# Date 2008-01-16 Time 06:42:20 PST -0800 (1200494540.30 s)
#phil __OFF__

Command line arguments: "../1254.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10435
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1254

-------------------------------------------------------------------------------
  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: (72.0062, 46.6953, 84.2302, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1542 1.95127
Completeness in resolution range: 0.9224
Completeness with d_max=infinity: 0.919715

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1542
                             d_min =   1.9513

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: (72.0062, 46.6953, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1542 1.95127
Completeness in resolution range: 0.9224
Completeness with d_max=infinity: 0.919715

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1547 -  4.1773 [2233/2263]  2014   219   9.8%
  bin  2:  4.1773 -  3.3272 [2138/2157]  1921   217  10.1%
  bin  3:  3.3272 -  2.9100 [2114/2134]  1896   218  10.3%
  bin  4:  2.9100 -  2.6455 [2113/2138]  1911   202   9.6%
  bin  5:  2.6455 -  2.4567 [2057/2076]  1853   204   9.9%
  bin  6:  2.4567 -  2.3124 [2071/2118]  1854   217  10.5%
  bin  7:  2.3124 -  2.1969 [2065/2097]  1859   206  10.0%
  bin  8:  2.1969 -  2.1016 [2056/2093]  1857   199   9.7%
  bin  9:  2.1016 -  2.0209 [1963/2085]  1760   203  10.3%
  bin 10:  2.0209 -  1.9513 [ 779/2076]   705    74   9.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1254/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.59 -     2.25: 26
        2.25 -     2.91: 1487
        2.91 -     3.58: 4515
        3.58 -     4.24: 9252
        4.24 -     4.90: 13207
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.589 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.621 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.656 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.744 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.793 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28482 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_1254/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1254/model_refine_001.geo

CPU time processing inputs: 8.85


============================ 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 = 72.00625 46.69535 84.23025 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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4508   r_free= 0.4515   ksol= 0.00   Bsol= 0.00   scale= 0.906    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.257823                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6601 0.99   1447  162 0.3575 0.3679       6.516       6.544|
|  2:  4.6601 -  3.7168 0.99   1393  154 0.3843 0.3551      6.7616       6.761|
|  3:  3.7168 -  3.2523 0.99   1372  149 0.4304 0.4314      6.6368      6.6817|
|  4:  3.2523 -  2.9573 0.99   1358  156 0.4262 0.4263      6.4679      6.4692|
|  5:  2.9573 -  2.7467 0.99   1343  149 0.4724 0.4691      6.3353      6.3252|
|  6:  2.7467 -  2.5856 0.98   1340  150 0.4930 0.4787      6.2481      6.2251|
|  7:  2.5856 -  2.4567 0.99   1342  140 0.4958 0.4477      6.2266      6.1639|
|  8:  2.4567 -  2.3502 0.98   1330  161 0.4901 0.4943      6.1287      6.1619|
|  9:  2.3502 -  2.2600 0.98   1332  143 0.4967 0.4840      6.1155      6.0789|
| 10:  2.2600 -  2.1822 0.98   1306  152 0.5089 0.5266       6.068      6.1022|
| 11:  2.1822 -  2.1142 0.99   1359  138 0.4966 0.5765      6.0104      6.0428|
| 12:  2.1142 -  2.0539 0.98   1292  144 0.4987 0.5459      5.9448      5.9514|
| 13:  2.0539 -  2.0000 0.80   1077  131 0.5139 0.5138      5.8615      5.8259|
| 14:  2.0000 -  1.9513 0.25    339   30 0.5371 0.4934      5.8074      5.7898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1547 -  4.6601  1447   162  0.72  32.11   0.83     0.77      62260.44|
|  2:  4.6601 -  3.7168  1393   154  0.73  32.78   0.93     0.84      93385.43|
|  3:  3.7168 -  3.2523  1372   149  0.62  42.32   0.91     0.81     103208.08|
|  4:  3.2523 -  2.9573  1358   156  0.53  49.49   0.94     0.74      95891.30|
|  5:  2.9573 -  2.7467  1343   149  0.43  57.28   0.89     0.61      78534.87|
|  6:  2.7467 -  2.5856  1340   150  0.41  58.71   0.90     0.59      67723.09|
|  7:  2.5856 -  2.4567  1342   140  0.43  57.86   0.91     0.58      59396.31|
|  8:  2.4567 -  2.3502  1330   161  0.43  57.60   0.93     0.63      53224.40|
|  9:  2.3502 -  2.2600  1332   143  0.41  59.39   0.95     0.60      49866.08|
| 10:  2.2600 -  2.1822  1306   152  0.35  64.00   0.95     0.52      49781.84|
| 11:  2.1822 -  2.1142  1359   138  0.26  70.36   0.96     0.40      50403.50|
| 12:  2.1142 -  2.0539  1292   144  0.23  72.71   0.95     0.37      46827.01|
| 13:  2.0539 -  2.0000  1077   131  0.26  70.75   0.93     0.42      39809.69|
| 14:  2.0000 -  1.9513   339    30  0.32  66.14   0.93     0.51      30557.69|
|alpha:            min =        0.37 max =            0.84 mean =         0.61|
|beta:             min =    30557.69 max =       103208.08 mean =     65365.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.48|
|phase err.(test): min =        0.00 max =           89.93 mean =        55.60|
|-----------------------------------------------------------------------------|

============================== 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 = 8.978277              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.008   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.375846              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.874   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.589 -  1.920:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.920 -  2.251:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.251 -  2.582:       36 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.582 -  2.913:     1451 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.913 -  3.245:     1918 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.245 -  3.576:     2597 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.576 -  3.907:     4729 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.907 -  4.238:     4523 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.238 -  4.569:     6050 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.569 -  4.900:     7157 |
|-----------------------------------------------------------------------------|
|-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 |        0.181 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.589 |       0.462 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.808)------------------------------------------|
|    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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4508   r_free= 0.4515   ksol= 0.00   Bsol= 0.00   scale= 0.906    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.257823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4411   r_free= 0.4427   ksol= 0.30   Bsol= 21.64   scale= 0.943   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,-2.82,2.14,-0.00,0.00,0.00); trace/3= 0.43                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.252192                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.120910              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.335   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.063335              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.523   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4411      final r-factor (work) = 0.3360          |
| start r-factor (free) = 0.4427      final r-factor (free) = 0.3760          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4279 = 7.12 * 0.50 * 6.2484 + 1.00 * 0.1809                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.9318 = 7.12 * 0.50 * 6.1295 + 1.00 * 0.1080                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3360      final r-factor (work) = 0.3061          |
| start r-factor (free) = 0.3760      final r-factor (free) = 0.3783          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5241 = 1.06 * 1.00 * 6.1295 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4347 = 1.06 * 1.00 * 6.0162 + 1.00 * 0.0374                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.808)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.34   18.85    None  None   None       |
|    all(noH): 2823   0      0.00    99.34   18.85    None  None   None       |
|    Sol.    : 438    0      0.00    94.25   40.52    None  None   None       |
|    Mac.    : 2385   0      0.00    99.34   14.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.934:  967   |   5:    49.672 -  59.606:   90        |
|      1:     9.934 -  19.869:  897   |   6:    59.606 -  69.540:   52        |
|      2:    19.869 -  29.803:  441   |   7:    69.540 -  79.475:   27        |
|      3:    29.803 -  39.737:  209   |   8:    79.475 -  89.409:    9        |
|      4:    39.737 -  49.672:  127   |   9:    89.409 -  99.343:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3061 r_free = 0.3783             target_work(ml) = 6.019         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3057 r_free = 0.3777             target_work(ml) = 6.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3057   r_free= 0.3777   ksol= 0.30   Bsol= 21.64   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,-2.82,2.14,-0.00,0.00,0.00); trace/3= 0.43                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.018101                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3048   r_free= 0.3766   ksol= 0.33   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,-1.57,1.02,-0.00,0.00,0.00); trace/3= 0.08                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.016373                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.129342              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.401   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.961382              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.863   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3048      final r-factor (work) = 0.2274          |
| start r-factor (free) = 0.3766      final r-factor (free) = 0.2948          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5440 = 6.13 * 0.50 * 6.0157 + 1.00 * 0.1080                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2217 = 6.13 * 0.50 * 5.9168 + 1.00 * 0.0888                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2274      final r-factor (work) = 0.2058          |
| start r-factor (free) = 0.2948      final r-factor (free) = 0.2723          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7090 = 0.96 * 1.00 * 5.9168 + 1.00 * 0.0207                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5238 = 0.96 * 1.00 * 5.7311 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.808)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.22  18.60    None  None   None       |
|    all(noH): 2823   0      0.00    101.22  18.60    None  None   None       |
|    Sol.    : 438    0      2.93    98.53   44.30    None  None   None       |
|    Mac.    : 2385   0      0.00    101.22  13.89    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 -  10.122: 1048   |   5:    50.609 -  60.731:   90        |
|      1:    10.122 -  20.244:  993   |   6:    60.731 -  70.853:   59        |
|      2:    20.244 -  30.365:  301   |   7:    70.853 -  80.975:   30        |
|      3:    30.365 -  40.487:  149   |   8:    80.975 -  91.096:   14        |
|      4:    40.487 -  50.609:  134   |   9:    91.096 - 101.218:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2058 r_free = 0.2723             target_work(ml) = 5.696         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2057 r_free = 0.2722             target_work(ml) = 5.695         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2057   r_free= 0.2722   ksol= 0.33   Bsol= 50.00   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,-1.57,1.02,-0.00,0.00,0.00); trace/3= 0.08                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.695086                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2049   r_free= 0.2710   ksol= 0.34   Bsol= 57.04   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-1.74,-0.56,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.690278                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.490297              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.986   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.280016              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.421  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2049      final r-factor (work) = 0.1571          |
| start r-factor (free) = 0.2710      final r-factor (free) = 0.2105          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8257 = 5.49 * 0.50 * 5.7326 + 1.00 * 0.0888                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4239 = 5.49 * 0.50 * 5.5949 + 1.00 * 0.0651                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1571      final r-factor (work) = 0.1451          |
| start r-factor (free) = 0.2105      final r-factor (free) = 0.1943          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5807 = 0.28 * 1.00 * 5.5949 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5327 = 0.28 * 1.00 * 5.4138 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.808)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.34   17.77    None  None   None       |
|    all(noH): 2823   0      0.00    96.34   17.77    None  None   None       |
|    Sol.    : 438    0      5.74    95.16   42.78    None  None   None       |
|    Mac.    : 2385   0      0.00    96.34   13.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.634:  957   |   5:    48.170 -  57.804:  115        |
|      1:     9.634 -  19.268: 1158   |   6:    57.804 -  67.438:   50        |
|      2:    19.268 -  28.902:  247   |   7:    67.438 -  77.072:   33        |
|      3:    28.902 -  38.536:  131   |   8:    77.072 -  86.707:    9        |
|      4:    38.536 -  48.170:  116   |   9:    86.707 -  96.341:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1451 r_free = 0.1943             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1450 r_free = 0.1940             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1940   ksol= 0.34   Bsol= 57.04   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-1.74,-0.56,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.367496                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1936   ksol= 0.33   Bsol= 53.12   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.51,-2.38,-1.59,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.368437                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.928886              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.932  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.599110              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.705   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1450      final r-factor (work) = 0.1243          |
| start r-factor (free) = 0.1936      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7145 = 3.93 * 0.50 * 5.4211 + 1.00 * 0.0651                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4978 = 3.93 * 0.50 * 5.3069 + 1.00 * 0.0727                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1243      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1943 = 0.60 * 1.00 * 5.3069 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1343 = 0.60 * 1.00 * 5.2151 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.808)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    100.55  17.65    None  None   None       |
|    all(noH): 2823   0      0.88    100.55  17.65    None  None   None       |
|    Sol.    : 438    0      5.89    89.50   42.82    None  None   None       |
|    Mac.    : 2385   0      0.88    100.55  13.02    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:     0.879 -  10.846: 1241   |   5:    50.716 -  60.683:  101        |
|      1:    10.846 -  20.814:  954   |   6:    60.683 -  70.650:   40        |
|      2:    20.814 -  30.781:  208   |   7:    70.650 -  80.618:   25        |
|      3:    30.781 -  40.748:  135   |   8:    80.618 -  90.585:   11        |
|      4:    40.748 -  50.716:  104   |   9:    90.585 - 100.552:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1662             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1659             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1659   ksol= 0.33   Bsol= 53.12   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.51,-2.38,-1.59,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198868                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1661   ksol= 0.32   Bsol= 52.09   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-2.49,-1.90,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.201017                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.634190              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.441  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.129000              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.476  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3351 = 1.63 * 0.50 * 5.2166 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3043 = 1.63 * 0.50 * 5.2039 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6811 = 0.13 * 1.00 * 5.2039 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6793 = 0.13 * 1.00 * 5.2087 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.808)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.78    95.82   16.94    None  None   None       |
|    all(noH): 2823   0      1.78    95.82   16.94    None  None   None       |
|    Sol.    : 438    0      6.18    85.02   39.29    None  None   None       |
|    Mac.    : 2385   0      1.78    95.82   12.84    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:     1.777 -  11.181: 1297   |   5:    48.798 -  58.202:   86        |
|      1:    11.181 -  20.585:  930   |   6:    58.202 -  67.606:   29        |
|      2:    20.585 -  29.989:  204   |   7:    67.606 -  77.011:   23        |
|      3:    29.989 -  39.394:  137   |   8:    77.011 -  86.415:    9        |
|      4:    39.394 -  48.798:  104   |   9:    86.415 -  95.819:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1203 r_free = 0.1631             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1201 r_free = 0.1629             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1629   ksol= 0.32   Bsol= 52.09   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-2.49,-1.90,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.200983                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6601 0.99   1447  162 0.1017 0.1308      5.4081      5.5931|
|  2:  4.6601 -  3.7168 0.99   1393  154 0.0915 0.1137      5.4891      5.6833|
|  3:  3.7168 -  3.2523 0.99   1372  149 0.1141 0.1703      5.5168       5.881|
|  4:  3.2523 -  2.9573 0.99   1358  156 0.1351 0.1651      5.5087      5.6265|
|  5:  2.9573 -  2.7467 0.99   1343  149 0.1434 0.1734      5.3728      5.5263|
|  6:  2.7467 -  2.5856 0.98   1340  150 0.1357 0.1811      5.2568      5.4489|
|  7:  2.5856 -  2.4567 0.99   1342  140 0.1340 0.1891      5.2095      5.4481|
|  8:  2.4567 -  2.3502 0.98   1330  161 0.1237 0.1691      5.0861        5.26|
|  9:  2.3502 -  2.2600 0.98   1332  143 0.1254 0.1993      5.0603      5.3558|
| 10:  2.2600 -  2.1822 0.98   1306  152 0.1211 0.1629      4.9938      5.2142|
| 11:  2.1822 -  2.1142 0.99   1359  138 0.1202 0.1956       4.969      5.3345|
| 12:  2.1142 -  2.0539 0.98   1292  144 0.1233 0.1817      4.9224      5.1443|
| 13:  2.0539 -  2.0000 0.80   1077  131 0.1271 0.1665      4.8286      5.0222|
| 14:  2.0000 -  1.9513 0.25    339   30 0.1124 0.1460      4.6629      4.8414|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1547 -  4.6601  1447   162  0.94   9.47   0.98     0.95       7542.09|
|  2:  4.6601 -  3.7168  1393   154  0.95   8.37   1.01     1.00       9786.23|
|  3:  3.7168 -  3.2523  1372   149  0.93  12.39   1.02     1.02      11181.50|
|  4:  3.2523 -  2.9573  1358   156  0.91  15.19   1.00     0.97      11150.12|
|  5:  2.9573 -  2.7467  1343   149  0.90  16.40   0.99     0.97       8601.02|
|  6:  2.7467 -  2.5856  1340   150  0.90  16.55   0.98     0.96       7370.82|
|  7:  2.5856 -  2.4567  1342   140  0.91  15.57   0.99     0.97       6371.98|
|  8:  2.4567 -  2.3502  1330   161  0.90  15.81   0.99     0.96       5491.43|
|  9:  2.3502 -  2.2600  1332   143  0.89  16.77   1.00     0.97       5193.74|
| 10:  2.2600 -  2.1822  1306   152  0.90  15.71   1.00     0.96       4534.26|
| 11:  2.1822 -  2.1142  1359   138  0.89  16.92   1.00     0.96       4647.24|
| 12:  2.1142 -  2.0539  1292   144  0.90  17.12   1.00     1.00       4384.14|
| 13:  2.0539 -  2.0000  1077   131  0.90  16.79   1.00     0.98       3503.04|
| 14:  2.0000 -  1.9513   339    30  0.90  15.55   0.99     0.97       2461.85|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2461.85 max =        11181.50 mean =      6905.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.77|
|phase err.(test): min =        0.00 max =           87.97 mean =        14.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1628   ksol= 0.32   Bsol= 52.02   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.43,-1.91,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.200920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1628   ksol= 0.32   Bsol= 52.02   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.43,-1.91,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.200920                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6601 0.99   1447  162 0.1017 0.1307      5.4077      5.5924|
|  2:  4.6601 -  3.7168 0.99   1393  154 0.0915 0.1137      5.4888       5.683|
|  3:  3.7168 -  3.2523 0.99   1372  149 0.1141 0.1702      5.5167      5.8808|
|  4:  3.2523 -  2.9573 0.99   1358  156 0.1351 0.1651      5.5087      5.6266|
|  5:  2.9573 -  2.7467 0.99   1343  149 0.1434 0.1734      5.3729      5.5262|
|  6:  2.7467 -  2.5856 0.98   1340  150 0.1357 0.1813      5.2569      5.4493|
|  7:  2.5856 -  2.4567 0.99   1342  140 0.1340 0.1891      5.2095       5.448|
|  8:  2.4567 -  2.3502 0.98   1330  161 0.1237 0.1690      5.0863      5.2599|
|  9:  2.3502 -  2.2600 0.98   1332  143 0.1254 0.1993      5.0603       5.356|
| 10:  2.2600 -  2.1822 0.98   1306  152 0.1210 0.1628      4.9935      5.2135|
| 11:  2.1822 -  2.1142 0.99   1359  138 0.1203 0.1956      4.9688      5.3344|
| 12:  2.1142 -  2.0539 0.98   1292  144 0.1233 0.1817      4.9225      5.1445|
| 13:  2.0539 -  2.0000 0.80   1077  131 0.1270 0.1665      4.8286      5.0225|
| 14:  2.0000 -  1.9513 0.25    339   30 0.1125 0.1465      4.6639      4.8439|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1547 -  4.6601  1447   162  0.94   9.47   0.98     0.95       7535.10|
|  2:  4.6601 -  3.7168  1393   154  0.95   8.36   1.01     1.00       9779.26|
|  3:  3.7168 -  3.2523  1372   149  0.93  12.38   1.02     1.02      11175.82|
|  4:  3.2523 -  2.9573  1358   156  0.91  15.19   1.00     0.97      11149.94|
|  5:  2.9573 -  2.7467  1343   149  0.90  16.40   0.99     0.97       8603.06|
|  6:  2.7467 -  2.5856  1340   150  0.90  16.56   0.98     0.96       7372.80|
|  7:  2.5856 -  2.4567  1342   140  0.91  15.57   0.99     0.97       6373.40|
|  8:  2.4567 -  2.3502  1330   161  0.90  15.81   0.99     0.96       5493.98|
|  9:  2.3502 -  2.2600  1332   143  0.89  16.77   1.00     0.97       5193.44|
| 10:  2.2600 -  2.1822  1306   152  0.90  15.70   0.99     0.95       4532.05|
| 11:  2.1822 -  2.1142  1359   138  0.89  16.91   0.99     0.96       4642.27|
| 12:  2.1142 -  2.0539  1292   144  0.90  17.11   1.00     1.00       4382.39|
| 13:  2.0539 -  2.0000  1077   131  0.90  16.80   0.99     0.98       3506.66|
| 14:  2.0000 -  1.9513   339    30  0.90  15.57   0.99     0.96       2468.20|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2468.20 max =        11175.82 mean =      6903.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.77|
|phase err.(test): min =        0.00 max =           87.97 mean =        14.22|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.808)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    95.76   16.88    None  None   None       |
|    all(noH): 2823   0      1.71    95.76   16.88    None  None   None       |
|    Sol.    : 438    0      6.12    84.96   39.22    None  None   None       |
|    Mac.    : 2385   0      1.71    95.76   12.77    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:     1.713 -  11.117: 1297   |   5:    48.734 -  58.138:   86        |
|      1:    11.117 -  20.521:  930   |   6:    58.138 -  67.543:   29        |
|      2:    20.521 -  29.926:  204   |   7:    67.543 -  76.947:   23        |
|      3:    29.926 -  39.330:  137   |   8:    76.947 -  86.351:    9        |
|      4:    39.330 -  48.734:  104   |   9:    86.351 -  95.755:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.557 - 5.984
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 334
   mapped sites are within: 0.732 - 5.984

peak=    6.236 closest distance to " O   HOH Z 103 " =    1.089
peak=    6.236 closest distance to " NH2AARG A 102 " =    1.054
peak=    5.555 closest distance to " CB  GLN A 223 " =    1.477
peak=    5.431 closest distance to " O   HOH Z 111 " =    2.039
peak=    5.411 closest distance to " CG  PRO A  54 " =    1.292
peak=    5.084 closest distance to " CB  SER A  63 " =    1.353
peak=    4.999 closest distance to " CG  PRO A 198 " =    1.395
peak=    4.992 closest distance to " CG  PRO A  90 " =    1.137
peak=    4.914 closest distance to " O   HOH Z 278 " =    1.088
peak=    4.902 closest distance to " O   HOH Z 260 " =    1.456
peak=    4.892 closest distance to " O   HOH Z 186 " =    1.517
peak=    4.845 closest distance to " CB  PRO A  54 " =    0.918
peak=    4.791 closest distance to " O   HOH Z 214 " =    1.296
peak=    4.781 closest distance to " O   HOH Z 183 " =    1.647
peak=    4.726 closest distance to " O   HOH Z 126 " =    1.611
peak=    4.726 closest distance to " O   HOH Z 182 " =    1.503
peak=    4.698 closest distance to " O   HOH Z 282 " =    1.757
peak=    4.647 closest distance to " CB  ARG A 275 " =    0.918
peak=    4.590 closest distance to " CB  ASN A 148 " =    1.293
peak=    4.568 closest distance to " CB  LEU A 228 " =    1.085
peak=    4.557 closest distance to " O   HOH Z 368 " =    1.923
peak=    4.553 closest distance to " O   HOH Z 236 " =    1.975
peak=    4.552 closest distance to " NE2 GLN A  11 " =    1.150
peak=    4.548 closest distance to " O   HOH Z  48 " =    1.742
peak=    4.502 closest distance to " C   PRO A 198 " =    1.547
peak=    4.475 closest distance to " O   HOH Z 134 " =    1.564
peak=    4.464 closest distance to " O   HOH Z  78 " =    2.157
peak=    4.425 closest distance to " CB  GLU A 128 " =    1.036
peak=    4.406 closest distance to " O   HOH Z 207 " =    1.652
peak=    4.393 closest distance to " O   HOH Z  15 " =    2.165
peak=    4.384 closest distance to " O   HOH Z 108 " =    1.850
peak=    4.376 closest distance to " CB  SER A 216 " =    0.857
peak=    4.339 closest distance to " O   HOH Z 126 " =    1.891
peak=    4.328 closest distance to " O   HOH Z 232 " =    2.214
peak=    4.318 closest distance to " O   HOH Z 403 " =    1.530
peak=    4.302 closest distance to " CB  GLU A 152 " =    1.184
peak=    4.300 closest distance to " CB  SER A   3 " =    1.505
peak=    4.286 closest distance to " CG  PRO A 243 " =    1.053
peak=    4.280 closest distance to " O   HOH Z  49 " =    1.825
peak=    4.275 closest distance to " O   HOH Z 247 " =    1.397
peak=    4.244 closest distance to " O   HOH Z  21 " =    1.732
peak=    4.239 closest distance to " OD2 ASP A 286 " =    2.911
peak=    4.194 closest distance to " O   HOH Z 144 " =    1.623
peak=    4.183 closest distance to " O   HOH Z  68 " =    1.724
peak=    4.160 closest distance to " O   HOH Z 193 " =    1.878
peak=    4.151 closest distance to " OE1 GLN A  58 " =    1.187
peak=    4.132 closest distance to " O   HOH Z 344 " =    3.184
peak=    4.112 closest distance to " CG  PRO A 280 " =    0.841
peak=    4.102 closest distance to " CD BLYS A 290 " =    1.101
peak=    4.094 closest distance to " CB  TYR A 169 " =    0.766
peak=    4.093 closest distance to " ND2 ASN A 187 " =    1.610
peak=    4.085 closest distance to " O   HOH Z 425 " =    1.553
peak=    4.074 closest distance to " OD1 ASN A  69 " =    2.562
peak=    4.069 closest distance to " O   HOH Z 132 " =    2.233
peak=    4.045 closest distance to " CA  ALA A  21 " =    1.129
peak=    4.024 closest distance to " O   HOH Z 193 " =    1.773
peak=    4.017 closest distance to " O   HOH Z 281 " =    4.178
peak=    4.001 closest distance to " O   HOH Z  88 " =    3.698
peak=    4.001 closest distance to " CB  GLN A 183 " =    1.130
peak=    4.000 closest distance to " O   ASP A 132 " =    3.797
peak=    3.976 closest distance to " CA  GLU A 152 " =    1.333
peak=    3.975 closest distance to " O   HOH Z 261 " =    1.762
peak=    3.973 closest distance to " CG  LEU A 167 " =    1.207
peak=    3.962 closest distance to " CB  TRP A 179 " =    1.488
peak=    3.958 closest distance to " CD1 LEU A 300 " =    1.291
peak=    3.945 closest distance to " O   HOH Z 369 " =    1.890
peak=    3.942 closest distance to " NH1AARG A 145 " =    1.036
peak=    3.941 closest distance to " O   HOH Z 128 " =    2.042
peak=    3.940 closest distance to " CA  THR A 221 " =    0.915
peak=    3.921 closest distance to " O   HOH Z 389 " =    1.970
peak=    3.920 closest distance to " CZ  PHE A 192 " =    0.927
peak=    3.919 closest distance to " CD  LYS A 119 " =    1.340
peak=    3.915 closest distance to " CB  TRP A 266 " =    0.946
peak=    3.906 closest distance to " N   ASN A  39 " =    1.330
peak=    3.905 closest distance to " CA  TYR A  30 " =    1.078
peak=    3.904 closest distance to " CD  LYS A 166 " =    1.336
peak=    3.897 closest distance to " O   HOH Z 227 " =    1.735
peak=    3.895 closest distance to " NE AARG A 275 " =    1.546
peak=    3.881 closest distance to " O   HOH Z 427 " =    2.955
peak=    3.878 closest distance to " O   HOH Z 298 " =    1.733
peak=    3.866 closest distance to " CB  PRO A 198 " =    0.900
peak=    3.866 closest distance to " O   HOH Z 316 " =    3.175
peak=    3.857 closest distance to " O   HOH Z  61 " =    1.649
peak=    3.852 closest distance to " O   HOH Z  80 " =    1.650
peak=    3.850 closest distance to " O   HOH Z 409 " =    2.533
peak=    3.840 closest distance to " O   HOH Z 295 " =    1.549
peak=    3.831 closest distance to " O   HOH Z 313 " =    1.840
peak=    3.828 closest distance to " CG2 THR A 221 " =    1.001
peak=    3.827 closest distance to " CB  VAL A 265 " =    1.220
peak=    3.798 closest distance to " N   TYR A  15 " =    0.869
peak=    3.798 closest distance to " CB  MET A  47 " =    1.028
peak=    3.797 closest distance to " O   HOH Z 189 " =    2.357
peak=    3.792 closest distance to " NH2AARG A 190 " =    1.588
peak=    3.788 closest distance to " CD BARG A 102 " =    1.363
peak=    3.788 closest distance to " O   HOH Z 112 " =    1.413
peak=    3.781 closest distance to " O   HOH Z 124 " =    1.339
peak=    3.777 closest distance to " O   HOH Z 437 " =    1.854
peak=    3.768 closest distance to " CA  THR A 264 " =    0.826
peak=    3.767 closest distance to " O   HOH Z 352 " =    1.840
peak=    3.747 closest distance to " O   HOH Z 272 " =    1.973
peak=    3.720 closest distance to " O   HOH Z 411 " =    3.601
peak=    3.715 closest distance to " OD1 ASN A 217 " =    1.568
peak=    3.706 closest distance to " O   HOH Z  10 " =    1.875
peak=    3.698 closest distance to " O   HOH Z   6 " =    2.141
peak=    3.698 closest distance to " CA  TYR A 186 " =    1.441
peak=    3.696 closest distance to " O   HOH Z 346 " =    1.630
peak=    3.692 closest distance to " CA  LEU A 282 " =    1.111
peak=    3.691 closest distance to " CZ  PHE A 208 " =    1.155
peak=    3.690 closest distance to " CB  VAL A 202 " =    1.629
peak=    3.687 closest distance to " OD1 ASP A 231 " =    1.829
peak=    3.673 closest distance to " CA  ASP A 191 " =    0.771
peak=    3.668 closest distance to " CD  ARG A 159 " =    0.792
peak=    3.668 closest distance to " O   HOH Z 374 " =    2.751
peak=    3.665 closest distance to " CG  GLN A  88 " =    1.008
peak=    3.665 closest distance to " CA  ASN A 215 " =    1.279
peak=    3.657 closest distance to " O   HOH Z  20 " =    2.044
peak=    3.656 closest distance to " O   HOH Z  66 " =    2.069
peak=    3.655 closest distance to " CB  ARG A 139 " =    0.916
peak=    3.654 closest distance to " N   ARG A 156 " =    1.396
peak=    3.653 closest distance to " CB  ASN A 187 " =    0.987
peak=    3.651 closest distance to " CA  MET A  40 " =    1.075
peak=    3.647 closest distance to " O   HOH Z 116 " =    1.728
peak=    3.643 closest distance to " CG2 VAL A 257 " =    0.933
peak=    3.642 closest distance to " CA  ASP A 124 " =    0.778
peak=    3.638 closest distance to " CB  ASP A 124 " =    0.757
peak=    3.637 closest distance to " CB  ARG A 102 " =    0.777
peak=    3.637 closest distance to " ND1 HIS A  86 " =    1.737
peak=    3.635 closest distance to " O   HOH Z  58 " =    1.948
peak=    3.628 closest distance to " CA  LYS A  48 " =    1.316
peak=    3.627 closest distance to " O   HOH Z 271 " =    2.210
peak=    3.625 closest distance to " O   HOH Z  98 " =    1.686
peak=    3.623 closest distance to " CA  SER A  87 " =    0.874
peak=    3.622 closest distance to " O   HOH Z 193 " =    2.168
peak=    3.622 closest distance to " CB  THR A 157 " =    1.103
peak=    3.619 closest distance to " O   HOH Z 117 " =    1.503
peak=    3.612 closest distance to " CG  TRP A 179 " =    2.222
peak=    3.610 closest distance to " CB  LEU A 143 " =    1.052
peak=    3.606 closest distance to " O   HOH Z  64 " =    2.241
peak=    3.587 closest distance to " CB  ALA A 291 " =    1.452
peak=    3.583 closest distance to " CG1 ILE A  33 " =    1.296
peak=    3.582 closest distance to " NE  ARG A  66 " =    3.731
peak=    3.580 closest distance to " CA  GLU A 152 " =    0.942
peak=    3.578 closest distance to " O   HOH Z 163 " =    2.010
peak=    3.575 closest distance to " O   HOH Z 125 " =    2.225
peak=    3.567 closest distance to " O   HOH Z 108 " =    1.762
peak=    3.563 closest distance to " O   HOH Z 359 " =    3.876
peak=    3.552 closest distance to " NH1 ARG A  56 " =    1.010
peak=    3.552 closest distance to " O   SER A  87 " =    2.314
peak=    3.530 closest distance to " O   HOH Z  11 " =    1.623
peak=    3.528 closest distance to " O   HOH Z   4 " =    2.001
peak=    3.524 closest distance to " O   HOH Z 373 " =    1.856
peak=    3.518 closest distance to " CG1 VAL A 153 " =    0.941
peak=    3.512 closest distance to " O   MET A 105 " =    1.688
peak=    3.511 closest distance to " CD2 HIS A  81 " =    1.290
peak=    3.507 closest distance to " O   ALA A   1 " =    1.551
peak=    3.504 closest distance to " O   HOH Z 133 " =    2.231
peak=    3.499 closest distance to " CB  MET A  40 " =    0.821
peak=    3.499 closest distance to " O   HOH Z 334 " =    1.500
peak=    3.499 closest distance to " CD1 ILE A  33 " =    1.550
peak=    3.497 closest distance to " O   HOH Z 423 " =    1.546
peak=    3.491 closest distance to " O   HOH Z 426 " =    3.432
peak=    3.487 closest distance to " O   HOH Z 410 " =    1.749
peak=    3.485 closest distance to " CB  ILE A 234 " =    0.977
peak=    3.481 closest distance to " O   HOH Z 371 " =    2.971
peak=    3.478 closest distance to " O   HOH Z 180 " =    2.085
peak=    3.477 closest distance to " CA  ALA A 154 " =    1.094
peak=    3.475 closest distance to " CA  THR A  42 " =    0.941
peak=    3.468 closest distance to " O   HOH Z  66 " =    2.273
peak=    3.463 closest distance to " O   HOH Z 276 " =    1.234
peak=    3.457 closest distance to " O   HOH Z  63 " =    2.352
peak=    3.455 closest distance to " O   HOH Z 132 " =    0.992
peak=    3.448 closest distance to " O   HOH Z   7 " =    1.243
peak=    3.448 closest distance to " CZ  PHE A 218 " =    0.989
peak=    3.446 closest distance to " CA  ALA A 158 " =    1.069
peak=    3.446 closest distance to " CB  ALA A  34 " =    1.115
peak=    3.441 closest distance to " NH2 ARG A 156 " =    1.287
peak=    3.436 closest distance to " CD2 LEU A 255 " =    1.350
peak=    3.436 closest distance to " O   HOH Z 156 " =    2.749
peak=    3.432 closest distance to " O   TRP A 274 " =    1.606
peak=    3.431 closest distance to " O   HOH Z 139 " =    2.960
peak=    3.429 closest distance to " O   HOH Z 387 " =    3.122
peak=    3.428 closest distance to " O   HOH Z 175 " =    2.214
peak=    3.425 closest distance to " O   HOH Z 284 " =    3.014
peak=    3.421 closest distance to " O   HOH Z 263 " =    2.177
peak=    3.420 closest distance to " N   ASN A 127 " =    1.336
peak=    3.420 closest distance to " CG AARG A 275 " =    1.100
peak=    3.418 closest distance to " O   HOH Z 273 " =    2.794
peak=    3.416 closest distance to " O   HOH Z 345 " =    1.792
peak=    3.416 closest distance to " CG BARG A 275 " =    1.500
peak=    3.415 closest distance to " CB  TRP A 179 " =    1.751
peak=    3.414 closest distance to " O   HOH Z 287 " =    1.884
peak=    3.400 closest distance to " O   HOH Z 175 " =    3.655
peak=    3.391 closest distance to " CG2 VAL A 112 " =    0.859
peak=    3.381 closest distance to " CA  GLY A 196 " =    0.914
peak=    3.379 closest distance to " O   HOH Z  93 " =    2.641
peak=    3.375 closest distance to " O   HOH Z  85 " =    2.281
peak=    3.372 closest distance to " NZ  LYS A  76 " =    1.212
peak=    3.371 closest distance to " NH2AARG A 145 " =    0.932
peak=    3.369 closest distance to " CB  PHE A  16 " =    1.079
peak=    3.368 closest distance to " CZ3 TRP A 123 " =    1.198
peak=    3.366 closest distance to " O   HOH Z 213 " =    1.822
peak=    3.362 closest distance to " O   HOH Z 128 " =    1.543
peak=    3.354 closest distance to " O   HOH Z 216 " =    2.466
peak=    3.351 closest distance to " CA  ALA A 299 " =    0.948
peak=    3.348 closest distance to " CD1 TRP A 266 " =    1.108
peak=    3.347 closest distance to " CB  ALA A 104 " =    0.794
peak=    3.346 closest distance to " NH2BARG A 145 " =    2.032
peak=    3.345 closest distance to " O   HOH Z 291 " =    1.949
peak=    3.321 closest distance to " O   HOH Z 215 " =    1.461
peak=    3.320 closest distance to " O   HOH Z 133 " =    1.734
peak=    3.319 closest distance to " O   ALA A 233 " =    1.784
peak=    3.318 closest distance to " CG  ARG A 159 " =    0.904
peak=    3.317 closest distance to " O   HOH Z  55 " =    2.261
peak=    3.315 closest distance to " O   HOH Z 217 " =    1.379
peak=    3.309 closest distance to " CE2 TYR A 247 " =    1.276
peak=    3.303 closest distance to " CA  ARG A 102 " =    1.227
peak=    3.302 closest distance to " NH1 ARG A  14 " =    1.072
peak=    3.301 closest distance to " CB  TRP A 123 " =    1.033
peak=    3.300 closest distance to " O   HOH Z 277 " =    2.499
peak=    3.297 closest distance to " CD  ARG A 269 " =    0.834
peak=    3.294 closest distance to " CB  ALA A 248 " =    0.971
peak=    3.294 closest distance to " O   ALA A  10 " =    1.539
peak=    3.291 closest distance to " O   HOH Z 194 " =    2.064
peak=    3.290 closest distance to " CA  ILE A 234 " =    0.937
peak=    3.289 closest distance to " OD1 ASP A 238 " =    1.023
peak=    3.289 closest distance to " O   HOH Z 332 " =    1.601
peak=    3.288 closest distance to " CD  ARG A  14 " =    1.340
peak=    3.286 closest distance to " CB  ALA A 161 " =    0.893
peak=    3.284 closest distance to " CE  LYS A  76 " =    0.878
peak=    3.282 closest distance to " O   HOH Z  49 " =    1.985
peak=    3.282 closest distance to " CD  ARG A 219 " =    1.013
peak=    3.281 closest distance to " CB  GLU A 277 " =    3.594
peak=    3.278 closest distance to " O   HOH Z 296 " =    1.559
peak=    3.278 closest distance to " O   HOH Z 214 " =    2.486
peak=    3.276 closest distance to " CB  GLU A 236 " =    1.091
peak=    3.275 closest distance to " O   HOH Z 211 " =    1.269
peak=    3.275 closest distance to " O   HOH Z  44 " =    1.731
peak=    3.272 closest distance to " CG2 VAL A  78 " =    1.010
peak=    3.271 closest distance to " CG  GLN A  55 " =    1.974
peak=    3.270 closest distance to " O   HOH Z 345 " =    3.417
peak=    3.270 closest distance to " CG1BVAL A  72 " =    1.502
peak=    3.265 closest distance to " CA  ALA A  43 " =    1.220
peak=    3.264 closest distance to " CB  ILE A 199 " =    0.960
peak=    3.262 closest distance to " CB  ALA A 184 " =    1.051
peak=    3.262 closest distance to " OD1BASN A 224 " =    2.107
peak=    3.259 closest distance to " CD  ARG A  66 " =    2.310
peak=    3.259 closest distance to " CB  ARG A 190 " =    1.784
peak=    3.253 closest distance to " ND1 HIS A  81 " =    1.539
peak=    3.232 closest distance to " O   HOH Z 152 " =    2.968
peak=    3.229 closest distance to " O   HOH Z 255 " =    1.664
peak=    3.223 closest distance to " CB  LYS A 117 " =    1.152
peak=    3.222 closest distance to " O   HOH Z 368 " =    2.605
peak=    3.218 closest distance to " CA  LYS A 117 " =    1.237
peak=    3.218 closest distance to " CB  ASN A  39 " =    0.931
peak=    3.217 closest distance to " O   HOH Z 415 " =    5.984
peak=    3.216 closest distance to " O   THR A 220 " =    1.403
peak=    3.215 closest distance to " OG1 THR A 294 " =    1.647
peak=    3.214 closest distance to " N   VAL A 126 " =    1.340
peak=    3.212 closest distance to " O   ARG A  56 " =    1.800
peak=    3.212 closest distance to " O   HOH Z 172 " =    3.617
peak=    3.209 closest distance to " OE1 GLU A 277 " =    1.796
peak=    3.209 closest distance to " O   HOH Z 299 " =    2.348
peak=    3.207 closest distance to " CB  TYR A 116 " =    1.007
peak=    3.206 closest distance to " OE1 GLN A  11 " =    2.040
peak=    3.206 closest distance to " CB  ILE A 120 " =    1.031
peak=    3.205 closest distance to " N   PHE A 130 " =    1.317
peak=    3.203 closest distance to " O   HOH Z 127 " =    2.263
peak=    3.196 closest distance to " NE2 GLN A  58 " =    5.581
peak=    3.194 closest distance to " O   HOH Z 162 " =    1.981
peak=    3.193 closest distance to " CB  SER A 276 " =    1.166
peak=    3.191 closest distance to " CH2 TRP A 150 " =    1.117
peak=    3.191 closest distance to " O   HOH Z  37 " =    2.768
peak=    3.190 closest distance to " CB  PHE A 283 " =    0.811
peak=    3.188 closest distance to " O   HOH Z 163 " =    2.019
peak=    3.188 closest distance to " CD1 ILE A 106 " =    0.772
peak=    3.188 closest distance to " NE  ARG A 156 " =    1.099
peak=    3.184 closest distance to " O   HOH Z 236 " =    1.652
peak=    3.183 closest distance to " CB  HIS A  81 " =    1.279
peak=    3.181 closest distance to " NZ  LYS A 166 " =    2.956
peak=    3.178 closest distance to " CA  ALA A 160 " =    0.909
peak=    3.177 closest distance to " NH1BARG A 145 " =    0.773
peak=    3.173 closest distance to " O   GLY A  57 " =    2.611
peak=    3.171 closest distance to " O   HOH Z  59 " =    2.098
peak=    3.171 closest distance to " O   HOH Z 115 " =    2.143
peak=    3.171 closest distance to " CB  SER A 212 " =    1.118
peak=    3.169 closest distance to " CB  PRO A 243 " =    1.221
peak=    3.168 closest distance to " O   HOH Z  44 " =    3.291
peak=    3.165 closest distance to " OG BSER A 164 " =    2.368
peak=    3.165 closest distance to " O   TYR A 116 " =    1.335
peak=    3.161 closest distance to " O   HOH Z 329 " =    3.610
peak=    3.159 closest distance to " O   HOH Z 379 " =    1.982
peak=    3.158 closest distance to " N   SER A 210 " =    0.997
peak=    3.156 closest distance to " O   HOH Z 128 " =    2.349
peak=    3.155 closest distance to " O   HOH Z 418 " =    2.533
peak=    3.154 closest distance to " O   ALA A 165 " =    1.362
peak=    3.152 closest distance to " NZ  LYS A 117 " =    3.361
peak=    3.152 closest distance to " O   HOH Z 337 " =    1.897
peak=    3.150 closest distance to " O   HOH Z  73 " =    1.485
peak=    3.146 closest distance to " CG2 VAL A 174 " =    1.355
peak=    3.143 closest distance to " CD  PRO A 280 " =    0.938
peak=    3.141 closest distance to " O   HOH Z 305 " =    3.698
peak=    3.137 closest distance to " O   HOH Z  22 " =    1.997
peak=    3.134 closest distance to " CG BARG A 102 " =    1.920
peak=    3.133 closest distance to " CG2 THR A 264 " =    0.760
peak=    3.132 closest distance to " O   HOH Z 158 " =    2.860
peak=    3.128 closest distance to " CD1AILE A 234 " =    1.121
peak=    3.125 closest distance to " CG2 ILE A 109 " =    1.042
peak=    3.122 closest distance to " OG ASER A 134 " =    1.203
peak=    3.122 closest distance to " NZ ALYS A 290 " =    1.212
peak=    3.121 closest distance to " O   HOH Z  17 " =    1.976
peak=    3.117 closest distance to " O   HOH Z 244 " =    1.759
peak=    3.109 closest distance to " O   HOH Z 368 " =    3.639
peak=    3.107 closest distance to " C   GLU A 277 " =    1.410
peak=    3.105 closest distance to " O   HOH Z 337 " =    3.827
peak=    3.095 closest distance to " O   HOH Z 184 " =    1.368
peak=    3.094 closest distance to " O   HOH Z 334 " =    1.473
peak=    3.093 closest distance to " O   HOH Z 149 " =    1.897
peak=    3.090 closest distance to " O   HOH Z   1 " =    2.042
peak=    3.087 closest distance to " CB  ALA A 256 " =    1.466
peak=    3.086 closest distance to " O   HOH Z 391 " =    2.945
peak=    3.082 closest distance to " O   HOH Z 419 " =    1.831
peak=    3.081 closest distance to " O   HOH Z  97 " =    1.962
peak=    3.075 closest distance to " O   HOH Z 281 " =    1.957
peak=    3.074 closest distance to " CG  PRO A 213 " =    1.009
peak=    3.073 closest distance to " NE2 GLN A  58 " =    2.922
peak=    3.066 closest distance to " NZ  LYS A 181 " =    0.732
peak=    3.059 closest distance to " O   HOH Z   1 " =    1.671
peak=    3.058 closest distance to " O   HOH Z 171 " =    2.107
peak=    3.046 closest distance to " O   HOH Z  53 " =    2.608
peak=    3.037 closest distance to " O   HOH Z 334 " =    1.640
peak=    3.013 closest distance to " CA  ASP A 140 " =    1.221

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.432 - 5.519
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 178 from: 185
   mapped sites are within: 0.735 - 5.519

peak=   -5.194 closest distance to " O   HOH Z 290 " =    0.933
peak=   -4.624 closest distance to " O   HOH Z 377 " =    1.190
peak=   -4.386 closest distance to " CG  MET A 105 " =    0.932
peak=   -4.318 closest distance to " O   HOH Z  98 " =    1.805
peak=   -4.313 closest distance to " CD2 LEU A 143 " =    2.552
peak=   -4.270 closest distance to " O   HOH Z 231 " =    1.418
peak=   -4.238 closest distance to " C   ALA A 158 " =    1.347
peak=   -4.219 closest distance to " O   PRO A 198 " =    1.267
peak=   -4.206 closest distance to " CB  PRO A 243 " =    2.624
peak=   -4.191 closest distance to " ND2 ASN A  45 " =    0.905
peak=   -4.184 closest distance to " CD  GLN A  88 " =    0.776
peak=   -4.177 closest distance to " OE1 GLN A  88 " =    1.076
peak=   -4.158 closest distance to " O   HOH Z  43 " =    1.320
peak=   -4.061 closest distance to " N   ALA A  43 " =    2.287
peak=   -4.027 closest distance to " CG  ASP A 231 " =    0.739
peak=   -4.013 closest distance to " O   HOH Z 222 " =    1.122
peak=   -4.000 closest distance to " CG  LYS A 193 " =    2.460
peak=   -3.990 closest distance to " O   HOH Z 266 " =    4.290
peak=   -3.963 closest distance to " CB  ASP A  27 " =    2.467
peak=   -3.951 closest distance to " O   HOH Z 275 " =    1.654
peak=   -3.929 closest distance to " O   HOH Z 388 " =    1.871
peak=   -3.840 closest distance to " CD1 LEU A 228 " =    2.466
peak=   -3.831 closest distance to " O   HOH Z 166 " =    1.200
peak=   -3.820 closest distance to " O   HOH Z 185 " =    2.426
peak=   -3.770 closest distance to " OG ASER A 134 " =    1.341
peak=   -3.768 closest distance to " O   GLY A 196 " =    1.127
peak=   -3.765 closest distance to " CA  GLY A 241 " =    2.293
peak=   -3.753 closest distance to " O   GLY A 211 " =    1.472
peak=   -3.752 closest distance to " CD  ARG A  14 " =    3.182
peak=   -3.742 closest distance to " O   HOH Z  98 " =    1.247
peak=   -3.721 closest distance to " CE  MET A  93 " =    1.136
peak=   -3.719 closest distance to " O   HOH Z  97 " =    1.299
peak=   -3.712 closest distance to " CG  ARG A 269 " =    2.490
peak=   -3.711 closest distance to " O   VAL A 153 " =    2.524
peak=   -3.695 closest distance to " OD1 ASN A  39 " =    2.227
peak=   -3.670 closest distance to " CB  ALA A 291 " =    2.255
peak=   -3.661 closest distance to " C   ASN A 285 " =    2.615
peak=   -3.660 closest distance to " O   HOH Z  52 " =    1.134
peak=   -3.650 closest distance to " O   HOH Z  71 " =    0.868
peak=   -3.645 closest distance to " O   VAL A  67 " =    2.741
peak=   -3.638 closest distance to " CD  ARG A 195 " =    5.118
peak=   -3.635 closest distance to " O   HOH Z 436 " =    1.225
peak=   -3.635 closest distance to " O   HOH Z  56 " =    0.811
peak=   -3.631 closest distance to " OD1 ASP A 191 " =    1.659
peak=   -3.624 closest distance to " CG  GLN A 223 " =    1.578
peak=   -3.622 closest distance to " CG  GLN A  58 " =    1.240
peak=   -3.611 closest distance to " O   HOH Z 213 " =    1.312
peak=   -3.590 closest distance to " O   HOH Z 210 " =    0.914
peak=   -3.587 closest distance to " CB  LEU A 167 " =    2.136
peak=   -3.584 closest distance to " O   HOH Z 407 " =    3.561
peak=   -3.579 closest distance to " OG  SER A 245 " =    0.914
peak=   -3.577 closest distance to " OG ASER A 216 " =    1.084
peak=   -3.573 closest distance to " O   SER A  62 " =    2.137
peak=   -3.554 closest distance to " CB  CYS A 254 " =    2.233
peak=   -3.541 closest distance to " CA  SER A 146 " =    2.352
peak=   -3.529 closest distance to " CG  GLU A 152 " =    0.735
peak=   -3.514 closest distance to " O   HOH Z  92 " =    1.372
peak=   -3.504 closest distance to " CB  CYS A 201 " =    2.628
peak=   -3.492 closest distance to " O   ALA A 161 " =    1.529
peak=   -3.491 closest distance to " CB  ASN A  39 " =    1.994
peak=   -3.488 closest distance to " N   THR A 157 " =    1.701
peak=   -3.486 closest distance to " O   HOH Z 184 " =    1.533
peak=   -3.482 closest distance to " NH2AARG A 275 " =    5.519
peak=   -3.482 closest distance to " CB  PRO A  54 " =    2.468
peak=   -3.482 closest distance to " O   HOH Z 283 " =    1.763
peak=   -3.479 closest distance to " CG  LEU A  83 " =    1.920
peak=   -3.478 closest distance to " SG  CYS A 254 " =    3.030
peak=   -3.473 closest distance to " O   HOH Z  20 " =    2.357
peak=   -3.459 closest distance to " OXT GLY A 302 " =    2.881
peak=   -3.449 closest distance to " CD2 LEU A 237 " =    2.627
peak=   -3.439 closest distance to " CH2 TRP A 179 " =    1.253
peak=   -3.437 closest distance to " CD  LYS A 289 " =    2.589
peak=   -3.431 closest distance to " OG  SER A  97 " =    2.223
peak=   -3.427 closest distance to " CA  TRP A 274 " =    1.595
peak=   -3.427 closest distance to " CB  GLN A  55 " =    1.382
peak=   -3.409 closest distance to " CE3 TRP A 150 " =    1.548
peak=   -3.408 closest distance to " CG  PRO A 163 " =    2.350
peak=   -3.403 closest distance to " O   HOH Z 266 " =    4.741
peak=   -3.401 closest distance to " CD2 TYR A 293 " =    2.020
peak=   -3.397 closest distance to " O   HOH Z  11 " =    1.871
peak=   -3.395 closest distance to " O   HOH Z  76 " =    1.396
peak=   -3.395 closest distance to " CB  ALA A  43 " =    2.422
peak=   -3.394 closest distance to " CE2 TYR A  30 " =    2.912
peak=   -3.393 closest distance to " C   ASN A 187 " =    1.781
peak=   -3.391 closest distance to " CB  TRP A  85 " =    2.503
peak=   -3.386 closest distance to " CD2 PHE A  59 " =    2.582
peak=   -3.385 closest distance to " CD  ARG A 156 " =    1.891
peak=   -3.384 closest distance to " O   HOH Z  37 " =    2.395
peak=   -3.384 closest distance to " OG  SER A  87 " =    1.273
peak=   -3.380 closest distance to " O   HOH Z  10 " =    1.510
peak=   -3.373 closest distance to " CD  GLN A  88 " =    2.261
peak=   -3.372 closest distance to " CH2 TRP A 177 " =    2.170
peak=   -3.368 closest distance to " O   ALA A   7 " =    1.647
peak=   -3.357 closest distance to " CB  PRO A 163 " =    2.638
peak=   -3.351 closest distance to " O   HOH Z  13 " =    1.131
peak=   -3.349 closest distance to " C   GLN A 240 " =    2.065
peak=   -3.346 closest distance to " O   HOH Z 353 " =    2.329
peak=   -3.342 closest distance to " N   GLN A  58 " =    1.720
peak=   -3.338 closest distance to " CE  LYS A  76 " =    2.639
peak=   -3.337 closest distance to " O   HOH Z 241 " =    1.180
peak=   -3.332 closest distance to " N   HIS A 115 " =    2.094
peak=   -3.326 closest distance to " CG  ASP A 200 " =    1.282
peak=   -3.326 closest distance to " OD2 ASP A 171 " =    2.090
peak=   -3.313 closest distance to " O   ASN A 301 " =    1.435
peak=   -3.313 closest distance to " O   HOH Z 368 " =    2.511
peak=   -3.306 closest distance to " O   HOH Z 298 " =    1.225
peak=   -3.306 closest distance to " CZ  TYR A 169 " =    1.795
peak=   -3.302 closest distance to " O   HOH Z 186 " =    0.789
peak=   -3.298 closest distance to " CG1 VAL A 250 " =    2.678
peak=   -3.291 closest distance to " O   HOH Z 120 " =    2.883
peak=   -3.286 closest distance to " O   HOH Z 417 " =    2.421
peak=   -3.285 closest distance to " C   LEU A 143 " =    1.698
peak=   -3.285 closest distance to " OD2 ASP A  65 " =    1.644
peak=   -3.285 closest distance to " CG  GLU A 152 " =    2.196
peak=   -3.280 closest distance to " CB  ASP A 132 " =    2.238
peak=   -3.273 closest distance to " CB  SER A 271 " =    1.782
peak=   -3.271 closest distance to " NE BARG A 102 " =    1.172
peak=   -3.265 closest distance to " N   GLY A  23 " =    2.147
peak=   -3.263 closest distance to " OH  TYR A 172 " =    1.732
peak=   -3.252 closest distance to " CD  ARG A 159 " =    1.306
peak=   -3.247 closest distance to " O   HOH Z  24 " =    1.482
peak=   -3.244 closest distance to " O   ILE A 109 " =    2.689
peak=   -3.237 closest distance to " CD2 LEU A 237 " =    2.702
peak=   -3.235 closest distance to " O   PRO A 163 " =    1.880
peak=   -3.235 closest distance to " CD  GLN A 223 " =    0.777
peak=   -3.229 closest distance to " CG  GLU A  53 " =    1.340
peak=   -3.228 closest distance to " O   HOH Z 389 " =    1.774
peak=   -3.224 closest distance to " CZ  ARG A 259 " =    0.909
peak=   -3.223 closest distance to " O   HOH Z 166 " =    1.864
peak=   -3.221 closest distance to " O   HOH Z   3 " =    1.722
peak=   -3.220 closest distance to " OG BSER A 134 " =    1.748
peak=   -3.218 closest distance to " O   HOH Z 252 " =    4.264
peak=   -3.218 closest distance to " C   LEU A 222 " =    0.765
peak=   -3.217 closest distance to " CG1 VAL A 112 " =    2.566
peak=   -3.215 closest distance to " OG BSER A 134 " =    1.280
peak=   -3.213 closest distance to " O   HOH Z 423 " =    1.037
peak=   -3.212 closest distance to " CE  MET A 105 " =    2.086
peak=   -3.200 closest distance to " NE2 GLN A  58 " =    1.093
peak=   -3.198 closest distance to " O   HOH Z  90 " =    1.443
peak=   -3.184 closest distance to " O   GLY A  57 " =    1.056
peak=   -3.182 closest distance to " O   HOH Z 100 " =    0.782
peak=   -3.180 closest distance to " O   HOH Z 281 " =    2.902
peak=   -3.175 closest distance to " N   VAL A 232 " =    2.594
peak=   -3.170 closest distance to " CD  ARG A 139 " =    1.576
peak=   -3.168 closest distance to " CD1 ILE A 239 " =    2.046
peak=   -3.167 closest distance to " O   HOH Z 111 " =    2.267
peak=   -3.167 closest distance to " CG2BVAL A  41 " =    1.213
peak=   -3.164 closest distance to " ND2 ASN A 249 " =    1.869
peak=   -3.156 closest distance to " CG  TRP A 266 " =    1.695
peak=   -3.156 closest distance to " OG  SER A 206 " =    2.038
peak=   -3.155 closest distance to " OD2 ASP A 140 " =    1.249
peak=   -3.153 closest distance to " O   HOH Z 109 " =    1.136
peak=   -3.149 closest distance to " O   HOH Z 129 " =    4.374
peak=   -3.145 closest distance to " O   HOH Z 438 " =    1.256
peak=   -3.144 closest distance to " O   HOH Z 148 " =    2.041
peak=   -3.141 closest distance to " O   PHE A 218 " =    1.421
peak=   -3.139 closest distance to " O   HOH Z 310 " =    3.492
peak=   -3.135 closest distance to " O   HOH Z 383 " =    1.034
peak=   -3.133 closest distance to " O   HOH Z 137 " =    1.575
peak=   -3.132 closest distance to " N   ALA A 226 " =    2.155
peak=   -3.130 closest distance to " OH  TYR A 169 " =    0.976
peak=   -3.121 closest distance to " OD2 ASP A 171 " =    1.761
peak=   -3.109 closest distance to " CD1 TRP A 179 " =    0.835
peak=   -3.104 closest distance to " OG1 THR A   4 " =    1.873
peak=   -3.103 closest distance to " ND2 ASN A  60 " =    1.870
peak=   -3.096 closest distance to " O   HOH Z 435 " =    2.814
peak=   -3.094 closest distance to " OD1 ASN A 249 " =    1.087
peak=   -3.088 closest distance to " N   PRO A 213 " =    1.954
peak=   -3.080 closest distance to " O   HOH Z  97 " =    2.390
peak=   -3.077 closest distance to " O   PRO A 198 " =    1.212
peak=   -3.075 closest distance to " CD2 LEU A 237 " =    2.465
peak=   -3.075 closest distance to " CB  ASP A 132 " =    2.545
peak=   -3.071 closest distance to " CD  LYS A 119 " =    1.003
peak=   -3.069 closest distance to " O   HOH Z 396 " =    1.734
peak=   -3.062 closest distance to " O   HOH Z 426 " =    2.342
peak=   -3.062 closest distance to " CG1 VAL A 202 " =    2.934
peak=   -3.055 closest distance to " CA  GLY A 133 " =    1.896
peak=   -3.052 closest distance to " O   HOH Z 262 " =    2.089

================= 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    :  0.4508 0.4515   6.257823e+00   6.259274e+00
   1_bss:  0.4411 0.4427   6.252192e+00   6.248003e+00
   1_xyz:  0.3360 0.3760   6.067513e+00   6.143273e+00
   1_adp:  0.3061 0.3783   6.019486e+00   6.149940e+00
   1_occ:  0.3057 0.3777   6.018101e+00   6.148741e+00
   2_bss:  0.3048 0.3766   6.016373e+00   6.145896e+00
   2_xyz:  0.2274 0.2948   5.770081e+00   5.951299e+00
   2_adp:  0.2058 0.2723   5.695656e+00   5.892664e+00
   2_occ:  0.2057 0.2722   5.695086e+00   5.891736e+00
   3_bss:  0.2049 0.2710   5.690278e+00   5.887216e+00
   3_xyz:  0.1571 0.2105   5.444396e+00   5.669761e+00
   3_adp:  0.1451 0.1943   5.368566e+00   5.587897e+00
   3_occ:  0.1450 0.1940   5.367496e+00   5.586685e+00
   4_bss:  0.1450 0.1936   5.368437e+00   5.586256e+00
   4_xyz:  0.1243 0.1709   5.233849e+00   5.465576e+00
   4_adp:  0.1190 0.1662   5.199952e+00   5.440222e+00
   4_occ:  0.1188 0.1659   5.198868e+00   5.439124e+00
   5_bss:  0.1193 0.1661   5.201017e+00   5.440802e+00
   5_xyz:  0.1191 0.1648   5.201712e+00   5.433775e+00
   5_adp:  0.1203 0.1631   5.201842e+00   5.423754e+00
   5_occ:  0.1201 0.1629   5.200983e+00   5.423267e+00
   5_bss:  0.1201 0.1628   5.200920e+00   5.423223e+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:  0.297  21.641   1.978  -2.823   2.138  -0.000   0.000   0.000
   1_xyz:  0.297  21.641   1.978  -2.823   2.138  -0.000   0.000   0.000
   1_adp:  0.297  21.641   1.978  -2.823   2.138  -0.000   0.000   0.000
   1_occ:  0.297  21.641   1.978  -2.823   2.138  -0.000   0.000   0.000
   2_bss:  0.331  50.000   0.790  -1.570   1.016  -0.000   0.000   0.000
   2_xyz:  0.331  50.000   0.790  -1.570   1.016  -0.000   0.000   0.000
   2_adp:  0.331  50.000   0.790  -1.570   1.016  -0.000   0.000   0.000
   2_occ:  0.331  50.000   0.790  -1.570   1.016  -0.000   0.000   0.000
   3_bss:  0.336  57.043  -0.354  -1.742  -0.556  -0.000  -0.000  -0.000
   3_xyz:  0.336  57.043  -0.354  -1.742  -0.556  -0.000  -0.000  -0.000
   3_adp:  0.336  57.043  -0.354  -1.742  -0.556  -0.000  -0.000  -0.000
   3_occ:  0.336  57.043  -0.354  -1.742  -0.556  -0.000  -0.000  -0.000
   4_bss:  0.330  53.121  -1.514  -2.377  -1.586  -0.000  -0.000  -0.000
   4_xyz:  0.330  53.121  -1.514  -2.377  -1.586  -0.000  -0.000  -0.000
   4_adp:  0.330  53.121  -1.514  -2.377  -1.586  -0.000  -0.000  -0.000
   4_occ:  0.330  53.121  -1.514  -2.377  -1.586  -0.000  -0.000  -0.000
   5_bss:  0.324  52.088  -1.773  -2.492  -1.898  -0.000  -0.000  -0.000
   5_xyz:  0.324  52.088  -1.773  -2.492  -1.898  -0.000  -0.000  -0.000
   5_adp:  0.324  52.088  -1.773  -2.492  -1.898  -0.000  -0.000  -0.000
   5_occ:  0.324  52.088  -1.773  -2.492  -1.898  -0.000  -0.000  -0.000
   5_bss:  0.324  52.024  -1.796  -2.431  -1.914  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.494 0.4507  0.6095    65366.556
   1_bss:  54.050 0.4676  0.6456    61831.787
   1_xyz:  42.276 0.6146  0.8271    41490.949
   1_adp:  43.092 0.6037  0.8127    42255.108
   1_occ:  43.028 0.6044  0.8120    42074.941
   2_bss:  42.746 0.6077  0.8085    41670.534
   2_xyz:  31.160 0.7436  0.9607    23648.059
   2_adp:  28.250 0.7764  0.9793    20346.295
   2_occ:  28.235 0.7766  0.9791    20301.577
   3_bss:  27.981 0.7791  0.9478    19965.617
   3_xyz:  20.911 0.8518  0.9973    11692.651
   3_adp:  18.637 0.8745  1.0076     9872.002
   3_occ:  18.607 0.8747  1.0076     9840.465
   4_bss:  18.594 0.8748  0.9744     9842.947
   4_xyz:  15.864 0.8989  0.9857     7544.121
   4_adp:  15.236 0.9045  0.9846     7160.415
   4_occ:  15.204 0.9048  0.9847     7138.666
   5_bss:  15.233 0.9046  0.9765     7181.981
   5_xyz:  15.027 0.9066  0.9759     7002.755
   5_adp:  14.736 0.9094  0.9759     6916.520
   5_occ:  14.715 0.9096  0.9758     6905.583
   5_bss:  14.714 0.9096  0.9739     6904.257
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.8088e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.8088e-01
   1_xyz:   1.361  0.011  0.089 15.891  0.005  4.111   1.0802e-01
   1_adp:   1.361  0.011  0.089 15.891  0.005  4.111   1.0802e-01
   1_occ:   1.361  0.011  0.089 15.891  0.005  4.111   1.0802e-01
   2_bss:   1.361  0.011  0.089 15.891  0.005  4.111   1.0802e-01
   2_xyz:   1.260  0.010  0.082 14.737  0.004  4.108   8.8756e-02
   2_adp:   1.260  0.010  0.082 14.737  0.004  4.108   8.8756e-02
   2_occ:   1.260  0.010  0.082 14.737  0.004  4.108   8.8756e-02
   3_bss:   1.260  0.010  0.082 14.737  0.004  4.108   8.8756e-02
   3_xyz:   1.072  0.007  0.074 14.619  0.004  4.117   6.5137e-02
   3_adp:   1.072  0.007  0.074 14.619  0.004  4.117   6.5137e-02
   3_occ:   1.072  0.007  0.074 14.619  0.004  4.117   6.5137e-02
   4_bss:   1.072  0.007  0.074 14.619  0.004  4.117   6.5137e-02
   4_xyz:   1.140  0.009  0.079 14.746  0.005  4.110   7.2676e-02
   4_adp:   1.140  0.009  0.079 14.746  0.005  4.110   7.2676e-02
   4_occ:   1.140  0.009  0.079 14.746  0.005  4.110   7.2676e-02
   5_bss:   1.140  0.009  0.079 14.746  0.005  4.110   7.2676e-02
   5_xyz:   0.935  0.006  0.067 14.422  0.003  4.111   5.2198e-02
   5_adp:   0.935  0.006  0.067 14.422  0.003  4.111   5.2198e-02
   5_occ:   0.935  0.006  0.067 14.422  0.003  4.111   5.2198e-02
   5_bss:   0.935  0.006  0.067 14.422  0.003  4.111   5.2198e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.589   2.4061e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.589   2.4061e-01
   1_xyz:   9.157  0.058  0.378 87.499  0.028  1.978   9.4152e-02
   1_adp:   9.157  0.058  0.378 87.499  0.028  1.978   9.4152e-02
   1_occ:   9.157  0.058  0.378 87.499  0.028  1.978   9.4152e-02
   2_bss:   9.157  0.058  0.378 87.499  0.028  1.978   9.4152e-02
   2_xyz:   7.293  0.053  0.245 81.858  0.020  2.261   1.4430e-01
   2_adp:   7.293  0.053  0.245 81.858  0.020  2.261   1.4430e-01
   2_occ:   7.293  0.053  0.245 81.858  0.020  2.261   1.4430e-01
   3_bss:   7.293  0.053  0.245 81.858  0.020  2.261   1.4430e-01
   3_xyz:   8.852  0.035  0.371 87.181  0.028  2.316   5.6485e-02
   3_adp:   8.852  0.035  0.371 87.181  0.028  2.316   5.6485e-02
   3_occ:   8.852  0.035  0.371 87.181  0.028  2.316   5.6485e-02
   4_bss:   8.852  0.035  0.371 87.181  0.028  2.316   5.6485e-02
   4_xyz:   7.834  0.051  0.246 82.706  0.033  2.312   5.9274e-02
   4_adp:   7.834  0.051  0.246 82.706  0.033  2.312   5.9274e-02
   4_occ:   7.834  0.051  0.246 82.706  0.033  2.312   5.9274e-02
   5_bss:   7.834  0.051  0.246 82.706  0.033  2.312   5.9274e-02
   5_xyz:   7.801  0.047  0.200 84.070  0.030  2.398   3.5648e-02
   5_adp:   7.801  0.047  0.200 84.070  0.030  2.398   3.5648e-02
   5_occ:   7.801  0.047  0.200 84.070  0.030  2.398   3.5648e-02
   5_bss:   7.801  0.047  0.200 84.070  0.030  2.398   3.5648e-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:  99.34   0.00  18.85  99.34   0.00  14.88  94.25   0.00  40.52
   1_occ:  99.34   0.00  18.85  99.34   0.00  14.88  94.25   0.00  40.52
   2_bss:  99.34   0.00  18.85  99.34   0.00  14.88  94.25   0.00  40.52
   2_xyz:  99.34   0.00  18.85  99.34   0.00  14.88  94.25   0.00  40.52
   2_adp: 101.22   0.00  18.60 101.22   0.00  13.89  98.53   2.93  44.30
   2_occ: 101.22   0.00  18.60 101.22   0.00  13.89  98.53   2.93  44.30
   3_bss: 101.22   0.00  18.60 101.22   0.00  13.89  98.53   2.93  44.30
   3_xyz: 101.22   0.00  18.60 101.22   0.00  13.89  98.53   2.93  44.30
   3_adp:  96.34   0.00  17.77  96.34   0.00  13.18  95.16   5.74  42.78
   3_occ:  96.34   0.00  17.77  96.34   0.00  13.18  95.16   5.74  42.78
   4_bss:  96.34   0.00  17.77  96.34   0.00  13.18  95.16   5.74  42.78
   4_xyz:  96.34   0.00  17.77  96.34   0.00  13.18  95.16   5.74  42.78
   4_adp: 100.55   0.88  17.65 100.55   0.88  13.02  89.50   5.89  42.82
   4_occ: 100.55   0.88  17.65 100.55   0.88  13.02  89.50   5.89  42.82
   5_bss: 100.55   0.88  17.65 100.55   0.88  13.02  89.50   5.89  42.82
   5_xyz: 100.55   0.88  17.65 100.55   0.88  13.02  89.50   5.89  42.82
   5_adp:  95.82   1.78  16.94  95.82   1.78  12.84  85.02   6.18  39.29
   5_occ:  95.82   1.78  16.94  95.82   1.78  12.84  85.02   6.18  39.29
   5_bss:  95.76   1.71  16.88  95.76   1.71  12.77  84.96   6.12  39.22
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.898    0.009    0.316
   1_adp:    1.898    0.009    0.316
   1_occ:    1.898    0.009    0.316
   2_bss:    1.898    0.009    0.316
   2_xyz:    1.346    0.028    0.527
   2_adp:    1.346    0.028    0.527
   2_occ:    1.346    0.028    0.527
   3_bss:    1.346    0.028    0.527
   3_xyz:    1.308    0.055    0.629
   3_adp:    1.308    0.055    0.629
   3_occ:    1.308    0.055    0.629
   4_bss:    1.308    0.055    0.629
   4_xyz:    1.376    0.070    0.680
   4_adp:    1.376    0.070    0.680
   4_occ:    1.376    0.070    0.680
   5_bss:    1.376    0.070    0.680
   5_xyz:    1.370    0.072    0.688
   5_adp:    1.370    0.072    0.688
   5_occ:    1.370    0.072    0.688
   5_bss:    1.370    0.072    0.688
------------------------------------------------------------------------

CPU time actual refinement: 362.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1254/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_1254/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1254/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1254/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1254/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 362.65 
  Macro-tasks:
    bulk solvent and scale       = 46.66  
    individual site refinement   = 145.33 
    weights calculation          = 29.97  
    collect and process          = 6.63   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 228.67 
  Micro-tasks:
    mask                            = 2.26   
    f_calc                          = 119.69 
    alpha_beta                      = 8.59   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 121.85 
    fmodel                         = 7.83   
    r_factors                      = 0.20   
    phase_errors                   = 11.62  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 273.48 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.131 micro seconds
Total CPU time: 6.27 minutes
from_scatterers_fft:    656 calls, 119.31 s
gradients_fft:          601 calls, 110.59 s

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

# Date 2008-01-16 Time 06:48:36 PST -0800 (1200494916.50 s)
Start R-work = 0.4508, R-free = 0.4515 (no bulk solvent and anisotropic scale)
Final R-work = 0.1440, R-free = 0.1850 (no bulk solvent and anisotropic scale)

Start R-work = 0.4411, R-free = 0.4427
Final R-work = 0.1201, R-free = 0.1628