243 " =    1.592
peak=    3.219 closest distance to " N   SER A 146 " =    1.733
peak=    3.216 closest distance to " CB  SER A  62 " =    1.136
peak=    3.212 closest distance to " CB  GLN A 103 " =    0.847
peak=    3.211 closest distance to " O   ASN A  74 " =    1.523
peak=    3.209 closest distance to " C   TYR A 214 " =    1.563
peak=    3.207 closest distance to " CA  LEU A 101 " =    1.420
peak=    3.198 closest distance to " CG1 ILE A 151 " =    1.054
peak=    3.196 closest distance to " CA  ALA A 160 " =    0.925
peak=    3.195 closest distance to " CG  GLN A 278 " =    1.447
peak=    3.189 closest distance to " O   HOH Z 238 " =    3.766
peak=    3.187 closest distance to " O   HOH Z 407 " =    2.342
peak=    3.181 closest distance to " CB  ASP A 171 " =    1.335
peak=    3.176 closest distance to " O   HOH Z  64 " =    2.348
peak=    3.173 closest distance to " O   HOH Z  20 " =    1.695
peak=    3.171 closest distance to " CB  SER A 210 " =    0.751
peak=    3.170 closest distance to " OD2 ASP A 286 " =    3.330
peak=    3.155 closest distance to " O   HOH Z 299 " =    4.376
peak=    3.154 closest distance to " OD1 ASN A 217 " =    1.572
peak=    3.151 closest distance to " O   HOH Z 271 " =    2.419
peak=    3.151 closest distance to " O   HOH Z 358 " =    3.772
peak=    3.150 closest distance to " CZ3 TRP A 266 " =    1.141
peak=    3.150 closest distance to " OG  SER A  62 " =    3.045
peak=    3.143 closest distance to " CA  SER A  95 " =    1.031
peak=    3.143 closest distance to " CB  ALA A 114 " =    1.399
peak=    3.142 closest distance to " O   HOH Z 145 " =    2.341
peak=    3.125 closest distance to " O   ALA A 158 " =    1.342
peak=    3.120 closest distance to " O   HOH Z 302 " =    1.815
peak=    3.118 closest distance to " O   GLY A  57 " =    2.591
peak=    3.117 closest distance to " CA  LYS A 117 " =    1.189
peak=    3.107 closest distance to " CB  ALA A 291 " =    1.361
peak=    3.107 closest distance to " O   HOH Z 273 " =    2.825
peak=    3.103 closest distance to " CB  SER A  26 " =    1.729
peak=    3.102 closest distance to " CD1 ILE A 263 " =    1.317
peak=    3.100 closest distance to " O   HOH Z 227 " =    1.835
peak=    3.100 closest distance to " CE3 TRP A  85 " =    0.916
peak=    3.100 closest distance to " NH2AARG A 275 " =    3.584
peak=    3.099 closest distance to " OE2 GLU A  53 " =    2.060
peak=    3.096 closest distance to " CA  ALA A 100 " =    1.170
peak=    3.096 closest distance to " CB  GLU A 236 " =    1.102
peak=    3.095 closest distance to " O   HOH Z 130 " =    3.765
peak=    3.094 closest distance to " O   HOH Z 152 " =    2.730
peak=    3.093 closest distance to " O   HOH Z 245 " =    1.237
peak=    3.090 closest distance to " CD1AILE A 234 " =    0.947
peak=    3.088 closest distance to " O   HOH Z  43 " =    1.904
peak=    3.080 closest distance to " CB  ALA A  43 " =    0.793
peak=    3.072 closest distance to " CD1 ILE A 106 " =    0.767
peak=    3.060 closest distance to " O   HOH Z 403 " =    1.569
peak=    3.053 closest distance to " O   HOH Z 359 " =    1.387
peak=    3.040 closest distance to " O   HOH Z 359 " =    4.147

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.732 - 5.691
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 217
   mapped sites are within: 0.732 - 5.691

peak=   -4.741 closest distance to " O   HOH Z 377 " =    2.086
peak=   -4.576 closest distance to " CD  ARG A 156 " =    2.099
peak=   -4.368 closest distance to " CB  PRO A 243 " =    2.567
peak=   -4.351 closest distance to " SG  CYS A 254 " =    3.544
peak=   -4.283 closest distance to " O   HOH Z 231 " =    2.197
peak=   -4.264 closest distance to " CG  GLN A 223 " =    2.080
peak=   -4.248 closest distance to " OG BSER A 134 " =    1.310
peak=   -4.222 closest distance to " O   VAL A  67 " =    2.740
peak=   -4.059 closest distance to " CZ3 TRP A 179 " =    1.152
peak=   -4.055 closest distance to " O   HOH Z 351 " =    1.509
peak=   -4.038 closest distance to " O   PRO A 198 " =    1.295
peak=   -4.016 closest distance to " O   HOH Z 266 " =    5.274
peak=   -3.960 closest distance to " CG1 VAL A 112 " =    3.018
peak=   -3.919 closest distance to " N   ALA A  43 " =    2.619
peak=   -3.915 closest distance to " O   HOH Z 185 " =    2.247
peak=   -3.913 closest distance to " O   HOH Z 389 " =    2.093
peak=   -3.903 closest distance to " CB  ALA A  43 " =    2.579
peak=   -3.895 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -3.894 closest distance to " O   HOH Z  38 " =    1.379
peak=   -3.858 closest distance to " O   HOH Z 407 " =    3.288
peak=   -3.847 closest distance to " CG1 VAL A 112 " =    2.637
peak=   -3.841 closest distance to " O   HOH Z 372 " =    2.492
peak=   -3.824 closest distance to " O   HOH Z 313 " =    1.785
peak=   -3.815 closest distance to " O   HOH Z 198 " =    1.965
peak=   -3.799 closest distance to " CB  TRP A  85 " =    2.487
peak=   -3.788 closest distance to " CA  GLY A 203 " =    2.352
peak=   -3.782 closest distance to " CE  MET A 105 " =    2.350
peak=   -3.776 closest distance to " OG  SER A  97 " =    2.167
peak=   -3.776 closest distance to " C   HIS A 108 " =    1.163
peak=   -3.762 closest distance to " CD2 LEU A 143 " =    2.640
peak=   -3.751 closest distance to " CD  GLN A  58 " =    0.942
peak=   -3.739 closest distance to " O   HOH Z 435 " =    2.919
peak=   -3.738 closest distance to " O   HOH Z 290 " =    1.256
peak=   -3.728 closest distance to " CA  GLY A 241 " =    2.307
peak=   -3.706 closest distance to " O   HOH Z 394 " =    1.450
peak=   -3.703 closest distance to " CB  ALA A 291 " =    2.229
peak=   -3.702 closest distance to " C   LEU A 222 " =    0.732
peak=   -3.699 closest distance to " O   HOH Z  73 " =    2.084
peak=   -3.698 closest distance to " CG1BVAL A  41 " =    2.855
peak=   -3.683 closest distance to " CD1 PHE A  59 " =    1.937
peak=   -3.667 closest distance to " N   ASP A 286 " =    2.523
peak=   -3.663 closest distance to " CD  ARG A 195 " =    5.264
peak=   -3.663 closest distance to " OXT GLY A 302 " =    3.093
peak=   -3.662 closest distance to " O   PRO A 163 " =    2.033
peak=   -3.660 closest distance to " O   HOH Z 111 " =    1.777
peak=   -3.645 closest distance to " ND2 ASN A  45 " =    1.992
peak=   -3.639 closest distance to " NH2AARG A 275 " =    5.527
peak=   -3.638 closest distance to " CE2 PHE A 218 " =    2.382
peak=   -3.624 closest distance to " O   PHE A 218 " =    1.522
peak=   -3.619 closest distance to " CD1 LEU A 101 " =    2.341
peak=   -3.617 closest distance to " O   ALA A  10 " =    1.650
peak=   -3.603 closest distance to " OD1 ASP A 171 " =    1.670
peak=   -3.592 closest distance to " ND2 ASN A 249 " =    2.382
peak=   -3.583 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.581 closest distance to " CG1 VAL A 250 " =    2.607
peak=   -3.581 closest distance to " O   HOH Z 359 " =    3.234
peak=   -3.570 closest distance to " CA  ASP A  27 " =    2.495
peak=   -3.569 closest distance to " NH2BARG A 275 " =    1.802
peak=   -3.566 closest distance to " N   THR A 157 " =    1.558
peak=   -3.560 closest distance to " CB  PHE A 192 " =    1.990
peak=   -3.554 closest distance to " O   HOH Z 198 " =    1.578
peak=   -3.552 closest distance to " CG2 THR A 178 " =    2.272
peak=   -3.548 closest distance to " OG BSER A 134 " =    1.732
peak=   -3.543 closest distance to " O   HOH Z 211 " =    1.485
peak=   -3.538 closest distance to " CB  ASP A 286 " =    2.194
peak=   -3.535 closest distance to " ND2 ASN A  60 " =    1.535
peak=   -3.529 closest distance to " O   PRO A 198 " =    1.369
peak=   -3.526 closest distance to " O   HOH Z 298 " =    1.240
peak=   -3.523 closest distance to " CB  ALA A 291 " =    2.133
peak=   -3.510 closest distance to " O   TYR A 247 " =    2.862
peak=   -3.508 closest distance to " O   PRO A 243 " =    2.495
peak=   -3.505 closest distance to " O   HOH Z 243 " =    2.015
peak=   -3.501 closest distance to " O   SER A 135 " =    1.425
peak=   -3.494 closest distance to " CD2 TYR A 293 " =    1.965
peak=   -3.482 closest distance to " O   HOH Z 426 " =    1.639
peak=   -3.477 closest distance to " O   HOH Z 102 " =    1.579
peak=   -3.474 closest distance to " CD1 LEU A 228 " =    2.388
peak=   -3.470 closest distance to " O   HOH Z 253 " =    3.988
peak=   -3.456 closest distance to " O   GLY A 211 " =    1.345
peak=   -3.454 closest distance to " O   HOH Z 131 " =    4.117
peak=   -3.449 closest distance to " O   HOH Z  22 " =    2.508
peak=   -3.447 closest distance to " O   HOH Z  10 " =    1.491
peak=   -3.447 closest distance to " O   HOH Z  43 " =    1.643
peak=   -3.445 closest distance to " CB  ASN A  39 " =    2.274
peak=   -3.433 closest distance to " OD1 ASN A 148 " =    1.576
peak=   -3.429 closest distance to " CA  GLY A  98 " =    1.887
peak=   -3.421 closest distance to " CG  PHE A 283 " =    2.660
peak=   -3.421 closest distance to " ND2 ASN A  69 " =    1.768
peak=   -3.419 closest distance to " N   ASP A 171 " =    2.333
peak=   -3.416 closest distance to " CB  PRO A  54 " =    2.498
peak=   -3.413 closest distance to " OG  SER A  87 " =    1.339
peak=   -3.405 closest distance to " O   HOH Z 176 " =    0.875
peak=   -3.400 closest distance to " C   GLY A  17 " =    1.177
peak=   -3.399 closest distance to " CB  PRO A 163 " =    2.467
peak=   -3.392 closest distance to " OD1 ASP A 191 " =    1.905
peak=   -3.389 closest distance to " CB  ALA A 100 " =    2.194
peak=   -3.386 closest distance to " O   GLY A  80 " =    2.446
peak=   -3.385 closest distance to " OD1 ASN A 187 " =    1.608
peak=   -3.372 closest distance to " C   LEU A 143 " =    1.284
peak=   -3.371 closest distance to " O   HOH Z 191 " =    5.691
peak=   -3.371 closest distance to " ND2BASN A 224 " =    1.697
peak=   -3.364 closest distance to " O   ILE A 109 " =    2.601
peak=   -3.364 closest distance to " O   HOH Z 348 " =    2.200
peak=   -3.364 closest distance to " C   ALA A 158 " =    1.503
peak=   -3.363 closest distance to " CG1 VAL A 197 " =    2.245
peak=   -3.360 closest distance to " CB  CYS A 254 " =    2.198
peak=   -3.359 closest distance to " O   ARG A 145 " =    1.570
peak=   -3.353 closest distance to " CD  ARG A 139 " =    1.564
peak=   -3.351 closest distance to " O   HOH Z 114 " =    3.194
peak=   -3.344 closest distance to " O   HOH Z  11 " =    1.791
peak=   -3.337 closest distance to " O   HOH Z  52 " =    1.367
peak=   -3.337 closest distance to " CG  GLN A  88 " =    0.867
peak=   -3.334 closest distance to " CE BMET A  47 " =    1.436
peak=   -3.331 closest distance to " O   HOH Z  51 " =    1.642
peak=   -3.327 closest distance to " O   HOH Z 345 " =    2.229
peak=   -3.324 closest distance to " CB  ALA A 248 " =    2.382
peak=   -3.323 closest distance to " CA  ASP A 298 " =    1.036
peak=   -3.322 closest distance to " O   HOH Z  90 " =    1.657
peak=   -3.317 closest distance to " CB  TYR A  15 " =    2.247
peak=   -3.315 closest distance to " O   HOH Z 281 " =    2.707
peak=   -3.314 closest distance to " O   VAL A 189 " =    2.511
peak=   -3.311 closest distance to " O   HOH Z 196 " =    2.187
peak=   -3.306 closest distance to " CD1 LEU A 297 " =    2.551
peak=   -3.304 closest distance to " O   HOH Z 111 " =    1.371
peak=   -3.301 closest distance to " ND2 ASN A  45 " =    1.238
peak=   -3.300 closest distance to " CE2 PHE A  61 " =    2.674
peak=   -3.297 closest distance to " O   HOH Z 275 " =    1.791
peak=   -3.297 closest distance to " O   HOH Z 353 " =    2.163
peak=   -3.296 closest distance to " C   ASN A 187 " =    1.913
peak=   -3.289 closest distance to " CG2 ILE A 263 " =    2.318
peak=   -3.288 closest distance to " CD2 PHE A 225 " =    1.116
peak=   -3.288 closest distance to " CZ  PHE A  59 " =    1.596
peak=   -3.288 closest distance to " OD1AASN A 224 " =    1.794
peak=   -3.276 closest distance to " CG  TRP A 266 " =    1.708
peak=   -3.275 closest distance to " OE1 GLN A  88 " =    1.127
peak=   -3.274 closest distance to " O   SER A 210 " =    1.919
peak=   -3.270 closest distance to " OD2 ASP A 140 " =    1.681
peak=   -3.265 closest distance to " NE  ARG A  36 " =    1.952
peak=   -3.265 closest distance to " O   VAL A  67 " =    2.914
peak=   -3.261 closest distance to " CG1 VAL A 125 " =    1.876
peak=   -3.261 closest distance to " O   HOH Z  63 " =    1.668
peak=   -3.260 closest distance to " O   HOH Z 323 " =    1.505
peak=   -3.254 closest distance to " CD1 PHE A  61 " =    2.965
peak=   -3.248 closest distance to " O   HOH Z 337 " =    1.543
peak=   -3.246 closest distance to " CA  GLY A 241 " =    3.273
peak=   -3.245 closest distance to " ND2 ASN A 249 " =    2.157
peak=   -3.242 closest distance to " SD  MET A 188 " =    2.288
peak=   -3.240 closest distance to " NH2 ARG A 219 " =    1.743
peak=   -3.235 closest distance to " N   MET A 105 " =    2.522
peak=   -3.232 closest distance to " N   SER A 276 " =    1.281
peak=   -3.231 closest distance to " N   ALA A 248 " =    1.582
peak=   -3.226 closest distance to " OH  TYR A 172 " =    1.749
peak=   -3.223 closest distance to " O   HOH Z 140 " =    1.627
peak=   -3.222 closest distance to " O   HOH Z 174 " =    2.676
peak=   -3.219 closest distance to " CE3 TRP A 150 " =    2.207
peak=   -3.219 closest distance to " OH  TYR A 247 " =    1.838
peak=   -3.219 closest distance to " O   HOH Z 252 " =    4.382
peak=   -3.218 closest distance to " O   HOH Z 100 " =    1.441
peak=   -3.218 closest distance to " ND2 ASN A 187 " =    1.555
peak=   -3.217 closest distance to " NE2 GLN A  88 " =    1.910
peak=   -3.213 closest distance to " C   GLY A  13 " =    0.979
peak=   -3.210 closest distance to " O   HOH Z 298 " =    2.455
peak=   -3.209 closest distance to " NH1 ARG A 195 " =    2.685
peak=   -3.208 closest distance to " CG2 VAL A 189 " =    1.966
peak=   -3.207 closest distance to " O   HOH Z 348 " =    1.841
peak=   -3.206 closest distance to " NZ  LYS A 166 " =    1.188
peak=   -3.203 closest distance to " CB  ALA A   9 " =    2.416
peak=   -3.197 closest distance to " O   HOH Z 417 " =    3.040
peak=   -3.191 closest distance to " O   HOH Z 241 " =    1.422
peak=   -3.190 closest distance to " O   HOH Z 317 " =    1.587
peak=   -3.190 closest distance to " O   HOH Z 292 " =    1.836
peak=   -3.186 closest distance to " O   HOH Z 184 " =    1.734
peak=   -3.182 closest distance to " O   HOH Z 414 " =    2.495
peak=   -3.179 closest distance to " CG1 VAL A  67 " =    2.853
peak=   -3.178 closest distance to " O   HOH Z   6 " =    1.526
peak=   -3.177 closest distance to " O   VAL A 189 " =    1.612
peak=   -3.177 closest distance to " O   HOH Z 350 " =    1.868
peak=   -3.165 closest distance to " O   HOH Z 266 " =    5.033
peak=   -3.143 closest distance to " CE3 TRP A 123 " =    1.290
peak=   -3.142 closest distance to " O   HOH Z 385 " =    2.018
peak=   -3.140 closest distance to " O   HOH Z 409 " =    4.506
peak=   -3.135 closest distance to " O   HOH Z   9 " =    2.018
peak=   -3.133 closest distance to " O   HOH Z 189 " =    2.073
peak=   -3.127 closest distance to " CB  GLN A  11 " =    1.778
peak=   -3.126 closest distance to " NH1 ARG A  36 " =    2.041
peak=   -3.117 closest distance to " CD1 ILE A 199 " =    2.620
peak=   -3.115 closest distance to " CD1 ILE A 239 " =    2.350
peak=   -3.115 closest distance to " CZ  TYR A 169 " =    1.699
peak=   -3.114 closest distance to " O   HOH Z 174 " =    2.975
peak=   -3.112 closest distance to " O   HOH Z 219 " =    4.804
peak=   -3.110 closest distance to " OG  SER A 245 " =    1.293
peak=   -3.107 closest distance to " CG  PRO A 163 " =    2.372
peak=   -3.105 closest distance to " O   HOH Z 318 " =    2.026
peak=   -3.103 closest distance to " O   HOH Z 114 " =    1.573
peak=   -3.102 closest distance to " C   LYS A  76 " =    1.623
peak=   -3.101 closest distance to " CB  ASP A 132 " =    2.380
peak=   -3.099 closest distance to " O   HOH Z 114 " =    0.931
peak=   -3.097 closest distance to " CD2 PHE A  61 " =    2.031
peak=   -3.091 closest distance to " N   ALA A 226 " =    2.107
peak=   -3.085 closest distance to " NH2 ARG A  79 " =    1.530
peak=   -3.084 closest distance to " O   ASP A  27 " =    1.894
peak=   -3.084 closest distance to " CG  GLU A 277 " =    1.258
peak=   -3.077 closest distance to " CG1 VAL A 268 " =    2.437
peak=   -3.074 closest distance to " CD1 TRP A 179 " =    1.121
peak=   -3.072 closest distance to " CD2 HIS A 207 " =    2.376
peak=   -3.066 closest distance to " O   HOH Z  13 " =    1.757
peak=   -3.058 closest distance to " SG ACYS A 201 " =    1.945
peak=   -3.057 closest distance to " ND2 ASN A  60 " =    1.936
peak=   -3.055 closest distance to " CD2 PHE A 130 " =    2.886
peak=   -3.046 closest distance to " O   TRP A  70 " =    1.459
peak=   -3.043 closest distance to " CA  GLY A 241 " =    2.868
peak=   -3.041 closest distance to " O   GLN A 240 " =    2.476
peak=   -3.032 closest distance to " CD2 TYR A 293 " =    2.133
peak=   -3.025 closest distance to " O   HOH Z 234 " =    4.222
peak=   -3.014 closest distance to " N   SER A 141 " =    1.830
peak=   -3.006 closest distance to " O   HOH Z 118 " =    1.126

================= 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    :  0.3683 0.3613   6.131046e+00   6.113381e+00
   1_bss:  0.3581 0.3544   6.117788e+00   6.095944e+00
   1_xyz:  0.1968 0.2240   5.596619e+00   5.687707e+00
   1_adp:  0.1784 0.2325   5.542821e+00   5.725445e+00
   1_occ:  0.1779 0.2320   5.541374e+00   5.724517e+00
   2_bss:  0.1764 0.2297   5.541313e+00   5.722618e+00
   2_xyz:  0.1386 0.1858   5.328547e+00   5.539429e+00
   2_adp:  0.1336 0.1753   5.285731e+00   5.488077e+00
   2_occ:  0.1334 0.1753   5.285344e+00   5.488199e+00
   3_bss:  0.1335 0.1749   5.284366e+00   5.485697e+00
   3_xyz:  0.1180 0.1603   5.183363e+00   5.406472e+00
   3_adp:  0.1144 0.1594   5.163659e+00   5.398848e+00
   3_occ:  0.1144 0.1594   5.163646e+00   5.398990e+00
   4_bss:  0.1144 0.1594   5.163571e+00   5.399002e+00
   4_xyz:  0.1140 0.1596   5.164737e+00   5.403337e+00
   4_adp:  0.1139 0.1589   5.162012e+00   5.399599e+00
   4_occ:  0.1138 0.1589   5.161858e+00   5.399538e+00
   5_bss:  0.1138 0.1588   5.161902e+00   5.399668e+00
   5_xyz:  0.1089 0.1581   5.137243e+00   5.392593e+00
   5_adp:  0.1086 0.1588   5.137019e+00   5.394443e+00
   5_occ:  0.1085 0.1587   5.136851e+00   5.394266e+00
   5_bss:  0.1087 0.1581   5.135629e+00   5.390551e+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:  0.335  59.326   0.000   0.000   0.000   0.000   0.000   0.000
   1_xyz:  0.335  59.326   0.000   0.000   0.000   0.000   0.000   0.000
   1_adp:  0.335  59.326   0.000   0.000   0.000   0.000   0.000   0.000
   1_occ:  0.335  59.326   0.000   0.000   0.000   0.000   0.000   0.000
   2_bss:  0.336  66.558  -1.893  -2.230  -1.137  -0.000  -0.000  -0.000
   2_xyz:  0.336  66.558  -1.893  -2.230  -1.137  -0.000  -0.000  -0.000
   2_adp:  0.336  66.558  -1.893  -2.230  -1.137  -0.000  -0.000  -0.000
   2_occ:  0.336  66.558  -1.893  -2.230  -1.137  -0.000  -0.000  -0.000
   3_bss:  0.332  66.558  -2.279  -2.607  -1.071  -0.000  -0.000  -0.000
   3_xyz:  0.332  66.558  -2.279  -2.607  -1.071  -0.000  -0.000  -0.000
   3_adp:  0.332  66.558  -2.279  -2.607  -1.071  -0.000  -0.000  -0.000
   3_occ:  0.332  66.558  -2.279  -2.607  -1.071  -0.000  -0.000  -0.000
   4_bss:  0.328  66.558  -2.242  -2.590  -1.021  -0.000  -0.000  -0.000
   4_xyz:  0.328  66.558  -2.242  -2.590  -1.021  -0.000  -0.000  -0.000
   4_adp:  0.328  66.558  -2.242  -2.590  -1.021  -0.000  -0.000  -0.000
   4_occ:  0.328  66.558  -2.242  -2.590  -1.021  -0.000  -0.000  -0.000
   5_bss:  0.320  60.064  -2.121  -2.478  -0.865  -0.000  -0.000  -0.000
   5_xyz:  0.320  60.064  -2.121  -2.478  -0.865  -0.000  -0.000  -0.000
   5_adp:  0.320  60.064  -2.121  -2.478  -0.865  -0.000  -0.000  -0.000
   5_occ:  0.320  60.064  -2.121  -2.478  -0.865  -0.000  -0.000  -0.000
   5_bss:  0.322  60.720  -1.961  -2.342  -0.726  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.547 0.6620  0.8346    36855.047
   1_bss:  37.744 0.6698  0.8491    34730.445
   1_xyz:  20.953 0.8538  1.0158    12393.382
   1_adp:  22.058 0.8420  1.0081    13221.424
   1_occ:  22.021 0.8423  1.0076    13159.229
   2_bss:  21.918 0.8434  0.9483    13102.781
   2_xyz:  17.441 0.8852  0.9737     8673.460
   2_adp:  16.089 0.8979  0.9772     7862.826
   2_occ:  16.092 0.8978  0.9770     7863.505
   3_bss:  16.056 0.8981  0.9689     7810.633
   3_xyz:  14.376 0.9120  0.9760     6590.674
   3_adp:  14.180 0.9137  0.9712     6451.315
   3_occ:  14.182 0.9137  0.9712     6453.652
   4_bss:  14.182 0.9137  0.9723     6453.145
   4_xyz:  14.252 0.9133  0.9716     6525.748
   4_adp:  14.158 0.9141  0.9672     6484.496
   4_occ:  14.157 0.9141  0.9672     6481.941
   5_bss:  14.162 0.9141  0.9715     6480.901
   5_xyz:  14.015 0.9151  0.9729     6421.001
   5_adp:  14.065 0.9148  0.9664     6436.543
   5_occ:  14.061 0.9148  0.9664     6433.362
   5_bss:  14.007 0.9151  0.9713     6349.610
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6180e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6180e-01
   1_xyz:   1.093  0.008  0.074 15.442  0.005  4.112   7.2804e-02
   1_adp:   1.093  0.008  0.074 15.442  0.005  4.112   7.2804e-02
   1_occ:   1.093  0.008  0.074 15.442  0.005  4.112   7.2804e-02
   2_bss:   1.093  0.008  0.074 15.442  0.005  4.112   7.2804e-02
   2_xyz:   0.948  0.006  0.071 14.447  0.003  4.124   5.2125e-02
   2_adp:   0.948  0.006  0.071 14.447  0.003  4.124   5.2125e-02
   2_occ:   0.948  0.006  0.071 14.447  0.003  4.124   5.2125e-02
   3_bss:   0.948  0.006  0.071 14.447  0.003  4.124   5.2125e-02
   3_xyz:   1.015  0.008  0.076 14.669  0.003  4.113   6.1781e-02
   3_adp:   1.015  0.008  0.076 14.669  0.003  4.113   6.1781e-02
   3_occ:   1.015  0.008  0.076 14.669  0.003  4.113   6.1781e-02
   4_bss:   1.015  0.008  0.076 14.669  0.003  4.113   6.1781e-02
   4_xyz:   0.946  0.007  0.072 14.493  0.003  4.114   5.4742e-02
   4_adp:   0.946  0.007  0.072 14.493  0.003  4.114   5.4742e-02
   4_occ:   0.946  0.007  0.072 14.493  0.003  4.114   5.4742e-02
   5_bss:   0.946  0.007  0.072 14.493  0.003  4.114   5.4742e-02
   5_xyz:   1.103  0.010  0.083 14.883  0.004  4.117   7.3864e-02
   5_adp:   1.103  0.010  0.083 14.883  0.004  4.117   7.3864e-02
   5_occ:   1.103  0.010  0.083 14.883  0.004  4.117   7.3864e-02
   5_bss:   1.103  0.010  0.083 14.883  0.004  4.117   7.3864e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4220e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4220e-01
   1_xyz:   9.226  0.057  0.269 84.310  0.046  2.226   1.2616e-01
   1_adp:   9.226  0.057  0.269 84.310  0.046  2.226   1.2616e-01
   1_occ:   9.226  0.057  0.269 84.310  0.046  2.226   1.2616e-01
   2_bss:   9.226  0.057  0.269 84.310  0.046  2.226   1.2616e-01
   2_xyz:   8.224  0.049  0.216 81.438  0.023  2.371   3.5545e-02
   2_adp:   8.224  0.049  0.216 81.438  0.023  2.371   3.5545e-02
   2_occ:   8.224  0.049  0.216 81.438  0.023  2.371   3.5545e-02
   3_bss:   8.224  0.049  0.216 81.438  0.023  2.371   3.5545e-02
   3_xyz:   8.132  0.042  0.236 84.201  0.025  2.338   4.2768e-02
   3_adp:   8.132  0.042  0.236 84.201  0.025  2.338   4.2768e-02
   3_occ:   8.132  0.042  0.236 84.201  0.025  2.338   4.2768e-02
   4_bss:   8.132  0.042  0.236 84.201  0.025  2.338   4.2768e-02
   4_xyz:   7.852  0.047  0.215 83.169  0.027  2.383   3.4954e-02
   4_adp:   7.852  0.047  0.215 83.169  0.027  2.383   3.4954e-02
   4_occ:   7.852  0.047  0.215 83.169  0.027  2.383   3.4954e-02
   5_bss:   7.852  0.047  0.215 83.169  0.027  2.383   3.4954e-02
   5_xyz:   7.779  0.049  0.273 83.898  0.029  2.291   5.9314e-02
   5_adp:   7.779  0.049  0.273 83.898  0.029  2.291   5.9314e-02
   5_occ:   7.779  0.049  0.273 83.898  0.029  2.291   5.9314e-02
   5_bss:   7.779  0.049  0.273 83.898  0.029  2.291   5.9314e-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:  86.09   1.13  17.57  72.59   1.13  13.22  86.09   3.43  41.30
   1_occ:  86.09   1.13  17.57  72.59   1.13  13.22  86.09   3.43  41.30
   2_bss:  86.09   1.13  17.57  72.59   1.13  13.22  86.09   3.43  41.30
   2_xyz:  86.09   1.13  17.57  72.59   1.13  13.22  86.09   3.43  41.30
   2_adp:  82.74   1.48  17.17  70.73   1.48  13.00  82.74   6.00  39.88
   2_occ:  82.74   1.48  17.17  70.73   1.48  13.00  82.74   6.00  39.88
   3_bss:  82.74   1.48  17.17  70.73   1.48  13.00  82.74   6.00  39.88
   3_xyz:  82.74   1.48  17.17  70.73   1.48  13.00  82.74   6.00  39.88
   3_adp:  87.89   0.00  17.49  81.91   0.00  13.05  87.89   6.06  41.71
   3_occ:  87.89   0.00  17.49  81.91   0.00  13.05  87.89   6.06  41.71
   4_bss:  87.89   0.00  17.49  81.91   0.00  13.05  87.89   6.06  41.71
   4_xyz:  87.89   0.00  17.49  81.91   0.00  13.05  87.89   6.06  41.71
   4_adp:  88.02   0.45  17.31  82.43   0.45  12.91  88.02   5.90  41.26
   4_occ:  88.02   0.45  17.31  82.43   0.45  12.91  88.02   5.90  41.26
   5_bss:  88.02   0.45  17.31  82.43   0.45  12.91  88.02   5.90  41.26
   5_xyz:  88.02   0.45  17.31  82.43   0.45  12.91  88.02   5.90  41.26
   5_adp:  91.26   0.00  17.18  86.59   0.00  12.80  91.26   5.86  41.09
   5_occ:  91.26   0.00  17.18  86.59   0.00  12.80  91.26   5.86  41.09
   5_bss:  91.26   0.00  17.19  86.60   0.00  12.80  91.26   5.86  41.09
------------------------------------------------------------------------
 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:    1.102    0.026    0.348
   1_adp:    1.102    0.026    0.348
   1_occ:    1.102    0.026    0.348
   2_bss:    1.102    0.026    0.348
   2_xyz:    1.013    0.025    0.405
   2_adp:    1.013    0.025    0.405
   2_occ:    1.013    0.025    0.405
   3_bss:    1.013    0.025    0.405
   3_xyz:    1.071    0.027    0.455
   3_adp:    1.071    0.027    0.455
   3_occ:    1.071    0.027    0.455
   4_bss:    1.071    0.027    0.455
   4_xyz:    1.192    0.032    0.462
   4_adp:    1.192    0.032    0.462
   4_occ:    1.192    0.032    0.462
   5_bss:    1.192    0.032    0.462
   5_xyz:    1.263    0.057    0.473
   5_adp:    1.263    0.057    0.473
   5_occ:    1.263    0.057    0.473
   5_bss:    1.263    0.057    0.473
------------------------------------------------------------------------

CPU time actual refinement: 265.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1008/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_1008/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1008/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1008/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1008/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 265.72 
  Macro-tasks:
    bulk solvent and scale       = 31.94  
    individual site refinement   = 106.94 
    weights calculation          = 24.67  
    collect and process          = 5.57   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 169.21 
  Micro-tasks:
    mask                            = 1.48   
    f_calc                          = 82.81  
    alpha_beta                      = 6.99   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 90.32  
    fmodel                         = 5.34   
    r_factors                      = 0.18   
    phase_errors                   = 9.19   
    foms                           = 0.18   
    TOTAL for micro-tasks          = 197.47 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.812 micro seconds
Total CPU time: 4.62 minutes
from_scatterers_fft:    627 calls, 82.51 s
gradients_fft:          572 calls, 78.99 s

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

# Date 2008-01-16 Time 06:10:49 PST -0800 (1200492649.22 s)
Start R-work = 0.3683, R-free = 0.3613 (no bulk solvent and anisotropic scale)
Final R-work = 0.1311, R-free = 0.1772 (no bulk solvent and anisotropic scale)

Start R-work = 0.3581, R-free = 0.3544
Final R-work = 0.1087, R-free = 0.1581