# Date 2008-01-16 Time 03:56:20 PST -0800 (1200484580.21 s)
#phil __OFF__

Command line arguments: "../108.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7286
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 108

-------------------------------------------------------------------------------
  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: (68.4938, 47.8686, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.95101
Completeness in resolution range: 0.903343
Completeness with d_max=infinity: 0.900685

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0027
                             d_min =   1.9510

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: (68.4938, 47.8686, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0027 1.95101
Completeness in resolution range: 0.903343
Completeness with d_max=infinity: 0.900685

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0031 -  4.1760 [2275/2303]  2043   232  10.2%
  bin  2:  4.1760 -  3.3265 [2193/2216]  1973   220  10.0%
  bin  3:  3.3265 -  2.9095 [2157/2182]  1950   207   9.6%
  bin  4:  2.9095 -  2.6450 [2123/2150]  1906   217  10.2%
  bin  5:  2.6450 -  2.4563 [2108/2141]  1888   220  10.4%
  bin  6:  2.4563 -  2.3121 [2131/2159]  1926   205   9.6%
  bin  7:  2.3121 -  2.1966 [2085/2121]  1881   204   9.8%
  bin  8:  2.1966 -  2.1013 [2093/2135]  1885   208   9.9%
  bin  9:  2.1013 -  2.0206 [1923/2151]  1732   191   9.9%
  bin 10:  2.0206 -  1.9510 [ 501/2127]   446    55  11.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_108/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        0.96 -     1.75: 9
        1.75 -     2.54: 65
        2.54 -     3.32: 3861
        3.32 -     4.11: 9361
        4.11 -     4.90: 14975
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  0.961 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.159 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.217 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.360 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.388 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28266 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_108/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_108/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 68.49375 47.8686 88.1178 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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4949   r_free= 0.4973   ksol= 0.00   Bsol= 0.00   scale= 0.868    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.298117                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6582 0.99   1479  162 0.3898 0.4106      6.5991      6.6287|
|  2:  4.6582 -  3.7159 0.99   1419  157 0.4400 0.4582      6.8454      6.8722|
|  3:  3.7159 -  3.2516 0.99   1395  158 0.4799 0.4791      6.6912      6.7049|
|  4:  3.2516 -  2.9568 0.98   1375  146 0.4971 0.4670      6.5166      6.5042|
|  5:  2.9568 -  2.7463 0.99   1387  157 0.5206 0.5266      6.3642      6.3942|
|  6:  2.7463 -  2.5852 0.99   1364  155 0.5265 0.5301      6.2776      6.1865|
|  7:  2.5852 -  2.4563 0.98   1341  161 0.5286 0.4669      6.2273      6.1557|
|  8:  2.4563 -  2.3498 0.98   1383  145 0.5514 0.5723      6.1682      6.2226|
|  9:  2.3498 -  2.2597 0.99   1346  142 0.5529 0.5259      6.1223      6.1635|
| 10:  2.2597 -  2.1819 0.99   1376  146 0.5348 0.5322      6.0762      6.0978|
| 11:  2.1819 -  2.1139 0.97   1338  160 0.5480 0.5530      6.0051      6.0234|
| 12:  2.1139 -  2.0536 0.98   1314  150 0.5407 0.5564      5.9494      5.9277|
| 13:  2.0536 -  1.9997 0.66    908   95 0.5238 0.5785      5.8685      5.8276|
| 14:  1.9997 -  1.9510 0.15    205   25 0.4919 0.4816      5.9222      5.7249|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.6582  1479   162  0.67  37.13   0.81     0.68      80469.60|
|  2:  4.6582 -  3.7159  1419   157  0.65  39.17   0.89     0.75     125296.59|
|  3:  3.7159 -  3.2516  1395   158  0.52  50.12   0.88     0.71     134202.77|
|  4:  3.2516 -  2.9568  1375   146  0.42  58.10   0.87     0.60     115302.20|
|  5:  2.9568 -  2.7463  1387   157  0.35  63.66   0.85     0.52      91090.00|
|  6:  2.7463 -  2.5852  1364   155  0.32  65.93   0.87     0.47      77004.53|
|  7:  2.5852 -  2.4563  1341   161  0.30  67.14   0.87     0.43      70673.33|
|  8:  2.4563 -  2.3498  1383   145  0.27  69.73   0.88     0.41      63688.39|
|  9:  2.3498 -  2.2597  1346   142  0.26  70.94   0.88     0.41      62187.27|
| 10:  2.2597 -  2.1819  1376   146  0.26  70.46   0.89     0.39      53768.78|
| 11:  2.1819 -  2.1139  1338   160  0.20  74.82   0.88     0.34      53689.01|
| 12:  2.1139 -  2.0536  1314   150  0.16  77.89   0.92     0.27      49596.05|
| 13:  2.0536 -  1.9997   908    95  0.13  80.68   0.93     0.22      45433.24|
| 14:  1.9997 -  1.9510   205    25  0.18  76.47   0.98     0.22      33522.74|
|alpha:            min =        0.22 max =            0.75 mean =         0.48|
|beta:             min =    33522.74 max =       134202.77 mean =     79388.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.89|
|phase err.(test): min =        0.00 max =           89.95 mean =        63.00|
|-----------------------------------------------------------------------------|

============================== 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 = 19.214121             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.469   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.000725              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.788   (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 |  0.961 -  1.355:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.355 -  1.748:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.748 -  2.142:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.142 -  2.536:       46 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.536 -  2.930:     1536 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.930 -  3.324:     2325 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.324 -  3.718:     3749 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.718 -  4.112:     5612 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.112 -  4.506:     6587 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.506 -  4.900:     8388 |
|-----------------------------------------------------------------------------|
|-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 |        0.233 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  0.961 |       1.201 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4949   r_free= 0.4973   ksol= 0.00   Bsol= 0.00   scale= 0.868    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.298117                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4890   r_free= 0.4881   ksol= 0.30   Bsol= 30.48   scale= 0.912   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,2.26,1.91,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.295618                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.476403             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.933   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.979634              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.331   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4890      final r-factor (work) = 0.3852          |
| start r-factor (free) = 0.4881      final r-factor (free) = 0.4143          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.9369 = 15.48 * 0.50 * 6.2940 + 1.00 * 0.2326                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.1486 = 15.48 * 0.50 * 6.2032 + 1.00 * 0.1467                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3852      final r-factor (work) = 0.3418          |
| start r-factor (free) = 0.4143      final r-factor (free) = 0.4240          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2862 = 1.98 * 1.00 * 6.2032 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.0919 = 1.98 * 1.00 * 6.0947 + 1.00 * 0.0266                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.83  20.92    None  None   None       |
|    all(noH): 2823   0      0.00    107.83  20.92    None  None   None       |
|    Sol.    : 438    0      0.00    107.83  41.12    None  None   None       |
|    Mac.    : 2385   0      0.00    97.92   17.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.783:  946   |   5:    53.914 -  64.697:   95        |
|      1:    10.783 -  21.566:  803   |   6:    64.697 -  75.480:   48        |
|      2:    21.566 -  32.349:  487   |   7:    75.480 -  86.263:   19        |
|      3:    32.349 -  43.131:  261   |   8:    86.263 -  97.045:    4        |
|      4:    43.131 -  53.914:  155   |   9:    97.045 - 107.828:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3418 r_free = 0.4240             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3415 r_free = 0.4237             target_work(ml) = 6.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3415   r_free= 0.4237   ksol= 0.30   Bsol= 30.48   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,2.26,1.91,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.099618                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3403   r_free= 0.4208   ksol= 0.31   Bsol= 45.01   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,1.18,1.23,0.00,0.00,0.00); trace/3= 0.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.095834                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.964000             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.474  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.683143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.338  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3403      final r-factor (work) = 0.2708          |
| start r-factor (free) = 0.4208      final r-factor (free) = 0.3307          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.5571 = 10.96 * 0.50 * 6.0946 + 1.00 * 0.1466                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.0988 = 10.96 * 0.50 * 6.0203 + 1.00 * 0.0954                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2708      final r-factor (work) = 0.2455          |
| start r-factor (free) = 0.3307      final r-factor (free) = 0.3103          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1397 = 0.68 * 1.00 * 6.0203 + 1.00 * 0.0270                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0283 = 0.68 * 1.00 * 5.8574 + 1.00 * 0.0269                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.40  19.51    None  None   None       |
|    all(noH): 2823   0      0.00    102.40  19.51    None  None   None       |
|    Sol.    : 438    0      2.20    102.40  41.92    None  None   None       |
|    Mac.    : 2385   0      0.00    91.22   15.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.241:  955   |   5:    51.202 -  61.443:   87        |
|      1:    10.241 -  20.481:  957   |   6:    61.443 -  71.683:   50        |
|      2:    20.481 -  30.721:  362   |   7:    71.683 -  81.924:   22        |
|      3:    30.721 -  40.962:  222   |   8:    81.924 -  92.164:    8        |
|      4:    40.962 -  51.202:  156   |   9:    92.164 - 102.404:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2455 r_free = 0.3103             target_work(ml) = 5.829         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2455 r_free = 0.3098             target_work(ml) = 5.828         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2455   r_free= 0.3098   ksol= 0.31   Bsol= 45.01   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,1.18,1.23,0.00,0.00,0.00); trace/3= 0.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.827842                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2449   r_free= 0.3095   ksol= 0.32   Bsol= 58.15   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-0.19,0.21,-0.00,0.00,0.00); trace/3= -0.81                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.827707                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.327362              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.722   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.894178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.386   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2449      final r-factor (work) = 0.1928          |
| start r-factor (free) = 0.3095      final r-factor (free) = 0.2461          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7722 = 4.33 * 0.50 * 5.8589 + 1.00 * 0.0954                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4883 = 4.33 * 0.50 * 5.7412 + 1.00 * 0.0662                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1928      final r-factor (work) = 0.1781          |
| start r-factor (free) = 0.2461      final r-factor (free) = 0.2369          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1499 = 0.89 * 1.00 * 5.7412 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0011 = 0.89 * 1.00 * 5.5768 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.01  19.56    None  None   None       |
|    all(noH): 2823   0      0.00    106.01  19.56    None  None   None       |
|    Sol.    : 438    0      5.12    106.01  46.71    None  None   None       |
|    Mac.    : 2385   0      0.00    96.40   14.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.601: 1073   |   5:    53.006 -  63.607:  107        |
|      1:    10.601 -  21.202: 1004   |   6:    63.607 -  74.208:   62        |
|      2:    21.202 -  31.804:  264   |   7:    74.208 -  84.809:   29        |
|      3:    31.804 -  42.405:  138   |   8:    84.809 -  95.410:   17        |
|      4:    42.405 -  53.006:  124   |   9:    95.410 - 106.012:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1781 r_free = 0.2369             target_work(ml) = 5.555         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1780 r_free = 0.2369             target_work(ml) = 5.555         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1780   r_free= 0.2369   ksol= 0.32   Bsol= 58.15   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-0.19,0.21,-0.00,0.00,0.00); trace/3= -0.81                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.554881                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1779   r_free= 0.2363   ksol= 0.33   Bsol= 63.27   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,-1.20,-0.64,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.555056                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.352801              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.860  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297998              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.560  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1779      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2363      final r-factor (free) = 0.2060          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6330 = 2.35 * 0.50 * 5.5821 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5179 = 2.35 * 0.50 * 5.4923 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1518      final r-factor (work) = 0.1465          |
| start r-factor (free) = 0.2060      final r-factor (free) = 0.1959          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6510 = 0.30 * 1.00 * 5.4923 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6217 = 0.30 * 1.00 * 5.4064 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.77    104.80  18.47    None  None   None       |
|    all(noH): 2823   0      1.77    104.80  18.47    None  None   None       |
|    Sol.    : 438    0      6.21    104.80  44.27    None  None   None       |
|    Mac.    : 2385   0      1.77    100.51  13.73    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:     1.766 -  12.070: 1350   |   5:    53.285 -  63.589:   84        |
|      1:    12.070 -  22.373:  867   |   6:    63.589 -  73.892:   52        |
|      2:    22.373 -  32.677:  189   |   7:    73.892 -  84.196:   17        |
|      3:    32.677 -  42.981:  128   |   8:    84.196 -  94.500:   11        |
|      4:    42.981 -  53.285:  121   |   9:    94.500 - 104.804:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1465 r_free = 0.1959             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1463 r_free = 0.1956             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1463   r_free= 0.1956   ksol= 0.33   Bsol= 63.27   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,-1.20,-0.64,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.378990                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1466   r_free= 0.1960   ksol= 0.33   Bsol= 64.86   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.61,-1.73,-0.89,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.380248                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.023044              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.573  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260802              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.057  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1466      final r-factor (work) = 0.1330          |
| start r-factor (free) = 0.1960      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5265 = 2.02 * 0.50 * 5.4074 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4568 = 2.02 * 0.50 * 5.3379 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1330      final r-factor (work) = 0.1306          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1761          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4027 = 0.26 * 1.00 * 5.3379 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3888 = 0.26 * 1.00 * 5.2884 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.80    104.75  18.05    None  None   None       |
|    all(noH): 2823   0      1.80    104.75  18.05    None  None   None       |
|    Sol.    : 438    0      5.65    104.75  42.95    None  None   None       |
|    Mac.    : 2385   0      1.80    100.02  13.47    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.804 -  12.099: 1374   |   5:    53.279 -  63.574:   75        |
|      1:    12.099 -  22.394:  875   |   6:    63.574 -  73.869:   46        |
|      2:    22.394 -  32.689:  173   |   7:    73.869 -  84.164:   16        |
|      3:    32.689 -  42.984:  126   |   8:    84.164 -  94.459:   10        |
|      4:    42.984 -  53.279:  126   |   9:    94.459 - 104.754:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1306 r_free = 0.1761             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1305 r_free = 0.1762             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1305   r_free= 0.1762   ksol= 0.33   Bsol= 64.86   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.61,-1.73,-0.89,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278451                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6582 0.99   1479  162 0.1037 0.1370      5.4287      5.6407|
|  2:  4.6582 -  3.7159 0.99   1419  157 0.0908 0.1067      5.4864      5.6361|
|  3:  3.7159 -  3.2516 0.99   1395  158 0.1254 0.1682      5.5923      5.9062|
|  4:  3.2516 -  2.9568 0.98   1375  146 0.1498 0.1885      5.5758      5.7546|
|  5:  2.9568 -  2.7463 0.99   1387  157 0.1624 0.1981      5.4863      5.6636|
|  6:  2.7463 -  2.5852 0.99   1364  155 0.1481 0.2298      5.3505      5.5653|
|  7:  2.5852 -  2.4563 0.98   1341  161 0.1487 0.1903      5.3076      5.4851|
|  8:  2.4563 -  2.3498 0.98   1383  145 0.1450 0.2161      5.2412      5.4795|
|  9:  2.3498 -  2.2597 0.99   1346  142 0.1375 0.1873      5.1423      5.3298|
| 10:  2.2597 -  2.1819 0.99   1376  146 0.1378 0.1920      5.0719      5.2575|
| 11:  2.1819 -  2.1139 0.97   1338  160 0.1328 0.1999      4.9988      5.3573|
| 12:  2.1139 -  2.0536 0.98   1314  150 0.1327 0.1705      4.9532      5.1448|
| 13:  2.0536 -  1.9997 0.66    908   95 0.1255 0.1907      4.8604      5.0658|
| 14:  1.9997 -  1.9510 0.15    205   25 0.1211 0.1942      4.8406      4.9742|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.6582  1479   162  0.94   9.58   0.97     0.94       7738.58|
|  2:  4.6582 -  3.7159  1419   157  0.95   8.69   1.01     1.00       9966.21|
|  3:  3.7159 -  3.2516  1395   158  0.92  12.99   1.02     1.02      12414.61|
|  4:  3.2516 -  2.9568  1375   146  0.89  17.04   1.01     1.01      13069.79|
|  5:  2.9568 -  2.7463  1387   157  0.87  19.11   1.00     0.98      11535.23|
|  6:  2.7463 -  2.5852  1364   155  0.87  19.40   0.98     0.94       9328.06|
|  7:  2.5852 -  2.4563  1341   161  0.87  19.36   0.99     0.96       8656.25|
|  8:  2.4563 -  2.3498  1383   145  0.87  19.45   1.00     0.95       7609.95|
|  9:  2.3498 -  2.2597  1346   142  0.88  18.76   0.99     0.94       6381.87|
| 10:  2.2597 -  2.1819  1376   146  0.88  18.14   1.00     0.97       5456.73|
| 11:  2.1819 -  2.1139  1338   160  0.88  18.17   0.99     0.94       4877.64|
| 12:  2.1139 -  2.0536  1314   150  0.89  17.74   0.99     0.99       4473.05|
| 13:  2.0536 -  1.9997   908    95  0.88  18.53   0.99     0.97       3944.56|
| 14:  1.9997 -  1.9510   205    25  0.91  15.20   0.96     0.92       3240.40|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3240.40 max =        13069.79 mean =      8195.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.54|
|phase err.(test): min =        0.00 max =           89.31 mean =        16.04|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1305   r_free= 0.1761   ksol= 0.33   Bsol= 60.40   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.55,-1.66,-0.83,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278387                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1305   r_free= 0.1761   ksol= 0.33   Bsol= 60.40   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.55,-1.66,-0.83,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278387                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0031 -  4.6582 0.99   1479  162 0.1034 0.1370       5.427      5.6382|
|  2:  4.6582 -  3.7159 0.99   1419  157 0.0905 0.1065       5.484      5.6336|
|  3:  3.7159 -  3.2516 0.99   1395  158 0.1254 0.1683      5.5914      5.9062|
|  4:  3.2516 -  2.9568 0.98   1375  146 0.1499 0.1887      5.5763      5.7553|
|  5:  2.9568 -  2.7463 0.99   1387  157 0.1626 0.1983      5.4874      5.6646|
|  6:  2.7463 -  2.5852 0.99   1364  155 0.1482 0.2299      5.3512       5.566|
|  7:  2.5852 -  2.4563 0.98   1341  161 0.1488 0.1903      5.3083      5.4855|
|  8:  2.4563 -  2.3498 0.98   1383  145 0.1450 0.2161      5.2416      5.4796|
|  9:  2.3498 -  2.2597 0.99   1346  142 0.1375 0.1873      5.1427      5.3303|
| 10:  2.2597 -  2.1819 0.99   1376  146 0.1378 0.1921      5.0721      5.2574|
| 11:  2.1819 -  2.1139 0.97   1338  160 0.1328 0.2000       4.999      5.3576|
| 12:  2.1139 -  2.0536 0.98   1314  150 0.1327 0.1706      4.9534       5.145|
| 13:  2.0536 -  1.9997 0.66    908   95 0.1255 0.1907      4.8607      5.0659|
| 14:  1.9997 -  1.9510 0.15    205   25 0.1211 0.1943      4.8407      4.9748|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0031 -  4.6582  1479   162  0.94   9.55   0.97     0.94       7706.93|
|  2:  4.6582 -  3.7159  1419   157  0.95   8.66   1.01     1.00       9921.37|
|  3:  3.7159 -  3.2516  1395   158  0.92  12.96   1.02     1.02      12371.95|
|  4:  3.2516 -  2.9568  1375   146  0.89  17.04   1.01     1.01      13071.72|
|  5:  2.9568 -  2.7463  1387   157  0.87  19.13   1.00     0.98      11561.79|
|  6:  2.7463 -  2.5852  1364   155  0.87  19.42   0.98     0.94       9343.16|
|  7:  2.5852 -  2.4563  1341   161  0.87  19.37   0.99     0.96       8669.27|
|  8:  2.4563 -  2.3498  1383   145  0.87  19.45   1.00     0.95       7614.18|
|  9:  2.3498 -  2.2597  1346   142  0.88  18.76   0.99     0.94       6386.84|
| 10:  2.2597 -  2.1819  1376   146  0.88  18.14   1.00     0.97       5458.02|
| 11:  2.1819 -  2.1139  1338   160  0.88  18.18   0.99     0.94       4880.34|
| 12:  2.1139 -  2.0536  1314   150  0.89  17.74   0.99     0.99       4474.68|
| 13:  2.0536 -  1.9997   908    95  0.88  18.54   0.99     0.97       3947.30|
| 14:  1.9997 -  1.9510   205    25  0.91  15.21   0.96     0.92       3243.24|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3243.24 max =        13071.72 mean =      8191.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.54|
|phase err.(test): min =        0.00 max =           89.41 mean =        16.04|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.857)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    104.69  17.98    None  None   None       |
|    all(noH): 2823   0      1.74    104.69  17.98    None  None   None       |
|    Sol.    : 438    0      5.59    104.69  42.89    None  None   None       |
|    Mac.    : 2385   0      1.74    99.95   13.41    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:     1.740 -  12.035: 1374   |   5:    53.215 -  63.510:   75        |
|      1:    12.035 -  22.330:  875   |   6:    63.510 -  73.805:   46        |
|      2:    22.330 -  32.625:  173   |   7:    73.805 -  84.100:   16        |
|      3:    32.625 -  42.920:  126   |   8:    84.100 -  94.395:   10        |
|      4:    42.920 -  53.215:  126   |   9:    94.395 - 104.690:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.435 - 4.660
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 297
   mapped sites are within: 0.755 - 4.660

peak=   11.206 closest distance to " O  BHOH Z  74 " =    1.399
peak=    8.295 closest distance to " O   HOH Z 203 " =    1.085
peak=    7.358 closest distance to " O   HOH Z 255 " =    1.403
peak=    7.068 closest distance to " O   HOH Z 117 " =    1.718
peak=    5.745 closest distance to " O   HOH Z  54 " =    2.137
peak=    5.503 closest distance to " O   HOH Z 248 " =    1.592
peak=    5.391 closest distance to " O   HOH Z 124 " =    1.304
peak=    5.156 closest distance to " O   HOH Z  49 " =    1.551
peak=    5.111 closest distance to " O   HOH Z 403 " =    2.119
peak=    5.046 closest distance to " O  BHOH Z 338 " =    1.412
peak=    5.017 closest distance to " O   HOH Z 210 " =    1.313
peak=    4.951 closest distance to " CZ3 TRP A 266 " =    1.062
peak=    4.934 closest distance to " CG  PRO A  54 " =    1.439
peak=    4.910 closest distance to " CB  GLN A 223 " =    1.379
peak=    4.814 closest distance to " O   HOH Z 102 " =    1.497
peak=    4.802 closest distance to " O   HOH Z 188 " =    2.759
peak=    4.795 closest distance to " O   HOH Z 113 " =    1.985
peak=    4.789 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.780 closest distance to " CD2 TRP A 179 " =    1.356
peak=    4.707 closest distance to " O   HOH Z 404 " =    1.338
peak=    4.673 closest distance to " O   HOH Z 394 " =    1.783
peak=    4.634 closest distance to " CA  TYR A  30 " =    0.987
peak=    4.555 closest distance to " O   HOH Z  97 " =    1.432
peak=    4.554 closest distance to " CZ  PHE A 218 " =    1.250
peak=    4.455 closest distance to " O   HOH Z 186 " =    2.510
peak=    4.419 closest distance to " NH1AARG A 275 " =    1.344
peak=    4.408 closest distance to " O   HOH Z  43 " =    2.510
peak=    4.408 closest distance to " CB  SER A  62 " =    0.996
peak=    4.407 closest distance to " O   HOH Z 412 " =    3.656
peak=    4.350 closest distance to " O   HOH Z 188 " =    1.518
peak=    4.315 closest distance to " O   HOH Z 417 " =    2.151
peak=    4.283 closest distance to " CG  PRO A  90 " =    1.326
peak=    4.267 closest distance to " O   HOH Z  69 " =    1.241
peak=    4.255 closest distance to " O   HOH Z 414 " =    1.772
peak=    4.169 closest distance to " O   HOH Z 402 " =    1.550
peak=    4.160 closest distance to " CG AARG A 275 " =    1.299
peak=    4.158 closest distance to " CA  ARG A  36 " =    1.093
peak=    4.158 closest distance to " O   HOH Z  65 " =    1.143
peak=    4.155 closest distance to " O   HOH Z 287 " =    1.557
peak=    4.146 closest distance to " CB  ASN A 148 " =    1.436
peak=    4.137 closest distance to " CG2BVAL A  41 " =    0.865
peak=    4.134 closest distance to " CA  ALA A 100 " =    1.081
peak=    4.108 closest distance to " CG  PRO A 243 " =    1.108
peak=    4.100 closest distance to " CB  PRO A  54 " =    1.023
peak=    4.069 closest distance to " O   HOH Z 369 " =    1.988
peak=    4.060 closest distance to " O   HOH Z  63 " =    1.985
peak=    4.010 closest distance to " O   HOH Z 277 " =    1.397
peak=    3.995 closest distance to " CB  GLN A 183 " =    1.205
peak=    3.977 closest distance to " O   GLY A  23 " =    2.435
peak=    3.966 closest distance to " O   HOH Z 126 " =    1.531
peak=    3.965 closest distance to " O   PRO A 198 " =    1.524
peak=    3.962 closest distance to " CB  TRP A 179 " =    1.292
peak=    3.951 closest distance to " O   HOH Z 130 " =    2.567
peak=    3.951 closest distance to " O   HOH Z 132 " =    2.695
peak=    3.947 closest distance to " O   HOH Z 433 " =    1.613
peak=    3.939 closest distance to " O   HOH Z 134 " =    1.703
peak=    3.938 closest distance to " O   HOH Z 403 " =    1.545
peak=    3.916 closest distance to " CG2AVAL A 121 " =    2.093
peak=    3.911 closest distance to " O   HOH Z 346 " =    1.628
peak=    3.911 closest distance to " O   HOH Z 128 " =    1.545
peak=    3.900 closest distance to " CA  ALA A  51 " =    0.990
peak=    3.897 closest distance to " CB  ASN A 187 " =    1.359
peak=    3.895 closest distance to " O   HOH Z 425 " =    1.445
peak=    3.890 closest distance to " O   HOH Z 261 " =    2.538
peak=    3.885 closest distance to " CB  SER A  63 " =    1.072
peak=    3.871 closest distance to " O   HOH Z 345 " =    1.767
peak=    3.867 closest distance to " CG  GLN A  11 " =    1.297
peak=    3.866 closest distance to " O   HOH Z 178 " =    0.947
peak=    3.860 closest distance to " CB  PRO A 198 " =    1.198
peak=    3.857 closest distance to " O   HOH Z 406 " =    1.671
peak=    3.857 closest distance to " CB  SER A  26 " =    1.812
peak=    3.841 closest distance to " O   HOH Z 298 " =    1.765
peak=    3.839 closest distance to " O   HOH Z 232 " =    2.475
peak=    3.834 closest distance to " O   HOH Z 116 " =    1.451
peak=    3.822 closest distance to " CZ  PHE A  38 " =    1.096
peak=    3.821 closest distance to " CA  THR A 246 " =    1.075
peak=    3.816 closest distance to " CA  GLU A 152 " =    0.863
peak=    3.811 closest distance to " CG  GLN A  58 " =    1.085
peak=    3.809 closest distance to " O   THR A 220 " =    1.123
peak=    3.802 closest distance to " NH2 ARG A  56 " =    1.174
peak=    3.801 closest distance to " CD  LYS A 166 " =    1.550
peak=    3.796 closest distance to " O   THR A 182 " =    1.567
peak=    3.790 closest distance to " CB  SER A 141 " =    1.187
peak=    3.787 closest distance to " O   HOH Z 250 " =    1.430
peak=    3.786 closest distance to " O   HOH Z 214 " =    1.276
peak=    3.780 closest distance to " O   GLN A  11 " =    0.962
peak=    3.773 closest distance to " O   HOH Z  76 " =    1.091
peak=    3.772 closest distance to " CD  ARG A 269 " =    0.976
peak=    3.752 closest distance to " CD  PRO A  54 " =    1.064
peak=    3.748 closest distance to " O   HOH Z 251 " =    1.674
peak=    3.745 closest distance to " O   HOH Z 234 " =    3.364
peak=    3.745 closest distance to " O   HOH Z 298 " =    2.248
peak=    3.739 closest distance to " CD  ARG A 139 " =    1.210
peak=    3.737 closest distance to " CE  LYS A  76 " =    0.905
peak=    3.737 closest distance to " O   HOH Z  40 " =    1.988
peak=    3.736 closest distance to " NZ  LYS A 117 " =    2.840
peak=    3.732 closest distance to " O   ALA A 165 " =    1.443
peak=    3.724 closest distance to " CB  GLU A 277 " =    3.770
peak=    3.717 closest distance to " O   HOH Z 207 " =    1.426
peak=    3.700 closest distance to " O   HOH Z 209 " =    2.145
peak=    3.697 closest distance to " O   HOH Z  80 " =    2.022
peak=    3.697 closest distance to " NH2BARG A 145 " =    2.244
peak=    3.692 closest distance to " O   HOH Z 365 " =    2.396
peak=    3.684 closest distance to " CA  ARG A 195 " =    1.207
peak=    3.684 closest distance to " CB  PRO A  90 " =    1.020
peak=    3.679 closest distance to " CB  ASP A 191 " =    1.170
peak=    3.675 closest distance to " O   HOH Z 112 " =    1.111
peak=    3.674 closest distance to " CB  LYS A 289 " =    1.138
peak=    3.657 closest distance to " O   HOH Z  54 " =    1.977
peak=    3.656 closest distance to " CG1 ILE A  33 " =    1.188
peak=    3.633 closest distance to " CB  GLU A 152 " =    1.035
peak=    3.632 closest distance to " N   CYS A 260 " =    0.914
peak=    3.628 closest distance to " CD2 LEU A 297 " =    1.096
peak=    3.625 closest distance to " O   HOH Z 299 " =    4.216
peak=    3.624 closest distance to " O   HOH Z 389 " =    1.848
peak=    3.622 closest distance to " NE2 GLN A  11 " =    1.277
peak=    3.616 closest distance to " O   HOH Z 368 " =    2.169
peak=    3.614 closest distance to " CG  PRO A 198 " =    1.445
peak=    3.613 closest distance to " O   HOH Z 193 " =    1.360
peak=    3.611 closest distance to " O   HOH Z  85 " =    1.554
peak=    3.608 closest distance to " O   HOH Z  88 " =    3.361
peak=    3.607 closest distance to " O   HOH Z  35 " =    2.242
peak=    3.594 closest distance to " CG1 ILE A  20 " =    1.340
peak=    3.592 closest distance to " CD  ARG A 195 " =    1.069
peak=    3.585 closest distance to " CB  ALA A 114 " =    0.814
peak=    3.585 closest distance to " OG BSER A 258 " =    2.904
peak=    3.584 closest distance to " N   ASN A  39 " =    1.227
peak=    3.561 closest distance to " OG BSER A 212 " =    2.504
peak=    3.558 closest distance to " O   HOH Z 421 " =    2.215
peak=    3.556 closest distance to " O   HOH Z  21 " =    1.831
peak=    3.556 closest distance to " CD  ARG A 159 " =    0.843
peak=    3.555 closest distance to " CB  ALA A 248 " =    1.372
peak=    3.554 closest distance to " CB  LEU A 300 " =    0.950
peak=    3.550 closest distance to " CG2 VAL A 197 " =    1.165
peak=    3.541 closest distance to " CB  ASN A 285 " =    0.936
peak=    3.541 closest distance to " CB  ARG A 219 " =    1.226
peak=    3.540 closest distance to " CB  VAL A 265 " =    1.194
peak=    3.532 closest distance to " CA  ALA A 160 " =    0.968
peak=    3.530 closest distance to " CA  VAL A 112 " =    1.099
peak=    3.526 closest distance to " O   TYR A 116 " =    1.479
peak=    3.523 closest distance to " O   HOH Z 298 " =    4.181
peak=    3.519 closest distance to " CD  LYS A  76 " =    1.823
peak=    3.514 closest distance to " O   THR A 251 " =    1.305
peak=    3.513 closest distance to " CB  PHE A  16 " =    1.232
peak=    3.508 closest distance to " O   HOH Z 380 " =    1.935
peak=    3.505 closest distance to " ND2 ASN A 187 " =    1.669
peak=    3.505 closest distance to " O   HOH Z 371 " =    2.658
peak=    3.502 closest distance to " O   HOH Z  39 " =    1.440
peak=    3.500 closest distance to " CB  PHE A 204 " =    0.949
peak=    3.488 closest distance to " O   HOH Z 264 " =    1.322
peak=    3.478 closest distance to " CA  ASP A 162 " =    1.142
peak=    3.478 closest distance to " O   HOH Z 144 " =    1.705
peak=    3.467 closest distance to " ND2BASN A 224 " =    0.817
peak=    3.464 closest distance to " CB  THR A  52 " =    0.755
peak=    3.461 closest distance to " O   HOH Z  63 " =    2.088
peak=    3.448 closest distance to " O   HOH Z 423 " =    1.828
peak=    3.444 closest distance to " CB  ALA A 291 " =    1.077
peak=    3.443 closest distance to " CG2BVAL A 121 " =    0.837
peak=    3.439 closest distance to " O   HOH Z   4 " =    1.727
peak=    3.438 closest distance to " O   HOH Z 219 " =    2.254
peak=    3.438 closest distance to " O   HOH Z 247 " =    1.403
peak=    3.437 closest distance to " CB  PRO A 243 " =    1.235
peak=    3.435 closest distance to " CA  ILE A 106 " =    0.839
peak=    3.429 closest distance to " O   HOH Z   1 " =    2.632
peak=    3.429 closest distance to " CD1 ILE A 199 " =    1.211
peak=    3.424 closest distance to " CB  ARG A  79 " =    0.810
peak=    3.422 closest distance to " O   HOH Z 285 " =    2.661
peak=    3.422 closest distance to " CB  GLU A 128 " =    1.160
peak=    3.421 closest distance to " O   HOH Z 272 " =    1.836
peak=    3.420 closest distance to " O   HOH Z 431 " =    1.282
peak=    3.418 closest distance to " OD1 ASN A 217 " =    1.568
peak=    3.410 closest distance to " CE1 TYR A 186 " =    1.277
peak=    3.409 closest distance to " O   HOH Z 126 " =    1.945
peak=    3.405 closest distance to " O   HOH Z 213 " =    1.723
peak=    3.401 closest distance to " ND2 ASN A 249 " =    0.933
peak=    3.401 closest distance to " CB  ARG A 190 " =    1.838
peak=    3.393 closest distance to " CG  ARG A 138 " =    1.386
peak=    3.392 closest distance to " O   HOH Z  68 " =    1.744
peak=    3.387 closest distance to " CE1 TYR A  30 " =    1.136
peak=    3.383 closest distance to " CB  THR A  31 " =    1.578
peak=    3.378 closest distance to " O   HOH Z 437 " =    1.523
peak=    3.378 closest distance to " CA  ASP A 149 " =    1.245
peak=    3.375 closest distance to " O   HOH Z 361 " =    3.228
peak=    3.370 closest distance to " CZ  ARG A  14 " =    1.275
peak=    3.367 closest distance to " O   HOH Z 417 " =    2.492
peak=    3.364 closest distance to " O   HOH Z 227 " =    1.695
peak=    3.360 closest distance to " CB  GLN A 194 " =    0.872
peak=    3.359 closest distance to " O   HOH Z 359 " =    1.774
peak=    3.356 closest distance to " O   HOH Z  78 " =    1.749
peak=    3.356 closest distance to " O   HOH Z 132 " =    2.164
peak=    3.352 closest distance to " O   HOH Z 316 " =    3.083
peak=    3.344 closest distance to " O   HOH Z  22 " =    2.476
peak=    3.344 closest distance to " O   HOH Z  15 " =    2.375
peak=    3.335 closest distance to " N   SER A 164 " =    0.986
peak=    3.334 closest distance to " NH2 ARG A 156 " =    1.071
peak=    3.332 closest distance to " NE  ARG A  24 " =    1.014
peak=    3.331 closest distance to " O   HOH Z 350 " =    2.042
peak=    3.327 closest distance to " O   HOH Z 343 " =    2.623
peak=    3.326 closest distance to " O   HOH Z 284 " =    2.886
peak=    3.325 closest distance to " O   HOH Z 163 " =    1.558
peak=    3.311 closest distance to " O   HOH Z 419 " =    1.695
peak=    3.304 closest distance to " CB  GLN A  88 " =    1.153
peak=    3.302 closest distance to " O   HOH Z 141 " =    1.720
peak=    3.302 closest distance to " O   HOH Z 426 " =    1.261
peak=    3.300 closest distance to " CA  SER A  12 " =    1.365
peak=    3.299 closest distance to " O   HOH Z  20 " =    1.409
peak=    3.298 closest distance to " O   GLY A 147 " =    1.627
peak=    3.297 closest distance to " O   HOH Z 306 " =    1.374
peak=    3.293 closest distance to " O   GLY A  91 " =    1.361
peak=    3.293 closest distance to " O   ASP A 200 " =    1.441
peak=    3.293 closest distance to " CB  ASN A 142 " =    1.094
peak=    3.292 closest distance to " OE1 GLN A  11 " =    2.129
peak=    3.289 closest distance to " O   HOH Z 279 " =    2.164
peak=    3.287 closest distance to " O   HOH Z 298 " =    1.772
peak=    3.284 closest distance to " CA  ARG A 156 " =    1.005
peak=    3.277 closest distance to " O   HOH Z 394 " =    3.491
peak=    3.276 closest distance to " N   HIS A 108 " =    1.838
peak=    3.275 closest distance to " O   HOH Z 193 " =    1.696
peak=    3.273 closest distance to " CD  GLN A 194 " =    1.653
peak=    3.271 closest distance to " CB  ALA A 233 " =    1.209
peak=    3.271 closest distance to " CA  THR A 221 " =    1.059
peak=    3.269 closest distance to " O   HOH Z 435 " =    1.894
peak=    3.268 closest distance to " OG  SER A 245 " =    1.395
peak=    3.265 closest distance to " CG2 ILE A 120 " =    1.276
peak=    3.261 closest distance to " CA  LEU A  83 " =    1.318
peak=    3.257 closest distance to " N   PHE A 130 " =    1.309
peak=    3.257 closest distance to " CA  THR A  82 " =    1.651
peak=    3.254 closest distance to " CB  ASN A  39 " =    0.872
peak=    3.250 closest distance to " CD  PRO A 213 " =    1.609
peak=    3.247 closest distance to " CA  GLY A 196 " =    0.894
peak=    3.244 closest distance to " C   ALA A 299 " =    1.105
peak=    3.233 closest distance to " CD1 LEU A   5 " =    1.457
peak=    3.223 closest distance to " CG  LEU A 237 " =    1.399
peak=    3.219 closest distance to " CA  TYR A 116 " =    1.515
peak=    3.218 closest distance to " O   HOH Z 313 " =    1.754
peak=    3.218 closest distance to " CA  ALA A  84 " =    0.970
peak=    3.214 closest distance to " CG2 ILE A  20 " =    1.315
peak=    3.198 closest distance to " CB  GLU A   2 " =    1.063
peak=    3.196 closest distance to " O   HOH Z 236 " =    1.639
peak=    3.195 closest distance to " CD1 LEU A  96 " =    0.804
peak=    3.194 closest distance to " O   HOH Z  44 " =    3.326
peak=    3.194 closest distance to " O   HOH Z 313 " =    1.986
peak=    3.189 closest distance to " CE  MET A  40 " =    0.991
peak=    3.188 closest distance to " OD2 ASP A  65 " =    1.090
peak=    3.188 closest distance to " N   THR A  52 " =    1.113
peak=    3.186 closest distance to " NH1AARG A 145 " =    1.559
peak=    3.183 closest distance to " CZ3 TRP A  85 " =    1.145
peak=    3.182 closest distance to " CG2 THR A 221 " =    1.221
peak=    3.179 closest distance to " O   HOH Z 234 " =    1.911
peak=    3.175 closest distance to " C   PHE A 208 " =    1.116
peak=    3.171 closest distance to " O   HOH Z 371 " =    1.523
peak=    3.168 closest distance to " O   HOH Z 282 " =    2.009
peak=    3.168 closest distance to " CB  ALA A   1 " =    1.194
peak=    3.161 closest distance to " O   HOH Z 299 " =    4.660
peak=    3.160 closest distance to " CA  ALA A 129 " =    1.241
peak=    3.159 closest distance to " CE3 TRP A 150 " =    1.135
peak=    3.158 closest distance to " OD2 ASP A 298 " =    3.449
peak=    3.158 closest distance to " OG1 THR A 264 " =    0.824
peak=    3.158 closest distance to " CG2 VAL A 257 " =    0.836
peak=    3.156 closest distance to " ND1 HIS A  81 " =    1.275
peak=    3.147 closest distance to " CA  SER A  87 " =    1.135
peak=    3.145 closest distance to " NH2AARG A 275 " =    2.629
peak=    3.145 closest distance to " CG  LEU A 167 " =    1.098
peak=    3.142 closest distance to " CG2AVAL A  72 " =    1.687
peak=    3.139 closest distance to " CG AARG A 102 " =    1.071
peak=    3.135 closest distance to " O   HOH Z 162 " =    1.976
peak=    3.128 closest distance to " O   HOH Z 357 " =    2.082
peak=    3.127 closest distance to " O   HOH Z 303 " =    2.369
peak=    3.123 closest distance to " CB  TRP A 179 " =    1.843
peak=    3.122 closest distance to " NH2AARG A 145 " =    1.224
peak=    3.121 closest distance to " CG2 ILE A 234 " =    1.293
peak=    3.119 closest distance to " CA  ASN A 217 " =    1.288
peak=    3.116 closest distance to " O   HOH Z 131 " =    2.438
peak=    3.113 closest distance to " CB  MET A 105 " =    0.852
peak=    3.110 closest distance to " O   HOH Z 427 " =    2.978
peak=    3.107 closest distance to " O   HOH Z 337 " =    1.691
peak=    3.106 closest distance to " CB  PRO A 213 " =    1.253
peak=    3.103 closest distance to " CA  GLY A 241 " =    1.014
peak=    3.102 closest distance to " O   HOH Z  85 " =    2.193
peak=    3.102 closest distance to " O   HOH Z   9 " =    2.630
peak=    3.101 closest distance to " CA  ASN A 176 " =    1.177
peak=    3.093 closest distance to " O   HOH Z 173 " =    2.112
peak=    3.091 closest distance to " CD  LYS A 119 " =    1.755
peak=    3.081 closest distance to " CB  TRP A 266 " =    1.079
peak=    3.080 closest distance to " CG  MET A 185 " =    1.173
peak=    3.079 closest distance to " CG2 ILE A 239 " =    0.829
peak=    3.067 closest distance to " CE1 HIS A  86 " =    1.379
peak=    3.066 closest distance to " NH1BARG A 145 " =    1.181
peak=    3.065 closest distance to " CB  ALA A  10 " =    1.159
peak=    3.064 closest distance to " CB  VAL A 202 " =    1.414
peak=    3.058 closest distance to " O   HOH Z 142 " =    1.534
peak=    3.044 closest distance to " CG2 THR A 220 " =    0.758
peak=    3.029 closest distance to " OD1 ASN A 301 " =    1.043

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.615 - 5.928
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 204
   mapped sites are within: 0.703 - 5.928

peak=   -4.575 closest distance to " O   PRO A 198 " =    1.296
peak=   -4.566 closest distance to " CG2BVAL A  41 " =    2.893
peak=   -4.497 closest distance to " O   HOH Z 422 " =    1.030
peak=   -4.468 closest distance to " CG2 ILE A  20 " =    2.917
peak=   -4.451 closest distance to " CG  GLN A  58 " =    0.953
peak=   -4.433 closest distance to " CG2 ILE A  49 " =    2.831
peak=   -4.395 closest distance to " O   HOH Z 221 " =    0.799
peak=   -4.212 closest distance to " CE2 PHE A  61 " =    2.829
peak=   -4.185 closest distance to " O  BHOH Z  74 " =    0.729
peak=   -4.159 closest distance to " CG  GLN A  11 " =    1.318
peak=   -4.123 closest distance to " CD2 LEU A 237 " =    2.525
peak=   -4.067 closest distance to " O   HOH Z 411 " =    5.624
peak=   -4.067 closest distance to " CB  ALA A  43 " =    2.511
peak=   -4.032 closest distance to " O   HOH Z 203 " =    1.770
peak=   -4.009 closest distance to " CD  GLN A 223 " =    1.445
peak=   -4.006 closest distance to " CD2 TYR A  30 " =    2.793
peak=   -3.999 closest distance to " CD2 TYR A 293 " =    1.878
peak=   -3.969 closest distance to " C   HIS A 108 " =    1.030
peak=   -3.946 closest distance to " O   HOH Z 193 " =    1.058
peak=   -3.903 closest distance to " O   HOH Z 377 " =    2.100
peak=   -3.883 closest distance to " O   HOH Z 150 " =    1.653
peak=   -3.881 closest distance to " NE  ARG A 156 " =    2.035
peak=   -3.831 closest distance to " CD  ARG A  14 " =    3.283
peak=   -3.815 closest distance to " CH2 TRP A 150 " =    1.100
peak=   -3.795 closest distance to " O   GLY A 241 " =    2.299
peak=   -3.793 closest distance to " OG BSER A 134 " =    1.335
peak=   -3.780 closest distance to " CD1 LEU A 101 " =    2.388
peak=   -3.773 closest distance to " O   GLN A  11 " =    1.193
peak=   -3.761 closest distance to " CG  PRO A 243 " =    1.647
peak=   -3.754 closest distance to " O   HOH Z 165 " =    1.664
peak=   -3.751 closest distance to " O   HOH Z 191 " =    5.928
peak=   -3.732 closest distance to " O   HOH Z 166 " =    1.650
peak=   -3.725 closest distance to " CG  GLU A  53 " =    1.335
peak=   -3.718 closest distance to " CA  ASP A 298 " =    1.093
peak=   -3.711 closest distance to " O   HOH Z  13 " =    1.899
peak=   -3.708 closest distance to " O   TRP A  92 " =    2.125
peak=   -3.708 closest distance to " OG  SER A  97 " =    2.194
peak=   -3.708 closest distance to " CG  MET A 105 " =    1.002
peak=   -3.690 closest distance to " O   HOH Z 423 " =    4.063
peak=   -3.674 closest distance to " O   SER A 146 " =    1.130
peak=   -3.674 closest distance to " O   HOH Z 205 " =    0.792
peak=   -3.656 closest distance to " NE2 GLN A 223 " =    1.154
peak=   -3.653 closest distance to " C   THR A 279 " =    1.238
peak=   -3.644 closest distance to " O   HOH Z 171 " =    2.533
peak=   -3.643 closest distance to " O   HOH Z 278 " =    0.992
peak=   -3.639 closest distance to " O   HOH Z 423 " =    2.468
peak=   -3.639 closest distance to " CG2 VAL A 189 " =    2.174
peak=   -3.626 closest distance to " O   HOH Z 351 " =    1.745
peak=   -3.624 closest distance to " O   HOH Z 285 " =    1.137
peak=   -3.605 closest distance to " O   VAL A 257 " =    1.300
peak=   -3.603 closest distance to " CB  ALA A 291 " =    2.398
peak=   -3.601 closest distance to " O   HOH Z 215 " =    2.250
peak=   -3.599 closest distance to " CA  GLY A 133 " =    2.009
peak=   -3.586 closest distance to " NE2 GLN A 194 " =    2.096
peak=   -3.586 closest distance to " O   HOH Z 366 " =    1.396
peak=   -3.572 closest distance to " O   HOH Z 203 " =    1.501
peak=   -3.571 closest distance to " O   HOH Z 198 " =    0.703
peak=   -3.565 closest distance to " O   HOH Z 290 " =    0.703
peak=   -3.562 closest distance to " CD1 ILE A 106 " =    2.216
peak=   -3.555 closest distance to " O   HOH Z 418 " =    1.021
peak=   -3.543 closest distance to " OXT GLY A 302 " =    2.978
peak=   -3.542 closest distance to " O   HOH Z  53 " =    1.058
peak=   -3.538 closest distance to " O   HOH Z 244 " =    1.380
peak=   -3.524 closest distance to " CZ  TYR A 172 " =    1.842
peak=   -3.521 closest distance to " C   ASN A 285 " =    2.320
peak=   -3.511 closest distance to " O   HOH Z  41 " =    1.906
peak=   -3.508 closest distance to " N   ALA A  43 " =    2.776
peak=   -3.503 closest distance to " CB  ALA A 248 " =    2.200
peak=   -3.498 closest distance to " CE3 TRP A 150 " =    2.346
peak=   -3.497 closest distance to " OD2 ASP A 171 " =    1.709
peak=   -3.494 closest distance to " OD2 ASP A 298 " =    0.953
peak=   -3.493 closest distance to " O   HOH Z  56 " =    0.968
peak=   -3.492 closest distance to " CB  ALA A 161 " =    2.535
peak=   -3.491 closest distance to " O   HOH Z 250 " =    1.774
peak=   -3.477 closest distance to " CE1 TYR A 247 " =    2.741
peak=   -3.473 closest distance to " ND2BASN A 224 " =    1.938
peak=   -3.470 closest distance to " O   HOH Z  52 " =    1.894
peak=   -3.467 closest distance to " NH2 ARG A  66 " =    0.985
peak=   -3.466 closest distance to " O   HOH Z 292 " =    3.111
peak=   -3.460 closest distance to " O   SER A 210 " =    1.791
peak=   -3.457 closest distance to " O   PRO A  54 " =    1.817
peak=   -3.456 closest distance to " CB  PRO A 243 " =    2.816
peak=   -3.454 closest distance to " O   HOH Z  67 " =    1.408
peak=   -3.449 closest distance to " CD1 PHE A  59 " =    2.051
peak=   -3.444 closest distance to " CG  GLN A  58 " =    1.274
peak=   -3.437 closest distance to " CZ  ARG A 156 " =    1.793
peak=   -3.435 closest distance to " NE2 GLN A  94 " =    1.933
peak=   -3.424 closest distance to " CA  ASP A  65 " =    1.418
peak=   -3.420 closest distance to " CD2 PHE A  61 " =    2.157
peak=   -3.419 closest distance to " OE2 GLU A   2 " =    1.352
peak=   -3.418 closest distance to " O   VAL A 174 " =    2.156
peak=   -3.410 closest distance to " O   HOH Z 150 " =    3.048
peak=   -3.409 closest distance to " CG  GLN A 103 " =    2.399
peak=   -3.407 closest distance to " O   SER A 271 " =    1.933
peak=   -3.406 closest distance to " CD1 LEU A  25 " =    2.453
peak=   -3.399 closest distance to " O   HOH Z 166 " =    1.662
peak=   -3.394 closest distance to " O   HOH Z  63 " =    1.189
peak=   -3.380 closest distance to " OE2 GLU A 152 " =    1.451
peak=   -3.375 closest distance to " ND2 ASN A 249 " =    2.161
peak=   -3.366 closest distance to " CD1 ILE A 109 " =    2.757
peak=   -3.361 closest distance to " O   SER A  95 " =    1.762
peak=   -3.359 closest distance to " O   HOH Z   1 " =    2.451
peak=   -3.359 closest distance to " CZ  PHE A  38 " =    2.239
peak=   -3.355 closest distance to " CD2 PHE A 225 " =    1.349
peak=   -3.353 closest distance to " O   HOH Z 152 " =    1.040
peak=   -3.352 closest distance to " O   HOH Z 102 " =    1.838
peak=   -3.348 closest distance to " CD1 TRP A 179 " =    1.095
peak=   -3.340 closest distance to " O   HOH Z 345 " =    2.845
peak=   -3.338 closest distance to " O   HOH Z 174 " =    3.633
peak=   -3.334 closest distance to " O   SER A   3 " =    0.921
peak=   -3.331 closest distance to " O   GLU A 128 " =    1.245
peak=   -3.330 closest distance to " CG  ASP A 286 " =    1.270
peak=   -3.329 closest distance to " CD2 PHE A 192 " =    2.166
peak=   -3.325 closest distance to " O   HOH Z 397 " =    1.063
peak=   -3.324 closest distance to " CA  TYR A  68 " =    2.908
peak=   -3.319 closest distance to " O   HOH Z 433 " =    0.972
peak=   -3.317 closest distance to " O   SER A 273 " =    1.035
peak=   -3.315 closest distance to " CG2 THR A 182 " =    2.275
peak=   -3.315 closest distance to " O   HOH Z 154 " =    1.636
peak=   -3.313 closest distance to " OG1 THR A  52 " =    2.712
peak=   -3.311 closest distance to " SG  CYS A 168 " =    1.072
peak=   -3.310 closest distance to " N   ASP A 191 " =    1.443
peak=   -3.309 closest distance to " CD  GLN A  88 " =    0.930
peak=   -3.306 closest distance to " O   HOH Z 434 " =    2.574
peak=   -3.303 closest distance to " CE BMET A  47 " =    1.411
peak=   -3.298 closest distance to " N   GLN A 223 " =    1.055
peak=   -3.294 closest distance to " O   HOH Z 274 " =    1.016
peak=   -3.294 closest distance to " CG1 VAL A 112 " =    2.447
peak=   -3.292 closest distance to " O   HOH Z 174 " =    2.320
peak=   -3.292 closest distance to " O   HOH Z 156 " =    3.460
peak=   -3.292 closest distance to " OD1 ASN A 148 " =    1.195
peak=   -3.288 closest distance to " ND2 ASN A  45 " =    2.005
peak=   -3.285 closest distance to " CZ  TYR A 169 " =    2.048
peak=   -3.285 closest distance to " N   SER A 134 " =    1.141
peak=   -3.285 closest distance to " O   HOH Z 297 " =    2.607
peak=   -3.278 closest distance to " CZ2 TRP A 179 " =    1.230
peak=   -3.277 closest distance to " CA  GLY A 241 " =    3.236
peak=   -3.274 closest distance to " CB  ASN A  45 " =    2.017
peak=   -3.274 closest distance to " O   HOH Z 280 " =    1.451
peak=   -3.264 closest distance to " O   ALA A  10 " =    1.483
peak=   -3.258 closest distance to " O   HOH Z 233 " =    2.520
peak=   -3.252 closest distance to " O   HOH Z 109 " =    2.000
peak=   -3.246 closest distance to " CG2 THR A  18 " =    2.903
peak=   -3.237 closest distance to " CE1 HIS A 207 " =    1.876
peak=   -3.233 closest distance to " O   HOH Z 287 " =    1.844
peak=   -3.231 closest distance to " CB  ALA A 184 " =    2.327
peak=   -3.229 closest distance to " OD2 ASP A 270 " =    0.929
peak=   -3.229 closest distance to " CA  ALA A 114 " =    0.945
peak=   -3.223 closest distance to " O   HOH Z 281 " =    2.491
peak=   -3.220 closest distance to " CG  GLU A  46 " =    2.513
peak=   -3.218 closest distance to " OXT GLY A 302 " =    3.275
peak=   -3.213 closest distance to " O   HOH Z 340 " =    1.569
peak=   -3.211 closest distance to " CG  ASP A 124 " =    0.966
peak=   -3.201 closest distance to " OG  SER A  97 " =    1.631
peak=   -3.199 closest distance to " NE2 GLN A  88 " =    1.604
peak=   -3.198 closest distance to " O   HOH Z 437 " =    1.203
peak=   -3.196 closest distance to " CG1AVAL A  41 " =    2.434
peak=   -3.189 closest distance to " SD  MET A 105 " =    2.353
peak=   -3.189 closest distance to " CB  TRP A  85 " =    2.684
peak=   -3.186 closest distance to " O   PHE A 218 " =    1.429
peak=   -3.181 closest distance to " O   HOH Z 231 " =    1.074
peak=   -3.172 closest distance to " N   ALA A 226 " =    1.813
peak=   -3.172 closest distance to " CA  ALA A 137 " =    2.510
peak=   -3.170 closest distance to " O   HOH Z 265 " =    1.400
peak=   -3.167 closest distance to " O   HOH Z 113 " =    1.642
peak=   -3.166 closest distance to " CB  ALA A   9 " =    2.415
peak=   -3.164 closest distance to " OE1 GLN A 223 " =    2.123
peak=   -3.157 closest distance to " O   HOH Z 126 " =    1.938
peak=   -3.156 closest distance to " O   HOH Z 424 " =    3.251
peak=   -3.150 closest distance to " SG ACYS A 201 " =    2.285
peak=   -3.146 closest distance to " O   GLY A  80 " =    2.799
peak=   -3.146 closest distance to " O   HOH Z 252 " =    3.595
peak=   -3.142 closest distance to " O   HOH Z 172 " =    5.654
peak=   -3.141 closest distance to " O   HOH Z 331 " =    1.012
peak=   -3.137 closest distance to " O   HOH Z 100 " =    0.946
peak=   -3.137 closest distance to " O   HOH Z 200 " =    1.219
peak=   -3.136 closest distance to " O   ARG A  79 " =    0.931
peak=   -3.133 closest distance to " CG  GLN A 223 " =    0.794
peak=   -3.129 closest distance to " O   GLN A  94 " =    2.248
peak=   -3.128 closest distance to " O   HOH Z  60 " =    1.467
peak=   -3.127 closest distance to " O   HOH Z  55 " =    1.955
peak=   -3.126 closest distance to " CB  HIS A  86 " =    1.259
peak=   -3.119 closest distance to " CB  GLN A  55 " =    1.489
peak=   -3.114 closest distance to " OH  TYR A 172 " =    1.736
peak=   -3.113 closest distance to " O   ILE A 106 " =    0.978
peak=   -3.108 closest distance to " O   ALA A  34 " =    2.548
peak=   -3.107 closest distance to " CD2 LEU A 237 " =    2.230
peak=   -3.106 closest distance to " O   HOH Z 109 " =    3.945
peak=   -3.105 closest distance to " OH  TYR A 169 " =    0.827
peak=   -3.103 closest distance to " NE  ARG A  79 " =    1.315
peak=   -3.100 closest distance to " O   HOH Z 198 " =    1.535
peak=   -3.088 closest distance to " O   HOH Z 197 " =    1.604
peak=   -3.081 closest distance to " CB  ASP A 162 " =    1.850
peak=   -3.077 closest distance to " CG1 VAL A  78 " =    2.758
peak=   -3.069 closest distance to " O   HOH Z 285 " =    2.084
peak=   -3.051 closest distance to " OG BSER A  99 " =    1.028
peak=   -3.033 closest distance to " O   ILE A 263 " =    2.338
peak=   -3.028 closest distance to " O   HOH Z 198 " =    2.232
peak=   -3.021 closest distance to " O   HOH Z 211 " =    1.273

================= 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    :  0.4949 0.4973   6.298117e+00   6.295581e+00
   1_bss:  0.4890 0.4881   6.295618e+00   6.292675e+00
   1_xyz:  0.3852 0.4143   6.148391e+00   6.200444e+00
   1_adp:  0.3418 0.4240   6.099963e+00   6.212488e+00
   1_occ:  0.3415 0.4237   6.099618e+00   6.213170e+00
   2_bss:  0.3403 0.4208   6.095834e+00   6.210404e+00
   2_xyz:  0.2708 0.3307   5.891576e+00   6.049233e+00
   2_adp:  0.2455 0.3103   5.828518e+00   6.001227e+00
   2_occ:  0.2455 0.3098   5.827842e+00   6.000619e+00
   3_bss:  0.2449 0.3095   5.827707e+00   5.999554e+00
   3_xyz:  0.1928 0.2461   5.613810e+00   5.808638e+00
   3_adp:  0.1781 0.2369   5.555178e+00   5.767164e+00
   3_occ:  0.1780 0.2369   5.554881e+00   5.766926e+00
   4_bss:  0.1779 0.2363   5.555056e+00   5.765168e+00
   4_xyz:  0.1518 0.2060   5.418910e+00   5.644635e+00
   4_adp:  0.1465 0.1959   5.379687e+00   5.591680e+00
   4_occ:  0.1463 0.1956   5.378990e+00   5.590698e+00
   5_bss:  0.1466 0.1960   5.380248e+00   5.591225e+00
   5_xyz:  0.1330 0.1795   5.294724e+00   5.511588e+00
   5_adp:  0.1306 0.1761   5.278666e+00   5.492919e+00
   5_occ:  0.1305 0.1762   5.278451e+00   5.492788e+00
   5_bss:  0.1305 0.1761   5.278387e+00   5.492689e+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:  0.299  30.482  -1.315   2.263   1.907   0.000   0.000   0.000
   1_xyz:  0.299  30.482  -1.315   2.263   1.907   0.000   0.000   0.000
   1_adp:  0.299  30.482  -1.315   2.263   1.907   0.000   0.000   0.000
   1_occ:  0.299  30.482  -1.315   2.263   1.907   0.000   0.000   0.000
   2_bss:  0.309  45.006  -1.430   1.182   1.227   0.000   0.000   0.000
   2_xyz:  0.309  45.006  -1.430   1.182   1.227   0.000   0.000   0.000
   2_adp:  0.309  45.006  -1.430   1.182   1.227   0.000   0.000   0.000
   2_occ:  0.309  45.006  -1.430   1.182   1.227   0.000   0.000   0.000
   3_bss:  0.323  58.149  -2.460  -0.189   0.210  -0.000   0.000   0.000
   3_xyz:  0.323  58.149  -2.460  -0.189   0.210  -0.000   0.000   0.000
   3_adp:  0.323  58.149  -2.460  -0.189   0.210  -0.000   0.000   0.000
   3_occ:  0.323  58.149  -2.460  -0.189   0.210  -0.000   0.000   0.000
   4_bss:  0.331  63.266  -3.294  -1.197  -0.636  -0.000  -0.000  -0.000
   4_xyz:  0.331  63.266  -3.294  -1.197  -0.636  -0.000  -0.000  -0.000
   4_adp:  0.331  63.266  -3.294  -1.197  -0.636  -0.000  -0.000  -0.000
   4_occ:  0.331  63.266  -3.294  -1.197  -0.636  -0.000  -0.000  -0.000
   5_bss:  0.332  64.858  -3.612  -1.729  -0.893  -0.000  -0.000  -0.000
   5_xyz:  0.332  64.858  -3.612  -1.729  -0.893  -0.000  -0.000  -0.000
   5_adp:  0.332  64.858  -3.612  -1.729  -0.893  -0.000  -0.000  -0.000
   5_occ:  0.332  64.858  -3.612  -1.729  -0.893  -0.000  -0.000  -0.000
   5_bss:  0.328  60.402  -3.547  -1.664  -0.828  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.904 0.3556  0.4844    79385.111
   1_bss:  62.080 0.3652  0.5184    77516.012
   1_xyz:  47.284 0.5542  0.7695    51411.887
   1_adp:  48.468 0.5387  0.7638    53708.865
   1_occ:  48.474 0.5386  0.7626    53717.220
   2_bss:  48.106 0.5429  0.7536    52721.034
   2_xyz:  36.301 0.6845  0.9213    30889.245
   2_adp:  33.174 0.7216  0.9401    26962.681
   2_occ:  33.144 0.7219  0.9400    26874.416
   3_bss:  33.023 0.7233  0.9054    26787.707
   3_xyz:  25.020 0.8101  0.9821    15959.566
   3_adp:  23.459 0.8271  0.9886    14665.084
   3_occ:  23.460 0.8271  0.9886    14663.943
   4_bss:  23.376 0.8278  0.9590    14579.442
   4_xyz:  19.983 0.8613  0.9738    10949.707
   4_adp:  18.690 0.8742  0.9727     9995.154
   4_occ:  18.676 0.8743  0.9728     9978.339
   5_bss:  18.681 0.8743  0.9605    10003.801
   5_xyz:  16.944 0.8899  0.9710     8457.972
   5_adp:  16.489 0.8941  0.9703     8199.794
   5_occ:  16.492 0.8941  0.9702     8195.035
   5_bss:  16.492 0.8941  0.9701     8191.114
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.3255e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.3255e-01
   1_xyz:   1.629  0.011  0.099 15.902  0.006  4.100   1.4667e-01
   1_adp:   1.629  0.011  0.099 15.902  0.006  4.100   1.4667e-01
   1_occ:   1.629  0.011  0.099 15.902  0.006  4.100   1.4667e-01
   2_bss:   1.629  0.011  0.099 15.902  0.006  4.100   1.4667e-01
   2_xyz:   1.330  0.009  0.093 15.351  0.005  4.129   9.5360e-02
   2_adp:   1.330  0.009  0.093 15.351  0.005  4.129   9.5360e-02
   2_occ:   1.330  0.009  0.093 15.351  0.005  4.129   9.5360e-02
   3_bss:   1.330  0.009  0.093 15.351  0.005  4.129   9.5360e-02
   3_xyz:   1.049  0.008  0.070 14.628  0.004  4.112   6.6224e-02
   3_adp:   1.049  0.008  0.070 14.628  0.004  4.112   6.6224e-02
   3_occ:   1.049  0.008  0.070 14.628  0.004  4.112   6.6224e-02
   4_bss:   1.049  0.008  0.070 14.628  0.004  4.112   6.6224e-02
   4_xyz:   1.009  0.006  0.073 14.351  0.003  4.121   5.6794e-02
   4_adp:   1.009  0.006  0.073 14.351  0.003  4.121   5.6794e-02
   4_occ:   1.009  0.006  0.073 14.351  0.003  4.121   5.6794e-02
   5_bss:   1.009  0.006  0.073 14.351  0.003  4.121   5.6794e-02
   5_xyz:   1.001  0.007  0.072 14.460  0.004  4.112   5.7338e-02
   5_adp:   1.001  0.007  0.072 14.460  0.004  4.112   5.7338e-02
   5_occ:   1.001  0.007  0.072 14.460  0.004  4.112   5.7338e-02
   5_bss:   1.001  0.007  0.072 14.460  0.004  4.112   5.7338e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.961   2.4687e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.961   2.4687e-01
   1_xyz:   9.199  0.085  0.320 81.606  0.032  1.874   7.8338e-02
   1_adp:   9.199  0.085  0.320 81.606  0.032  1.874   7.8338e-02
   1_occ:   9.199  0.085  0.320 81.606  0.032  1.874   7.8338e-02
   2_bss:   9.199  0.085  0.320 81.606  0.032  1.874   7.8338e-02
   2_xyz:  10.229  0.058  0.320 85.030  0.029  2.081   1.0008e-01
   2_adp:  10.229  0.058  0.320 85.030  0.029  2.081   1.0008e-01
   2_occ:  10.229  0.058  0.320 85.030  0.029  2.081   1.0008e-01
   3_bss:  10.229  0.058  0.320 85.030  0.029  2.081   1.0008e-01
   3_xyz:   7.036  0.054  0.252 79.613  0.037  2.261   7.1945e-02
   3_adp:   7.036  0.054  0.252 79.613  0.037  2.261   7.1945e-02
   3_occ:   7.036  0.054  0.252 79.613  0.037  2.261   7.1945e-02
   4_bss:   7.036  0.054  0.252 79.613  0.037  2.261   7.1945e-02
   4_xyz:   7.466  0.043  0.219 77.889  0.037  2.369   3.7242e-02
   4_adp:   7.466  0.043  0.219 77.889  0.037  2.369   3.7242e-02
   4_occ:   7.466  0.043  0.219 77.889  0.037  2.369   3.7242e-02
   5_bss:   7.466  0.043  0.219 77.889  0.037  2.369   3.7242e-02
   5_xyz:   7.040  0.048  0.233 82.249  0.038  2.348   3.6066e-02
   5_adp:   7.040  0.048  0.233 82.249  0.038  2.348   3.6066e-02
   5_occ:   7.040  0.048  0.233 82.249  0.038  2.348   3.6066e-02
   5_bss:   7.040  0.048  0.233 82.249  0.038  2.348   3.6066e-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: 107.83   0.00  20.92  97.92   0.00  17.21 107.83   0.00  41.12
   1_occ: 107.83   0.00  20.92  97.92   0.00  17.21 107.83   0.00  41.12
   2_bss: 107.83   0.00  20.92  97.92   0.00  17.21 107.83   0.00  41.12
   2_xyz: 107.83   0.00  20.92  97.92   0.00  17.21 107.83   0.00  41.12
   2_adp: 102.40   0.00  19.51  91.22   0.00  15.40 102.40   2.20  41.92
   2_occ: 102.40   0.00  19.51  91.22   0.00  15.40 102.40   2.20  41.92
   3_bss: 102.40   0.00  19.51  91.22   0.00  15.40 102.40   2.20  41.92
   3_xyz: 102.40   0.00  19.51  91.22   0.00  15.40 102.40   2.20  41.92
   3_adp: 106.01   0.00  19.56  96.40   0.00  14.57 106.01   5.12  46.71
   3_occ: 106.01   0.00  19.56  96.40   0.00  14.57 106.01   5.12  46.71
   4_bss: 106.01   0.00  19.56  96.40   0.00  14.57 106.01   5.12  46.71
   4_xyz: 106.01   0.00  19.56  96.40   0.00  14.57 106.01   5.12  46.71
   4_adp: 104.80   1.77  18.47 100.51   1.77  13.73 104.80   6.21  44.27
   4_occ: 104.80   1.77  18.47 100.51   1.77  13.73 104.80   6.21  44.27
   5_bss: 104.80   1.77  18.47 100.51   1.77  13.73 104.80   6.21  44.27
   5_xyz: 104.80   1.77  18.47 100.51   1.77  13.73 104.80   6.21  44.27
   5_adp: 104.75   1.80  18.05 100.02   1.80  13.47 104.75   5.65  42.95
   5_occ: 104.75   1.80  18.05 100.02   1.80  13.47 104.75   5.65  42.95
   5_bss: 104.69   1.74  17.98  99.95   1.74  13.41 104.69   5.59  42.89
------------------------------------------------------------------------
 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:    3.440    0.036    0.423
   1_adp:    3.440    0.036    0.423
   1_occ:    3.440    0.036    0.423
   2_bss:    3.440    0.036    0.423
   2_xyz:    3.485    0.037    0.634
   2_adp:    3.485    0.037    0.634
   2_occ:    3.485    0.037    0.634
   3_bss:    3.485    0.037    0.634
   3_xyz:    3.528    0.070    0.753
   3_adp:    3.528    0.070    0.753
   3_occ:    3.528    0.070    0.753
   4_bss:    3.528    0.070    0.753
   4_xyz:    3.531    0.059    0.819
   4_adp:    3.531    0.059    0.819
   4_occ:    3.531    0.059    0.819
   5_bss:    3.531    0.059    0.819
   5_xyz:    3.489    0.064    0.857
   5_adp:    3.489    0.064    0.857
   5_occ:    3.489    0.064    0.857
   5_bss:    3.489    0.064    0.857
------------------------------------------------------------------------

CPU time actual refinement: 344.01


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_108/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_108/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_108/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_108/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_108/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.86 
  Macro-tasks:
    bulk solvent and scale       = 38.13  
    individual site refinement   = 145.69 
    weights calculation          = 29.89  
    collect and process          = 6.49   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 220.30 
  Micro-tasks:
    mask                            = 2.56   
    f_calc                          = 111.66 
    alpha_beta                      = 8.46   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 120.23 
    fmodel                         = 6.28   
    r_factors                      = 0.15   
    phase_errors                   = 10.38  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 261.15 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.885 micro seconds
Total CPU time: 5.96 minutes
from_scatterers_fft:    642 calls, 111.33 s
gradients_fft:          587 calls, 106.73 s

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

# Date 2008-01-16 Time 04:02:17 PST -0800 (1200484937.49 s)
Start R-work = 0.4949, R-free = 0.4973 (no bulk solvent and anisotropic scale)
Final R-work = 0.1557, R-free = 0.1958 (no bulk solvent and anisotropic scale)

Start R-work = 0.4890, R-free = 0.4881
Final R-work = 0.1305, R-free = 0.1761