# Date 2008-01-16 Time 06:15:38 PST -0800 (1200492938.96 s)
#phil __OFF__

Command line arguments: "../1067.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4473
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1067

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.8686, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95158
Completeness in resolution range: 0.908834
Completeness with d_max=infinity: 0.906185

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0490
                             d_min =   1.9516

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95158
Completeness in resolution range: 0.908834
Completeness with d_max=infinity: 0.906185

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0495 -  4.1774 [2263/2292]  2039   224   9.9%
  bin  2:  4.1774 -  3.3275 [2171/2194]  1952   219  10.1%
  bin  3:  3.3275 -  2.9103 [2134/2159]  1918   216  10.1%
  bin  4:  2.9103 -  2.6458 [2130/2156]  1923   207   9.7%
  bin  5:  2.6458 -  2.4571 [2100/2134]  1891   209  10.0%
  bin  6:  2.4571 -  2.3127 [2110/2138]  1897   213  10.1%
  bin  7:  2.3127 -  2.1973 [2085/2121]  1874   211  10.1%
  bin  8:  2.1973 -  2.1019 [2081/2123]  1869   212  10.2%
  bin  9:  2.1019 -  2.0212 [1963/2119]  1771   192   9.8%
  bin 10:  2.0212 -  1.9516 [ 552/2118]   496    56  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1067/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.44 -     2.13: 22
        2.13 -     2.82: 922
        2.82 -     3.52: 4417
        3.52 -     4.21: 9293
        4.21 -     4.90: 13642
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.440 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.512 3.040 -x+1/2,-y+1,z-1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.515 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.536 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.548 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28291 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_1067/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1067/model_refine_001.geo

CPU time processing inputs: 7.81


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.8686 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 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4778   r_free= 0.4713   ksol= 0.00   Bsol= 0.00   scale= 0.882    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.287298                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6600 0.99   1471  166 0.3741 0.3831      6.5664      6.5704|
|  2:  4.6600 -  3.7171 0.99   1410  154 0.4114 0.4005      6.8289      6.8299|
|  3:  3.7171 -  3.2526 0.99   1379  148 0.4530 0.4155      6.6704      6.6665|
|  4:  3.2526 -  2.9577 0.98   1374  163 0.4756 0.4696      6.5079      6.4961|
|  5:  2.9577 -  2.7471 0.99   1379  148 0.4988 0.4795      6.3579      6.3299|
|  6:  2.7471 -  2.5860 0.99   1354  158 0.5193 0.5000      6.2735      6.1758|
|  7:  2.5860 -  2.4571 0.98   1356  138 0.5128 0.4938      6.2392      6.2089|
|  8:  2.4571 -  2.3505 0.98   1346  152 0.5273 0.5216      6.1439      6.1969|
|  9:  2.3505 -  2.2603 0.99   1344  150 0.5482 0.5378      6.1498      6.1188|
| 10:  2.2603 -  2.1826 0.99   1349  159 0.5259 0.5486      6.0798      6.1232|
| 11:  2.1826 -  2.1145 0.97   1345  140 0.5332 0.5873      6.0192      5.9858|
| 12:  2.1145 -  2.0542 0.98   1327  147 0.5163 0.5249      5.9241       5.963|
| 13:  2.0542 -  2.0003 0.71    952  116 0.5377 0.4813      5.8673      5.8576|
| 14:  2.0003 -  1.9516 0.17    244   20 0.5825 0.3829      5.7991      5.7026|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6600  1471   166  0.70  34.35   0.82     0.73      71505.55|
|  2:  4.6600 -  3.7171  1410   154  0.69  35.89   0.90     0.78     106097.67|
|  3:  3.7171 -  3.2526  1379   148  0.58  45.67   0.90     0.75     116483.43|
|  4:  3.2526 -  2.9577  1374   163  0.47  54.00   0.89     0.67     106188.74|
|  5:  2.9577 -  2.7471  1379   148  0.42  58.57   0.86     0.61      83363.61|
|  6:  2.7471 -  2.5860  1354   158  0.40  60.10   0.87     0.57      69129.87|
|  7:  2.5860 -  2.4571  1356   138  0.39  60.79   0.90     0.54      62202.90|
|  8:  2.4571 -  2.3505  1346   152  0.32  65.71   0.88     0.49      61464.51|
|  9:  2.3505 -  2.2603  1344   150  0.28  68.89   0.91     0.43      58353.19|
| 10:  2.2603 -  2.1826  1349   159  0.24  72.25   0.92     0.36      56819.94|
| 11:  2.1826 -  2.1145  1345   140  0.18  76.34   0.91     0.28      53296.57|
| 12:  2.1145 -  2.0542  1327   147  0.15  79.13   0.92     0.25      50718.68|
| 13:  2.0542 -  2.0003   952   116  0.16  78.49   0.91     0.26      42837.42|
| 14:  2.0003 -  1.9516   244    20  0.19  75.65   0.87     0.32      35614.53|
|alpha:            min =        0.25 max =            0.78 mean =         0.52|
|beta:             min =    35614.53 max =       116483.43 mean =     72631.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.96 mean =        60.25|
|phase err.(test): min =        0.00 max =           89.99 mean =        60.37|
|-----------------------------------------------------------------------------|

============================== 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 = 17.694447             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.007   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.443934              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.653   (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 |  1.440 -  1.786:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.786 -  2.132:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.132 -  2.478:       32 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.478 -  2.824:      890 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.824 -  3.170:     2021 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.170 -  3.516:     2396 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.516 -  3.862:     4604 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.862 -  4.208:     4689 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.208 -  4.554:     6191 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.554 -  4.900:     7451 |
|-----------------------------------------------------------------------------|
|-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 |        0.198 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.440 |       0.700 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.966)------------------------------------------|
|    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 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4778   r_free= 0.4713   ksol= 0.00   Bsol= 0.00   scale= 0.882    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.287298                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4707   r_free= 0.4660   ksol= 0.28   Bsol= 15.20   scale= 0.927   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,2.83,1.31,0.00,0.00,0.00); trace/3= 0.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.283900                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.538186             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.033   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.427717              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.312   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4707      final r-factor (work) = 0.3624          |
| start r-factor (free) = 0.4660      final r-factor (free) = 0.3988          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.7103 = 13.54 * 0.50 * 6.2803 + 1.00 * 0.1981                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.8970 = 13.54 * 0.50 * 6.1649 + 1.00 * 0.1662                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3624      final r-factor (work) = 0.3331          |
| start r-factor (free) = 0.3988      final r-factor (free) = 0.3995          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8081 = 1.43 * 1.00 * 6.1649 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6991 = 1.43 * 1.00 * 6.0664 + 1.00 * 0.0380                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.966)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.16  17.76    None  None   None       |
|    all(noH): 2823   0      0.00    121.16  17.76    None  None   None       |
|    Sol.    : 438    0      0.00    71.90   37.93    None  None   None       |
|    Mac.    : 2385   0      0.00    121.16  14.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.116: 1142   |   5:    60.580 -  72.695:    5        |
|      1:    12.116 -  24.232:  990   |   6:    72.695 -  84.811:    0        |
|      2:    24.232 -  36.348:  391   |   7:    84.811 -  96.927:    0        |
|      3:    36.348 -  48.464:  196   |   8:    96.927 - 109.043:    0        |
|      4:    48.464 -  60.580:   98   |   9:   109.043 - 121.159:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3331 r_free = 0.3995             target_work(ml) = 6.067         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3326 r_free = 0.3996             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3326   r_free= 0.3996   ksol= 0.28   Bsol= 15.20   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.21,2.83,1.31,0.00,0.00,0.00); trace/3= 0.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.065319                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3304   r_free= 0.3984   ksol= 0.33   Bsol= 61.26   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,1.52,0.44,0.00,0.00,0.00); trace/3= 0.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.064005                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.565239              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.965   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.352525              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.667  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3304      final r-factor (work) = 0.2503          |
| start r-factor (free) = 0.3984      final r-factor (free) = 0.3078          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1785 = 9.57 * 0.50 * 6.0659 + 1.00 * 0.1675                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.6593 = 9.57 * 0.50 * 5.9725 + 1.00 * 0.0953                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2503      final r-factor (work) = 0.2266          |
| start r-factor (free) = 0.3078      final r-factor (free) = 0.2937          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0966 = 1.35 * 1.00 * 5.9725 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8521 = 1.35 * 1.00 * 5.7921 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.966)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.71  19.39    None  None   None       |
|    all(noH): 2823   0      0.00    111.71  19.39    None  None   None       |
|    Sol.    : 438    0      3.48    111.71  45.74    None  None   None       |
|    Mac.    : 2385   0      0.00    100.67  14.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.171: 1190   |   5:    55.854 -  67.025:   75        |
|      1:    11.171 -  22.342:  879   |   6:    67.025 -  78.196:   48        |
|      2:    22.342 -  33.513:  291   |   7:    78.196 -  89.367:   32        |
|      3:    33.513 -  44.683:  172   |   8:    89.367 - 100.537:   17        |
|      4:    44.683 -  55.854:  113   |   9:   100.537 - 111.708:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2266 r_free = 0.2937             target_work(ml) = 5.772         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2265 r_free = 0.2936             target_work(ml) = 5.772         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2265   r_free= 0.2936   ksol= 0.33   Bsol= 61.26   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,1.52,0.44,0.00,0.00,0.00); trace/3= 0.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.772085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2259   r_free= 0.2928   ksol= 0.33   Bsol= 65.09   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,0.26,-0.70,0.00,-0.00,-0.00); trace/3= -0.54                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.768623                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.553154              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.328  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261152              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.466  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2259      final r-factor (work) = 0.1876          |
| start r-factor (free) = 0.2928      final r-factor (free) = 0.2449          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3860 = 3.55 * 0.50 * 5.7924 + 1.00 * 0.0953                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1801 = 3.55 * 0.50 * 5.6980 + 1.00 * 0.0572                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1876      final r-factor (work) = 0.1779          |
| start r-factor (free) = 0.2449      final r-factor (free) = 0.2248          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5064 = 0.26 * 1.00 * 5.6980 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4723 = 0.26 * 1.00 * 5.5754 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.966)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.68  18.27    None  None   None       |
|    all(noH): 2823   0      0.00    102.68  18.27    None  None   None       |
|    Sol.    : 438    0      5.53    102.68  44.15    None  None   None       |
|    Mac.    : 2385   0      0.00    99.83   13.52    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 -  10.268: 1130   |   5:    51.341 -  61.609:   92        |
|      1:    10.268 -  20.536:  981   |   6:    61.609 -  71.878:   44        |
|      2:    20.536 -  30.805:  257   |   7:    71.878 -  82.146:   32        |
|      3:    30.805 -  41.073:  149   |   8:    82.146 -  92.414:   15        |
|      4:    41.073 -  51.341:  114   |   9:    92.414 - 102.682:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1779 r_free = 0.2248             target_work(ml) = 5.538         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1777 r_free = 0.2247             target_work(ml) = 5.538         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1777   r_free= 0.2247   ksol= 0.33   Bsol= 65.09   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,0.26,-0.70,0.00,-0.00,-0.00); trace/3= -0.54                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.537928                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1778   r_free= 0.2247   ksol= 0.33   Bsol= 65.09   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-0.76,-1.46,-0.00,-0.00,-0.00); trace/3= -1.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.540209                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.715867              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.662  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.509709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.624   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1778      final r-factor (work) = 0.1465          |
| start r-factor (free) = 0.2247      final r-factor (free) = 0.1912          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6330 = 2.72 * 0.50 * 5.5789 + 1.00 * 0.0572                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4635 = 2.72 * 0.50 * 5.4533 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1465      final r-factor (work) = 0.1404          |
| start r-factor (free) = 0.1912      final r-factor (free) = 0.1890          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7940 = 0.51 * 1.00 * 5.4533 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7535 = 0.51 * 1.00 * 5.3497 + 1.00 * 0.0267                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.966)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.42  18.14    None  None   None       |
|    all(noH): 2823   0      0.00    101.42  18.14    None  None   None       |
|    Sol.    : 438    0      5.55    101.42  44.64    None  None   None       |
|    Mac.    : 2385   0      0.00    100.87  13.27    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 -  10.142: 1099   |   5:    50.712 -  60.854:   98        |
|      1:    10.142 -  20.285: 1040   |   6:    60.854 -  70.996:   47        |
|      2:    20.285 -  30.427:  232   |   7:    70.996 -  81.138:   33        |
|      3:    30.427 -  40.569:  129   |   8:    81.138 -  91.281:   16        |
|      4:    40.569 -  50.712:  118   |   9:    91.281 - 101.423:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1404 r_free = 0.1890             target_work(ml) = 5.342         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1404 r_free = 0.1890             target_work(ml) = 5.342         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1404   r_free= 0.1890   ksol= 0.33   Bsol= 65.09   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-0.76,-1.46,-0.00,-0.00,-0.00); trace/3= -1.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.342436                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1407   r_free= 0.1895   ksol= 0.32   Bsol= 59.75   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.14,-1.66,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.345039                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.758501              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.011  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.129507              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.867   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1407      final r-factor (work) = 0.1317          |
| start r-factor (free) = 0.1895      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7638 = 1.76 * 0.50 * 5.3518 + 1.00 * 0.0583                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7290 = 1.76 * 0.50 * 5.3193 + 1.00 * 0.0520                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1317      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.1810      final r-factor (free) = 0.1747          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7045 = 0.13 * 1.00 * 5.3193 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6935 = 0.13 * 1.00 * 5.2964 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.966)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.26    90.04   16.81    None  None   None       |
|    all(noH): 2823   0      2.26    90.04   16.81    None  None   None       |
|    Sol.    : 438    0      5.12    90.04   39.66    None  None   None       |
|    Mac.    : 2385   0      2.26    88.97   12.61    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:     2.256 -  11.034: 1321   |   5:    46.146 -  54.924:   94        |
|      1:    11.034 -  19.812:  870   |   6:    54.924 -  63.702:   39        |
|      2:    19.812 -  28.590:  201   |   7:    63.702 -  72.480:   26        |
|      3:    28.590 -  37.368:  132   |   8:    72.480 -  81.258:   12        |
|      4:    37.368 -  46.146:  121   |   9:    81.258 -  90.036:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1315 r_free = 0.1747             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1314 r_free = 0.1749             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1314   r_free= 0.1749   ksol= 0.32   Bsol= 59.75   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,-1.14,-1.66,-0.00,-0.00,-0.00); trace/3= -1.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.280175                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6600 0.99   1471  166 0.1034 0.1290      5.4157      5.5897|
|  2:  4.6600 -  3.7171 0.99   1410  154 0.0962 0.1186      5.5167      5.7474|
|  3:  3.7171 -  3.2526 0.99   1379  148 0.1224 0.1873      5.5943      5.9641|
|  4:  3.2526 -  2.9577 0.98   1374  163 0.1551 0.1812      5.6142      5.7614|
|  5:  2.9577 -  2.7471 0.99   1379  148 0.1581 0.1974      5.4673       5.592|
|  6:  2.7471 -  2.5860 0.99   1354  158 0.1461 0.2167      5.3394      5.5417|
|  7:  2.5860 -  2.4571 0.98   1356  138 0.1462 0.1881      5.2827      5.4743|
|  8:  2.4571 -  2.3505 0.98   1346  152 0.1462 0.1873      5.2118      5.4079|
|  9:  2.3505 -  2.2603 0.99   1344  150 0.1386 0.2020      5.1382      5.3594|
| 10:  2.2603 -  2.1826 0.99   1349  159 0.1367 0.1809         5.1      5.3295|
| 11:  2.1826 -  2.1145 0.97   1345  140 0.1310 0.1881      5.0107      5.2595|
| 12:  2.1145 -  2.0542 0.98   1327  147 0.1373 0.2122        4.98      5.2383|
| 13:  2.0542 -  2.0003 0.71    952  116 0.1381 0.1772      4.9003      5.0876|
| 14:  2.0003 -  1.9516 0.17    244   20 0.1407 0.1867       4.795      4.9865|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6600  1471   166  0.94   9.20   0.97     0.95       7275.84|
|  2:  4.6600 -  3.7171  1410   154  0.95   8.85   1.00     0.99      10137.36|
|  3:  3.7171 -  3.2526  1379   148  0.91  13.93   1.02     1.01      13415.62|
|  4:  3.2526 -  2.9577  1374   163  0.89  17.52   1.00     0.97      13897.77|
|  5:  2.9577 -  2.7471  1379   148  0.87  19.07   0.99     0.97      11111.89|
|  6:  2.7471 -  2.5860  1354   158  0.88  18.48   0.99     0.96       9017.69|
|  7:  2.5860 -  2.4571  1356   138  0.89  17.41   0.99     0.95       7404.86|
|  8:  2.4571 -  2.3505  1346   152  0.88  18.70   1.00     0.97       7163.14|
|  9:  2.3505 -  2.2603  1344   150  0.88  18.18   1.00     0.96       6009.04|
| 10:  2.2603 -  2.1826  1349   159  0.89  17.92   0.99     0.95       5611.91|
| 11:  2.1826 -  2.1145  1345   140  0.89  17.57   0.99     0.95       4878.91|
| 12:  2.1145 -  2.0542  1327   147  0.88  18.67   0.99     0.98       4855.27|
| 13:  2.0542 -  2.0003   952   116  0.88  18.92   1.00     0.98       4103.08|
| 14:  2.0003 -  1.9516   244    20  0.88  18.37   0.98     0.95       3263.63|
|alpha:            min =        0.95 max =            1.01 mean =         0.97|
|beta:             min =     3263.63 max =        13897.77 mean =      8120.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.39|
|phase err.(test): min =        0.00 max =           89.38 mean =        15.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1746   ksol= 0.32   Bsol= 51.27   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-1.31,-1.70,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.279782                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1746   ksol= 0.32   Bsol= 51.27   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-1.31,-1.70,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.279782                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6600 0.99   1471  166 0.1031 0.1283      5.4126      5.5811|
|  2:  4.6600 -  3.7171 0.99   1410  154 0.0955 0.1171      5.5096      5.7365|
|  3:  3.7171 -  3.2526 0.99   1379  148 0.1219 0.1866        5.59      5.9627|
|  4:  3.2526 -  2.9577 0.98   1374  163 0.1552 0.1808      5.6141      5.7604|
|  5:  2.9577 -  2.7471 0.99   1379  148 0.1584 0.1973      5.4685      5.5928|
|  6:  2.7471 -  2.5860 0.99   1354  158 0.1463 0.2171      5.3407      5.5443|
|  7:  2.5860 -  2.4571 0.98   1356  138 0.1465 0.1880      5.2845       5.474|
|  8:  2.4571 -  2.3505 0.98   1346  152 0.1463 0.1881      5.2132      5.4113|
|  9:  2.3505 -  2.2603 0.99   1344  150 0.1388 0.2023      5.1393      5.3609|
| 10:  2.2603 -  2.1826 0.99   1349  159 0.1370 0.1808      5.1013      5.3299|
| 11:  2.1826 -  2.1145 0.97   1345  140 0.1311 0.1887       5.011      5.2599|
| 12:  2.1145 -  2.0542 0.98   1327  147 0.1375 0.2127      4.9814      5.2402|
| 13:  2.0542 -  2.0003 0.71    952  116 0.1381 0.1770      4.9008      5.0866|
| 14:  2.0003 -  1.9516 0.17    244   20 0.1410 0.1866      4.7951      4.9875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6600  1471   166  0.94   9.13   0.97     0.95       7177.46|
|  2:  4.6600 -  3.7171  1410   154  0.95   8.73   1.00     0.99       9969.35|
|  3:  3.7171 -  3.2526  1379   148  0.92  13.81   1.02     1.01      13226.27|
|  4:  3.2526 -  2.9577  1374   163  0.89  17.48   1.00     0.97      13856.04|
|  5:  2.9577 -  2.7471  1379   148  0.87  19.06   0.99     0.96      11113.63|
|  6:  2.7471 -  2.5860  1354   158  0.88  18.50   0.98     0.96       9042.12|
|  7:  2.5860 -  2.4571  1356   138  0.89  17.41   0.98     0.95       7421.96|
|  8:  2.4571 -  2.3505  1346   152  0.88  18.73   1.00     0.97       7193.96|
|  9:  2.3505 -  2.2603  1344   150  0.88  18.21   1.00     0.95       6030.27|
| 10:  2.2603 -  2.1826  1349   159  0.89  17.94   0.98     0.94       5630.56|
| 11:  2.1826 -  2.1145  1345   140  0.89  17.58   0.98     0.94       4885.06|
| 12:  2.1145 -  2.0542  1327   147  0.88  18.69   0.98     0.97       4866.23|
| 13:  2.0542 -  2.0003   952   116  0.88  18.92   0.99     0.97       4106.07|
| 14:  2.0003 -  1.9516   244    20  0.88  18.35   0.97     0.94       3257.73|
|alpha:            min =        0.94 max =            1.01 mean =         0.96|
|beta:             min =     3257.73 max =        13856.04 mean =      8090.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.37|
|phase err.(test): min =        0.00 max =           89.46 mean =        15.69|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.966)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.17    89.95   16.72    None  None   None       |
|    all(noH): 2823   0      2.17    89.95   16.72    None  None   None       |
|    Sol.    : 438    0      5.03    89.95   39.58    None  None   None       |
|    Mac.    : 2385   0      2.17    88.89   12.53    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:     2.174 -  10.952: 1321   |   5:    46.064 -  54.842:   94        |
|      1:    10.952 -  19.730:  870   |   6:    54.842 -  63.620:   39        |
|      2:    19.730 -  28.508:  201   |   7:    63.620 -  72.398:   26        |
|      3:    28.508 -  37.286:  132   |   8:    72.398 -  81.176:   12        |
|      4:    37.286 -  46.064:  121   |   9:    81.176 -  89.954:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 349         
Filter by distance & map next to the model:
   mapped sites are within: 0.606 - 5.824
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 343 from: 349
   mapped sites are within: 0.726 - 5.824

peak=    5.606 closest distance to " CG  PRO A  54 " =    1.293
peak=    5.594 closest distance to " NH2BARG A 102 " =    1.073
peak=    5.503 closest distance to " O   HOH Z 111 " =    2.287
peak=    5.491 closest distance to " O   HOH Z 120 " =    1.097
peak=    5.361 closest distance to " CB  GLN A 223 " =    1.484
peak=    5.353 closest distance to " CB  SER A  63 " =    1.345
peak=    5.204 closest distance to " CG  PRO A  90 " =    1.268
peak=    5.134 closest distance to " O   HOH Z  11 " =    1.405
peak=    5.118 closest distance to " O   HOH Z 210 " =    1.441
peak=    4.953 closest distance to " O   HOH Z  15 " =    2.003
peak=    4.933 closest distance to " O   HOH Z 127 " =    1.278
peak=    4.864 closest distance to " O   HOH Z 134 " =    1.962
peak=    4.845 closest distance to " CG  PRO A 280 " =    0.861
peak=    4.840 closest distance to " O   HOH Z 332 " =    1.081
peak=    4.819 closest distance to " CG  PRO A 198 " =    1.362
peak=    4.782 closest distance to " O   HOH Z 132 " =    1.558
peak=    4.757 closest distance to " O   HOH Z 126 " =    1.850
peak=    4.739 closest distance to " O   HOH Z 124 " =    1.561
peak=    4.707 closest distance to " CG  GLN A  77 " =    0.875
peak=    4.664 closest distance to " CA  TYR A  30 " =    1.064
peak=    4.610 closest distance to " O   HOH Z  48 " =    1.782
peak=    4.608 closest distance to " O   PRO A 198 " =    1.621
peak=    4.564 closest distance to " CG  PRO A 213 " =    1.338
peak=    4.530 closest distance to " CB  PRO A 198 " =    1.026
peak=    4.489 closest distance to " O   HOH Z 352 " =    1.250
peak=    4.478 closest distance to " CB  ARG A 275 " =    0.944
peak=    4.471 closest distance to " O   HOH Z  80 " =    2.117
peak=    4.459 closest distance to " CG  PRO A 243 " =    1.147
peak=    4.448 closest distance to " N   ASN A  39 " =    1.281
peak=    4.444 closest distance to " O   HOH Z 234 " =    3.853
peak=    4.437 closest distance to " O   HOH Z 246 " =    1.482
peak=    4.426 closest distance to " CB  LEU A 228 " =    1.121
peak=    4.414 closest distance to " OE1 GLN A  11 " =    1.923
peak=    4.382 closest distance to " O   HOH Z 389 " =    1.882
peak=    4.301 closest distance to " O   HOH Z 214 " =    1.356
peak=    4.290 closest distance to " O   HOH Z  39 " =    2.020
peak=    4.283 closest distance to " O   HOH Z 260 " =    1.473
peak=    4.272 closest distance to " CB  PRO A  54 " =    0.745
peak=    4.245 closest distance to " O   HOH Z 211 " =    1.524
peak=    4.244 closest distance to " CB  TRP A 179 " =    1.383
peak=    4.241 closest distance to " O   HOH Z 142 " =    1.585
peak=    4.224 closest distance to " O   HOH Z 411 " =    3.226
peak=    4.213 closest distance to " CB  GLU A 128 " =    1.107
peak=    4.186 closest distance to " O   HOH Z 196 " =    1.508
peak=    4.153 closest distance to " O   HOH Z 298 " =    1.832
peak=    4.151 closest distance to " O   HOH Z 102 " =    1.300
peak=    4.149 closest distance to " O   HOH Z 163 " =    1.836
peak=    4.123 closest distance to " CG2 THR A 221 " =    0.973
peak=    4.122 closest distance to " CB  GLU A 152 " =    1.186
peak=    4.118 closest distance to " CB  GLN A  58 " =    0.873
peak=    4.117 closest distance to " O   HOH Z  67 " =    1.920
peak=    4.110 closest distance to " O   HOH Z 132 " =    1.831
peak=    4.109 closest distance to " O   HOH Z  43 " =    1.841
peak=    4.108 closest distance to " O   HOH Z 272 " =    1.936
peak=    4.105 closest distance to " O   HOH Z 246 " =    1.806
peak=    4.095 closest distance to " O   HOH Z 326 " =    1.540
peak=    4.092 closest distance to " O   HOH Z 193 " =    1.993
peak=    4.071 closest distance to " O   HOH Z 369 " =    2.191
peak=    4.064 closest distance to " O   HOH Z 371 " =    3.148
peak=    4.062 closest distance to " O   HOH Z  97 " =    1.868
peak=    4.059 closest distance to " CA  GLN A 223 " =    0.871
peak=    4.057 closest distance to " O   HOH Z 394 " =    1.619
peak=    4.047 closest distance to " O   HOH Z 349 " =    1.047
peak=    4.045 closest distance to " CB  GLN A  73 " =    0.940
peak=    4.045 closest distance to " CB  SER A 141 " =    0.987
peak=    4.035 closest distance to " O   HOH Z 108 " =    1.979
peak=    4.007 closest distance to " CB  SER A   3 " =    1.467
peak=    4.002 closest distance to " O   HOH Z 433 " =    1.634
peak=    3.998 closest distance to " CG  GLN A  11 " =    1.272
peak=    3.987 closest distance to " CA  GLU A 152 " =    0.951
peak=    3.986 closest distance to " O   HOH Z 189 " =    1.997
peak=    3.980 closest distance to " NH2 ARG A 156 " =    1.285
peak=    3.977 closest distance to " O   HOH Z 154 " =    1.511
peak=    3.976 closest distance to " O   HOH Z  98 " =    2.329
peak=    3.958 closest distance to " CB  TYR A 169 " =    0.864
peak=    3.953 closest distance to " O   HOH Z 207 " =    1.834
peak=    3.940 closest distance to " O   HOH Z 282 " =    1.714
peak=    3.937 closest distance to " CB  ARG A 190 " =    1.686
peak=    3.932 closest distance to " O   HOH Z  39 " =    1.779
peak=    3.909 closest distance to " OD1 ASN A 217 " =    1.806
peak=    3.909 closest distance to " O   HOH Z 215 " =    1.424
peak=    3.906 closest distance to " O   HOH Z 133 " =    1.636
peak=    3.888 closest distance to " CG1 ILE A  33 " =    1.248
peak=    3.886 closest distance to " O   HOH Z 132 " =    2.567
peak=    3.881 closest distance to " CG1 VAL A 153 " =    1.051
peak=    3.877 closest distance to " O   SER A  87 " =    2.124
peak=    3.872 closest distance to " O   HOH Z 192 " =    1.565
peak=    3.872 closest distance to " O   HOH Z 316 " =    3.032
peak=    3.855 closest distance to " CA  ALA A  21 " =    1.330
peak=    3.846 closest distance to " CB  GLN A 183 " =    1.207
peak=    3.846 closest distance to " CB  ASN A 187 " =    1.055
peak=    3.845 closest distance to " CG  ARG A  66 " =    2.781
peak=    3.824 closest distance to " NH1 ARG A 269 " =    0.863
peak=    3.817 closest distance to " O   HOH Z 118 " =    1.841
peak=    3.811 closest distance to " O   HOH Z 232 " =    2.313
peak=    3.808 closest distance to " O   HOH Z  47 " =    1.577
peak=    3.797 closest distance to " CA  ASP A 191 " =    0.833
peak=    3.794 closest distance to " CB  GLN A 194 " =    0.856
peak=    3.793 closest distance to " O   HOH Z  30 " =    1.975
peak=    3.788 closest distance to " CG2BVAL A  41 " =    1.033
peak=    3.776 closest distance to " CB  ILE A 199 " =    1.042
peak=    3.771 closest distance to " CD BLYS A 290 " =    0.981
peak=    3.771 closest distance to " NZ  LYS A 193 " =    1.461
peak=    3.770 closest distance to " O   HOH Z 104 " =    3.686
peak=    3.769 closest distance to " CG1 ILE A 120 " =    1.132
peak=    3.768 closest distance to " OD1 ASP A 238 " =    0.901
peak=    3.767 closest distance to " O   HOH Z  19 " =    1.982
peak=    3.765 closest distance to " CB  VAL A 202 " =    1.481
peak=    3.764 closest distance to " CD  LYS A 119 " =    1.388
peak=    3.764 closest distance to " O   HOH Z 287 " =    1.984
peak=    3.748 closest distance to " O   HOH Z  78 " =    2.338
peak=    3.727 closest distance to " C   SER A  32 " =    1.078
peak=    3.720 closest distance to " NH2BARG A 145 " =    1.998
peak=    3.706 closest distance to " OD2 ASP A 286 " =    2.934
peak=    3.704 closest distance to " O   HOH Z  44 " =    1.798
peak=    3.698 closest distance to " O   HOH Z 112 " =    1.530
peak=    3.695 closest distance to " CG2 VAL A  78 " =    1.026
peak=    3.693 closest distance to " O   HOH Z 374 " =    2.573
peak=    3.690 closest distance to " O   HOH Z 108 " =    1.739
peak=    3.689 closest distance to " CD2 LEU A 297 " =    0.919
peak=    3.683 closest distance to " O   HOH Z 199 " =    1.049
peak=    3.682 closest distance to " O   HOH Z 387 " =    2.381
peak=    3.677 closest distance to " O   HOH Z 227 " =    1.949
peak=    3.677 closest distance to " CB  TRP A 266 " =    0.931
peak=    3.673 closest distance to " NE AARG A 275 " =    1.424
peak=    3.663 closest distance to " NE2 HIS A 115 " =    0.790
peak=    3.653 closest distance to " CZ  PHE A 192 " =    1.043
peak=    3.637 closest distance to " CB  MET A  47 " =    1.059
peak=    3.630 closest distance to " CA  ASP A 124 " =    0.791
peak=    3.616 closest distance to " O   HOH Z 374 " =    1.083
peak=    3.611 closest distance to " CB  SER A  62 " =    0.875
peak=    3.610 closest distance to " O   HOH Z 313 " =    2.249
peak=    3.610 closest distance to " O   HOH Z 279 " =    2.250
peak=    3.598 closest distance to " CB  ALA A 100 " =    1.420
peak=    3.595 closest distance to " NZ  LYS A 117 " =    1.249
peak=    3.593 closest distance to " O   HOH Z 336 " =    1.623
peak=    3.587 closest distance to " O   HOH Z 223 " =    1.204
peak=    3.583 closest distance to " O   HOH Z  63 " =    2.103
peak=    3.579 closest distance to " O   HOH Z 368 " =    3.286
peak=    3.571 closest distance to " CG AARG A 275 " =    1.060
peak=    3.570 closest distance to " O   HOH Z 174 " =    2.189
peak=    3.569 closest distance to " O   HOH Z  21 " =    1.835
peak=    3.565 closest distance to " O   HOH Z 409 " =    2.903
peak=    3.564 closest distance to " O   HOH Z 291 " =    1.709
peak=    3.561 closest distance to " O   HOH Z 139 " =    3.386
peak=    3.558 closest distance to " CB  GLU A 277 " =    1.046
peak=    3.555 closest distance to " O   HOH Z 207 " =    1.941
peak=    3.554 closest distance to " O   HOH Z 344 " =    3.128
peak=    3.551 closest distance to " CD  ARG A 269 " =    0.907
peak=    3.542 closest distance to " O   HOH Z  44 " =    2.358
peak=    3.539 closest distance to " O   HOH Z 437 " =    1.699
peak=    3.537 closest distance to " O   HOH Z 406 " =    1.509
peak=    3.536 closest distance to " O   HOH Z 183 " =    1.395
peak=    3.535 closest distance to " OE1 GLN A  58 " =    5.824
peak=    3.533 closest distance to " CA  ASP A 162 " =    1.143
peak=    3.527 closest distance to " CD  ARG A 159 " =    0.813
peak=    3.520 closest distance to " CB  ARG A  79 " =    1.287
peak=    3.520 closest distance to " O   HOH Z 426 " =    1.395
peak=    3.516 closest distance to " CB  MET A  40 " =    0.746
peak=    3.515 closest distance to " O   HOH Z 363 " =    1.168
peak=    3.512 closest distance to " CD1 TRP A 266 " =    1.179
peak=    3.511 closest distance to " CZ  PHE A 218 " =    1.135
peak=    3.507 closest distance to " CB  GLU A 277 " =    3.704
peak=    3.505 closest distance to " CD1 LEU A  96 " =    0.761
peak=    3.499 closest distance to " CA  THR A 221 " =    0.908
peak=    3.499 closest distance to " O   HOH Z 248 " =    1.609
peak=    3.499 closest distance to " O   HOH Z 418 " =    1.671
peak=    3.496 closest distance to " O   HOH Z  88 " =    3.670
peak=    3.496 closest distance to " CB  PRO A  90 " =    1.134
peak=    3.486 closest distance to " CA  GLY A 196 " =    1.023
peak=    3.485 closest distance to " NH2AARG A 190 " =    1.557
peak=    3.484 closest distance to " CE  LYS A 119 " =    1.196
peak=    3.480 closest distance to " O   ALA A 165 " =    1.211
peak=    3.477 closest distance to " O   HOH Z 261 " =    1.866
peak=    3.476 closest distance to " CD  PRO A 280 " =    1.099
peak=    3.473 closest distance to " O   HOH Z 197 " =    1.963
peak=    3.469 closest distance to " NZ  LYS A 117 " =    3.292
peak=    3.468 closest distance to " O   HOH Z 200 " =    1.525
peak=    3.468 closest distance to " NZ  LYS A  76 " =    1.156
peak=    3.463 closest distance to " CB  PRO A  54 " =    1.319
peak=    3.460 closest distance to " CG2 VAL A 112 " =    1.403
peak=    3.460 closest distance to " CB  ALA A 291 " =    1.201
peak=    3.458 closest distance to " O   HOH Z  22 " =    2.163
peak=    3.456 closest distance to " OE1 GLN A  58 " =    1.291
peak=    3.455 closest distance to " O   HOH Z 420 " =    5.720
peak=    3.455 closest distance to " O   HOH Z 109 " =    2.390
peak=    3.455 closest distance to " O   THR A 251 " =    1.311
peak=    3.453 closest distance to " O   HOH Z 403 " =    1.821
peak=    3.451 closest distance to " N   THR A  52 " =    1.073
peak=    3.450 closest distance to " O   GLY A  91 " =    1.152
peak=    3.446 closest distance to " O   HOH Z 221 " =    1.369
peak=    3.439 closest distance to " CA  ILE A 263 " =    1.007
peak=    3.437 closest distance to " O   HOH Z 180 " =    2.155
peak=    3.434 closest distance to " OG  SER A  97 " =    3.510
peak=    3.433 closest distance to " CA  GLN A  88 " =    1.324
peak=    3.430 closest distance to " O   HOH Z 243 " =    1.370
peak=    3.420 closest distance to " SD  MET A  93 " =    1.395
peak=    3.419 closest distance to " CB  VAL A 265 " =    1.385
peak=    3.417 closest distance to " CA  ARG A 195 " =    1.101
peak=    3.413 closest distance to " O   HOH Z 128 " =    2.199
peak=    3.411 closest distance to " CD1 PHE A  59 " =    1.724
peak=    3.404 closest distance to " CA  LYS A  48 " =    1.405
peak=    3.401 closest distance to " O   HOH Z  49 " =    1.970
peak=    3.396 closest distance to " O   HOH Z  49 " =    1.110
peak=    3.395 closest distance to " O   HOH Z 145 " =    1.794
peak=    3.395 closest distance to " O   HOH Z   4 " =    1.916
peak=    3.392 closest distance to " CB  PHE A  16 " =    1.284
peak=    3.391 closest distance to " O   HOH Z 139 " =    4.374
peak=    3.391 closest distance to " O   HOH Z 368 " =    2.059
peak=    3.391 closest distance to " O   HOH Z 301 " =    1.610
peak=    3.390 closest distance to " O   HOH Z 128 " =    2.085
peak=    3.388 closest distance to " CB  SER A  26 " =    0.998
peak=    3.388 closest distance to " CD  LYS A 166 " =    1.426
peak=    3.384 closest distance to " CA  LEU A 282 " =    1.227
peak=    3.374 closest distance to " CD1 LEU A 300 " =    1.269
peak=    3.362 closest distance to " CA  ARG A  36 " =    1.184
peak=    3.359 closest distance to " O   SER A 164 " =    1.466
peak=    3.357 closest distance to " CA  SER A  87 " =    0.792
peak=    3.354 closest distance to " CH2 TRP A 274 " =    1.930
peak=    3.353 closest distance to " O   TRP A 274 " =    1.602
peak=    3.353 closest distance to " CB  ASN A 148 " =    1.140
peak=    3.351 closest distance to " OG ASER A 164 " =    0.787
peak=    3.350 closest distance to " O   HOH Z 217 " =    1.348
peak=    3.346 closest distance to " O   HOH Z 150 " =    1.653
peak=    3.336 closest distance to " O   HOH Z 245 " =    1.368
peak=    3.332 closest distance to " O   HOH Z 404 " =    1.476
peak=    3.331 closest distance to " O   HOH Z 234 " =    2.071
peak=    3.330 closest distance to " O   SER A  26 " =    1.716
peak=    3.326 closest distance to " O   HOH Z 426 " =    3.052
peak=    3.324 closest distance to " CB  TRP A 123 " =    1.208
peak=    3.322 closest distance to " O   HOH Z 185 " =    1.826
peak=    3.320 closest distance to " O   HOH Z  87 " =    2.416
peak=    3.319 closest distance to " O   HOH Z 214 " =    1.991
peak=    3.319 closest distance to " CB  ALA A 244 " =    0.955
peak=    3.317 closest distance to " O   HOH Z 203 " =    1.722
peak=    3.316 closest distance to " N   ASN A 252 " =    1.104
peak=    3.315 closest distance to " NE BARG A 102 " =    1.417
peak=    3.314 closest distance to " O   HOH Z 343 " =    2.429
peak=    3.313 closest distance to " O   HOH Z 425 " =    1.607
peak=    3.311 closest distance to " O   HOH Z  14 " =    2.385
peak=    3.311 closest distance to " O   HOH Z 438 " =    2.712
peak=    3.310 closest distance to " OH  TYR A  30 " =    1.465
peak=    3.308 closest distance to " NH1BARG A 145 " =    0.919
peak=    3.307 closest distance to " CB  ALA A  71 " =    1.322
peak=    3.298 closest distance to " O   HOH Z 280 " =    2.523
peak=    3.296 closest distance to " O   HOH Z 427 " =    3.256
peak=    3.287 closest distance to " CB  SER A  28 " =    0.956
peak=    3.286 closest distance to " CA  VAL A  41 " =    0.741
peak=    3.279 closest distance to " O   HOH Z 150 " =    3.373
peak=    3.277 closest distance to " CB  SER A 216 " =    0.784
peak=    3.273 closest distance to " CG2 THR A 251 " =    1.128
peak=    3.271 closest distance to " CD  PRO A  54 " =    1.065
peak=    3.271 closest distance to " CB  MET A 105 " =    1.197
peak=    3.269 closest distance to " CB  ASP A 124 " =    0.726
peak=    3.261 closest distance to " NH1 ARG A  14 " =    1.275
peak=    3.259 closest distance to " O   HOH Z 173 " =    1.835
peak=    3.256 closest distance to " C   GLY A  80 " =    1.227
peak=    3.256 closest distance to " O   HOH Z 364 " =    2.090
peak=    3.255 closest distance to " O   HOH Z 281 " =    3.953
peak=    3.254 closest distance to " O   HOH Z 193 " =    2.339
peak=    3.254 closest distance to " O   HOH Z 271 " =    1.251
peak=    3.253 closest distance to " O   MET A 105 " =    1.934
peak=    3.253 closest distance to " O   HOH Z 276 " =    1.349
peak=    3.251 closest distance to " O   HOH Z  93 " =    2.441
peak=    3.249 closest distance to " O   HOH Z   6 " =    1.862
peak=    3.239 closest distance to " NH1 ARG A 138 " =    1.045
peak=    3.239 closest distance to " CD2 LEU A 255 " =    1.263
peak=    3.238 closest distance to " O   HOH Z 432 " =    1.803
peak=    3.234 closest distance to " O   HOH Z 410 " =    1.547
peak=    3.230 closest distance to " CD1 LEU A 222 " =    0.864
peak=    3.229 closest distance to " O   HOH Z 383 " =    1.895
peak=    3.228 closest distance to " O   HOH Z  54 " =    1.675
peak=    3.224 closest distance to " O   HOH Z 406 " =    1.652
peak=    3.223 closest distance to " OG  SER A  62 " =    3.250
peak=    3.221 closest distance to " O   HOH Z 357 " =    2.043
peak=    3.218 closest distance to " CA  PRO A  90 " =    0.958
peak=    3.218 closest distance to " O   HOH Z 324 " =    1.585
peak=    3.216 closest distance to " O   HOH Z 184 " =    0.974
peak=    3.214 closest distance to " O   HOH Z  54 " =    2.281
peak=    3.213 closest distance to " CD  ARG A 195 " =    1.062
peak=    3.212 closest distance to " O   HOH Z 358 " =    1.456
peak=    3.210 closest distance to " CA  THR A 221 " =    1.283
peak=    3.207 closest distance to " CG2 THR A  42 " =    0.879
peak=    3.206 closest distance to " O   HOH Z 345 " =    3.287
peak=    3.203 closest distance to " CZ3 TRP A 274 " =    2.251
peak=    3.202 closest distance to " CA  GLY A  75 " =    1.088
peak=    3.201 closest distance to " OG  SER A 245 " =    1.587
peak=    3.199 closest distance to " CA  ALA A 158 " =    1.078
peak=    3.194 closest distance to " O   HOH Z 109 " =    3.012
peak=    3.193 closest distance to " O   HOH Z   1 " =    2.942
peak=    3.192 closest distance to " O   HOH Z 337 " =    3.977
peak=    3.191 closest distance to " CA  ILE A 106 " =    0.810
peak=    3.189 closest distance to " O   HOH Z 147 " =    1.723
peak=    3.187 closest distance to " CB  LYS A  76 " =    0.832
peak=    3.185 closest distance to " CA  ALA A 100 " =    1.216
peak=    3.184 closest distance to " O   HOH Z  88 " =    1.590
peak=    3.183 closest distance to " CB  LEU A  83 " =    0.778
peak=    3.182 closest distance to " O   HOH Z 238 " =    5.531
peak=    3.179 closest distance to " NH1 ARG A  56 " =    1.540
peak=    3.177 closest distance to " N   SER A 164 " =    0.952
peak=    3.177 closest distance to " O   HOH Z 299 " =    1.554
peak=    3.171 closest distance to " CE3 TRP A 274 " =    3.594
peak=    3.169 closest distance to " OD2 ASP A  50 " =    1.211
peak=    3.167 closest distance to " CB  GLU A 175 " =    1.315
peak=    3.166 closest distance to " O   HOH Z 155 " =    2.912
peak=    3.166 closest distance to " CB  ALA A 256 " =    1.116
peak=    3.162 closest distance to " OD1 ASN A  69 " =    2.429
peak=    3.161 closest distance to " OG1 THR A 294 " =    4.051
peak=    3.158 closest distance to " CB  TYR A 293 " =    1.566
peak=    3.153 closest distance to " CA  ALA A 160 " =    0.928
peak=    3.148 closest distance to " CG ALYS A 290 " =    1.176
peak=    3.146 closest distance to " CG  LEU A 167 " =    1.076
peak=    3.145 closest distance to " O   HOH Z 292 " =    1.765
peak=    3.145 closest distance to " O   HOH Z 144 " =    2.060
peak=    3.144 closest distance to " OD2 ASP A 162 " =    1.073
peak=    3.143 closest distance to " O   HOH Z 419 " =    2.861
peak=    3.142 closest distance to " CD1 TRP A 274 " =    1.024
peak=    3.141 closest distance to " O   HOH Z 270 " =    1.646
peak=    3.140 closest distance to " NZ  LYS A 119 " =    1.619
peak=    3.139 closest distance to " CA  ALA A 295 " =    1.155
peak=    3.131 closest distance to " CA  GLY A 241 " =    0.804
peak=    3.130 closest distance to " CA  ARG A  66 " =    1.210
peak=    3.125 closest distance to " O   HOH Z 244 " =    1.658
peak=    3.123 closest distance to " CB  TYR A 116 " =    1.378
peak=    3.111 closest distance to " O   HOH Z 172 " =    2.236
peak=    3.108 closest distance to " CB  ARG A 139 " =    0.803
peak=    3.106 closest distance to " CA  GLY A 211 " =    0.992
peak=    3.104 closest distance to " O   HOH Z 294 " =    1.619
peak=    3.101 closest distance to " CB  ALA A 154 " =    1.196
peak=    3.095 closest distance to " N   ARG A 156 " =    1.444
peak=    3.089 closest distance to " O   HOH Z 293 " =    1.868
peak=    3.085 closest distance to " O   PRO A 213 " =    1.325
peak=    3.083 closest distance to " CA  ILE A  33 " =    1.579
peak=    3.071 closest distance to " O   HOH Z 346 " =    1.557
peak=    3.060 closest distance to " CB  ASN A 148 " =    1.953
peak=    3.058 closest distance to " O   HOH Z 261 " =    1.640
peak=    3.053 closest distance to " O   HOH Z 162 " =    1.701
peak=    3.051 closest distance to " ND2 ASN A 187 " =    1.544
peak=    3.048 closest distance to " O   HOH Z 313 " =    1.859
peak=    3.033 closest distance to " CA  ALA A 248 " =    1.164
peak=    3.008 closest distance to " O   HOH Z  48 " =    3.209
peak=    3.001 closest distance to " OD2 ASP A 286 " =    3.353
peak=    3.000 closest distance to " O   HOH Z 240 " =    2.128

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 229         
Filter by distance & map next to the model:
   mapped sites are within: 0.327 - 5.319
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 229
   mapped sites are within: 0.702 - 5.319

peak=   -5.135 closest distance to " O   HOH Z 221 " =    0.955
peak=   -5.127 closest distance to " O   HOH Z 290 " =    0.804
peak=   -4.365 closest distance to " NH2 ARG A  66 " =    1.194
peak=   -4.270 closest distance to " N   ALA A  43 " =    2.603
peak=   -4.242 closest distance to " O   HOH Z 350 " =    1.017
peak=   -4.125 closest distance to " O   HOH Z  71 " =    1.183
peak=   -4.091 closest distance to " O   HOH Z  52 " =    2.158
peak=   -4.089 closest distance to " O   HOH Z  17 " =    0.976
peak=   -4.070 closest distance to " O   HOH Z 166 " =    1.795
peak=   -4.067 closest distance to " C   ASN A 285 " =    2.688
peak=   -4.044 closest distance to " CG  ASP A 231 " =    0.762
peak=   -4.040 closest distance to " CE  MET A  93 " =    1.167
peak=   -4.026 closest distance to " CZ  ARG A  66 " =    0.750
peak=   -4.010 closest distance to " CD  LYS A 119 " =    0.933
peak=   -3.991 closest distance to " OG  SER A  97 " =    2.275
peak=   -3.955 closest distance to " O   HOH Z  13 " =    1.289
peak=   -3.946 closest distance to " OG ASER A 134 " =    1.223
peak=   -3.937 closest distance to " OE2 GLU A   2 " =    1.100
peak=   -3.929 closest distance to " CD2 PHE A  59 " =    2.399
peak=   -3.919 closest distance to " O   HOH Z  93 " =    1.253
peak=   -3.915 closest distance to " OH  TYR A 169 " =    0.966
peak=   -3.911 closest distance to " O   HOH Z 332 " =    0.975
peak=   -3.909 closest distance to " O   GLY A 118 " =    2.291
peak=   -3.901 closest distance to " OG  SER A  32 " =    0.991
peak=   -3.894 closest distance to " O   VAL A  67 " =    2.749
peak=   -3.894 closest distance to " O   HOH Z 109 " =    3.697
peak=   -3.869 closest distance to " CD  GLN A  88 " =    0.750
peak=   -3.838 closest distance to " O   HOH Z 231 " =    0.997
peak=   -3.825 closest distance to " CA  VAL A 197 " =    1.001
peak=   -3.825 closest distance to " O   HOH Z 308 " =    1.663
peak=   -3.820 closest distance to " CG1 VAL A 112 " =    2.665
peak=   -3.818 closest distance to " OXT GLY A 302 " =    2.838
peak=   -3.815 closest distance to " CD1 LEU A 101 " =    2.782
peak=   -3.799 closest distance to " O   HOH Z 407 " =    0.761
peak=   -3.787 closest distance to " ND2 ASN A  45 " =    1.005
peak=   -3.786 closest distance to " CG  GLN A  58 " =    1.124
peak=   -3.784 closest distance to " CB  LEU A 167 " =    2.173
peak=   -3.771 closest distance to " O   HOH Z 266 " =    4.294
peak=   -3.761 closest distance to " O   HOH Z 120 " =    0.822
peak=   -3.760 closest distance to " O   HOH Z 259 " =    0.752
peak=   -3.757 closest distance to " CB  ASP A  50 " =    2.558
peak=   -3.756 closest distance to " CD  GLN A  77 " =    1.007
peak=   -3.738 closest distance to " CD1 PHE A  59 " =    1.854
peak=   -3.736 closest distance to " O   HOH Z 222 " =    1.197
peak=   -3.730 closest distance to " O   HOH Z   7 " =    0.929
peak=   -3.716 closest distance to " N   GLN A  58 " =    1.665
peak=   -3.716 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -3.697 closest distance to " O   HOH Z 423 " =    1.045
peak=   -3.690 closest distance to " CE  MET A 105 " =    2.000
peak=   -3.680 closest distance to " CD2 LEU A 237 " =    2.325
peak=   -3.672 closest distance to " CD2 LEU A 300 " =    2.765
peak=   -3.671 closest distance to " O   GLY A 196 " =    1.156
peak=   -3.665 closest distance to " CG2 THR A   4 " =    1.865
peak=   -3.660 closest distance to " OD1 ASP A 191 " =    1.628
peak=   -3.646 closest distance to " O   HOH Z  91 " =    2.411
peak=   -3.629 closest distance to " CA  VAL A  67 " =    2.817
peak=   -3.629 closest distance to " O   PRO A 198 " =    1.301
peak=   -3.614 closest distance to " N   ARG A 275 " =    1.563
peak=   -3.589 closest distance to " CD  GLN A  58 " =    0.871
peak=   -3.588 closest distance to " O   HOH Z 282 " =    1.651
peak=   -3.567 closest distance to " O   HOH Z 184 " =    1.284
peak=   -3.556 closest distance to " CH2 TRP A 179 " =    1.100
peak=   -3.549 closest distance to " C   ALA A 158 " =    1.158
peak=   -3.549 closest distance to " OE1 GLN A  88 " =    1.002
peak=   -3.543 closest distance to " O   ALA A 256 " =    1.485
peak=   -3.535 closest distance to " OD2 ASP A 171 " =    1.852
peak=   -3.534 closest distance to " CA  TYR A  68 " =    2.744
peak=   -3.527 closest distance to " O   HOH Z 422 " =    1.111
peak=   -3.525 closest distance to " O   HOH Z 388 " =    1.954
peak=   -3.524 closest distance to " CG2 THR A 221 " =    2.192
peak=   -3.515 closest distance to " O   HOH Z  37 " =    1.510
peak=   -3.511 closest distance to " CA  GLY A 241 " =    2.234
peak=   -3.504 closest distance to " CD  ARG A 139 " =    1.740
peak=   -3.500 closest distance to " O   HOH Z 185 " =    2.356
peak=   -3.496 closest distance to " O   HOH Z  92 " =    1.256
peak=   -3.493 closest distance to " O   HOH Z 150 " =    1.099
peak=   -3.492 closest distance to " O   HOH Z  15 " =    1.676
peak=   -3.489 closest distance to " O   HOH Z  11 " =    1.650
peak=   -3.486 closest distance to " O   LEU A 300 " =    2.548
peak=   -3.477 closest distance to " CE2 TRP A  85 " =    1.062
peak=   -3.475 closest distance to " C   THR A 279 " =    1.234
peak=   -3.473 closest distance to " O   HOH Z 313 " =    1.064
peak=   -3.472 closest distance to " C   HIS A 108 " =    1.075
peak=   -3.472 closest distance to " CB  GLN A  55 " =    1.436
peak=   -3.470 closest distance to " CD1 TRP A 179 " =    0.964
peak=   -3.467 closest distance to " O   HOH Z 423 " =    2.265
peak=   -3.464 closest distance to " OG1 THR A  82 " =    1.907
peak=   -3.464 closest distance to " O   HOH Z 414 " =    1.244
peak=   -3.451 closest distance to " O   HOH Z 418 " =    1.333
peak=   -3.449 closest distance to " NH2AARG A 275 " =    5.319
peak=   -3.438 closest distance to " CG  GLU A  53 " =    1.512
peak=   -3.432 closest distance to " CA  SER A 276 " =    1.372
peak=   -3.422 closest distance to " CB  TYR A  15 " =    2.309
peak=   -3.411 closest distance to " C   SER A 271 " =    1.273
peak=   -3.404 closest distance to " O   HOH Z 182 " =    0.837
peak=   -3.396 closest distance to " CD2 LEU A 143 " =    2.480
peak=   -3.395 closest distance to " O   HOH Z 437 " =    0.979
peak=   -3.383 closest distance to " CZ  TYR A 169 " =    1.831
peak=   -3.381 closest distance to " OD2 ASP A 171 " =    2.391
peak=   -3.379 closest distance to " CA  ASN A 148 " =    1.706
peak=   -3.376 closest distance to " O   HOH Z 396 " =    1.514
peak=   -3.369 closest distance to " O   HOH Z 426 " =    2.375
peak=   -3.355 closest distance to " N   SER A 134 " =    1.266
peak=   -3.348 closest distance to " O   HOH Z 325 " =    1.712
peak=   -3.347 closest distance to " O   HOH Z 298 " =    2.885
peak=   -3.347 closest distance to " CD  GLU A 236 " =    1.038
peak=   -3.345 closest distance to " O   HOH Z 151 " =    1.447
peak=   -3.344 closest distance to " O   ARG A 275 " =    2.226
peak=   -3.326 closest distance to " CD  PRO A 198 " =    1.088
peak=   -3.326 closest distance to " CG  ARG A 269 " =    2.299
peak=   -3.321 closest distance to " CB  SER A 146 " =    2.233
peak=   -3.321 closest distance to " C   VAL A 257 " =    1.166
peak=   -3.318 closest distance to " CE  MET A 105 " =    2.126
peak=   -3.316 closest distance to " OG ASER A 216 " =    1.077
peak=   -3.316 closest distance to " NH2 ARG A  66 " =    5.246
peak=   -3.316 closest distance to " CA  SER A 164 " =    1.984
peak=   -3.309 closest distance to " CB  ALA A 161 " =    2.623
peak=   -3.302 closest distance to " CD  GLN A 223 " =    0.841
peak=   -3.301 closest distance to " CD1 TYR A 247 " =    2.412
peak=   -3.300 closest distance to " N   GLY A  17 " =    1.612
peak=   -3.300 closest distance to " O   LEU A 167 " =    1.492
peak=   -3.295 closest distance to " O   HOH Z 118 " =    5.252
peak=   -3.295 closest distance to " CB  PHE A 208 " =    2.301
peak=   -3.293 closest distance to " C   LEU A 143 " =    1.723
peak=   -3.287 closest distance to " O   HOH Z 384 " =    2.068
peak=   -3.286 closest distance to " O   HOH Z  69 " =    0.887
peak=   -3.282 closest distance to " O   PHE A 218 " =    1.414
peak=   -3.281 closest distance to " C   SER A 206 " =    1.591
peak=   -3.278 closest distance to " ND2 ASN A  60 " =    1.341
peak=   -3.278 closest distance to " CD  LYS A 289 " =    2.510
peak=   -3.277 closest distance to " O   HOH Z  43 " =    1.963
peak=   -3.272 closest distance to " N   ALA A 226 " =    2.089
peak=   -3.270 closest distance to " O   HOH Z 190 " =    2.213
peak=   -3.268 closest distance to " O   GLN A 194 " =    1.179
peak=   -3.268 closest distance to " O   HOH Z 213 " =    1.250
peak=   -3.266 closest distance to " C   ASN A 187 " =    1.879
peak=   -3.262 closest distance to " N   GLY A 262 " =    2.089
peak=   -3.261 closest distance to " O   HOH Z 231 " =    2.054
peak=   -3.250 closest distance to " O   HOH Z 385 " =    3.969
peak=   -3.245 closest distance to " NZ  LYS A 119 " =    1.257
peak=   -3.244 closest distance to " CD2 LEU A 300 " =    2.759
peak=   -3.241 closest distance to " CA  GLU A  37 " =    1.363
peak=   -3.239 closest distance to " CA  GLY A  23 " =    2.317
peak=   -3.238 closest distance to " O   HOH Z 265 " =    1.619
peak=   -3.237 closest distance to " O   HOH Z 380 " =    4.567
peak=   -3.237 closest distance to " O   HOH Z 409 " =    3.016
peak=   -3.233 closest distance to " CA  VAL A 232 " =    2.355
peak=   -3.233 closest distance to " OE1 GLN A  55 " =    0.702
peak=   -3.232 closest distance to " CD1 LEU A  25 " =    2.477
peak=   -3.228 closest distance to " O   HOH Z 275 " =    1.543
peak=   -3.225 closest distance to " CE3 TRP A 150 " =    1.038
peak=   -3.224 closest distance to " CA  ASP A 286 " =    2.742
peak=   -3.221 closest distance to " O   HOH Z 100 " =    0.884
peak=   -3.217 closest distance to " CG2 VAL A 296 " =    2.060
peak=   -3.214 closest distance to " CD2 PHE A  61 " =    1.703
peak=   -3.212 closest distance to " OD2 ASP A  65 " =    1.516
peak=   -3.209 closest distance to " CB  ALA A 291 " =    2.236
peak=   -3.206 closest distance to " O   HOH Z  38 " =    1.220
peak=   -3.206 closest distance to " O   HOH Z 371 " =    1.597
peak=   -3.200 closest distance to " O   HOH Z 360 " =    2.466
peak=   -3.199 closest distance to " O   HOH Z  19 " =    1.974
peak=   -3.199 closest distance to " CH2 TRP A 177 " =    1.942
peak=   -3.198 closest distance to " O   HOH Z 176 " =    1.045
peak=   -3.198 closest distance to " CE3 TRP A 150 " =    1.763
peak=   -3.195 closest distance to " CG  GLN A  73 " =    0.829
peak=   -3.195 closest distance to " O   HOH Z 111 " =    1.177
peak=   -3.189 closest distance to " CB  ALA A  43 " =    2.529
peak=   -3.188 closest distance to " O   HOH Z 165 " =    2.124
peak=   -3.188 closest distance to " CB  CYS A 254 " =    2.659
peak=   -3.184 closest distance to " NE  ARG A 156 " =    1.843
peak=   -3.183 closest distance to " CB  PRO A 243 " =    2.582
peak=   -3.179 closest distance to " O   HOH Z 434 " =    4.077
peak=   -3.175 closest distance to " CB  GLU A 277 " =    1.256
peak=   -3.172 closest distance to " CB  ASN A  39 " =    2.139
peak=   -3.171 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.166 closest distance to " O   HOH Z 146 " =    0.989
peak=   -3.165 closest distance to " O   HOH Z  98 " =    1.528
peak=   -3.163 closest distance to " O   HOH Z 251 " =    1.383
peak=   -3.162 closest distance to " O   ARG A  66 " =    1.372
peak=   -3.161 closest distance to " O   HOH Z 283 " =    1.651
peak=   -3.156 closest distance to " O   ALA A 160 " =    1.529
peak=   -3.156 closest distance to " O   HOH Z  62 " =    0.936
peak=   -3.155 closest distance to " CD2 LEU A 167 " =    1.786
peak=   -3.154 closest distance to " CG  GLN A  11 " =    1.112
peak=   -3.151 closest distance to " O   VAL A 197 " =    1.235
peak=   -3.150 closest distance to " O   ASP A 191 " =    1.301
peak=   -3.148 closest distance to " O   HOH Z 407 " =    1.708
peak=   -3.147 closest distance to " CD1 LEU A 228 " =    2.551
peak=   -3.142 closest distance to " O   MET A 113 " =    1.108
peak=   -3.139 closest distance to " O   HOH Z 189 " =    1.626
peak=   -3.137 closest distance to " C   LEU A 101 " =    0.902
peak=   -3.136 closest distance to " O   HOH Z 427 " =    1.311
peak=   -3.133 closest distance to " NH1 ARG A 195 " =    2.262
peak=   -3.127 closest distance to " O   HOH Z  97 " =    1.083
peak=   -3.127 closest distance to " OG  SER A  62 " =    1.367
peak=   -3.127 closest distance to " O   HOH Z 377 " =    1.976
peak=   -3.123 closest distance to " O   HOH Z 352 " =    1.106
peak=   -3.122 closest distance to " O   HOH Z 132 " =    1.336
peak=   -3.112 closest distance to " CB  LEU A  25 " =    2.421
peak=   -3.106 closest distance to " O   VAL A 174 " =    1.911
peak=   -3.105 closest distance to " O   HOH Z 172 " =    5.045
peak=   -3.102 closest distance to " O   HOH Z 236 " =    1.909
peak=   -3.102 closest distance to " O   HOH Z 352 " =    0.843
peak=   -3.093 closest distance to " O   HOH Z 322 " =    1.018
peak=   -3.090 closest distance to " O   ALA A  34 " =    2.026
peak=   -3.086 closest distance to " O   MET A  47 " =    2.300
peak=   -3.076 closest distance to " CB  ALA A 227 " =    2.313
peak=   -3.074 closest distance to " O   ALA A 161 " =    2.662
peak=   -3.074 closest distance to " CB  PRO A 163 " =    2.891
peak=   -3.070 closest distance to " O   HOH Z  90 " =    1.927
peak=   -3.060 closest distance to " ND2 ASN A 215 " =    2.118
peak=   -3.058 closest distance to " O   HOH Z 297 " =    2.785
peak=   -3.058 closest distance to " O   HOH Z 340 " =    0.826
peak=   -3.049 closest distance to " CG  LYS A 193 " =    2.665
peak=   -3.048 closest distance to " N   LEU A 261 " =    1.312
peak=   -3.035 closest distance to " CD2 TRP A 274 " =    2.364

================= 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    :  0.4778 0.4713   6.287298e+00   6.278140e+00
   1_bss:  0.4707 0.4660   6.283900e+00   6.268531e+00
   1_xyz:  0.3624 0.3988   6.108011e+00   6.179514e+00
   1_adp:  0.3331 0.3995   6.066550e+00   6.182965e+00
   1_occ:  0.3326 0.3996   6.065319e+00   6.182582e+00
   2_bss:  0.3304 0.3984   6.064005e+00   6.180210e+00
   2_xyz:  0.2503 0.3078   5.836945e+00   6.003830e+00
   2_adp:  0.2266 0.2937   5.772409e+00   5.966584e+00
   2_occ:  0.2265 0.2936   5.772085e+00   5.966304e+00
   3_bss:  0.2259 0.2928   5.768623e+00   5.964211e+00
   3_xyz:  0.1876 0.2449   5.593878e+00   5.806202e+00
   3_adp:  0.1779 0.2248   5.538397e+00   5.733410e+00
   3_occ:  0.1777 0.2247   5.537928e+00   5.732916e+00
   4_bss:  0.1778 0.2247   5.540209e+00   5.733590e+00
   4_xyz:  0.1465 0.1912   5.367652e+00   5.582796e+00
   4_adp:  0.1404 0.1890   5.342434e+00   5.566486e+00
   4_occ:  0.1404 0.1890   5.342436e+00   5.566659e+00
   5_bss:  0.1407 0.1895   5.345039e+00   5.567685e+00
   5_xyz:  0.1317 0.1810   5.294275e+00   5.521610e+00
   5_adp:  0.1315 0.1747   5.280141e+00   5.493399e+00
   5_occ:  0.1314 0.1749   5.280175e+00   5.494120e+00
   5_bss:  0.1313 0.1746   5.279782e+00   5.493139e+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:  0.281  15.200  -1.209   2.828   1.312   0.000   0.000   0.000
   1_xyz:  0.281  15.200  -1.209   2.828   1.312   0.000   0.000   0.000
   1_adp:  0.281  15.200  -1.209   2.828   1.312   0.000   0.000   0.000
   1_occ:  0.281  15.200  -1.209   2.828   1.312   0.000   0.000   0.000
   2_bss:  0.333  61.261  -0.808   1.521   0.437   0.000   0.000   0.000
   2_xyz:  0.333  61.261  -0.808   1.521   0.437   0.000   0.000   0.000
   2_adp:  0.333  61.261  -0.808   1.521   0.437   0.000   0.000   0.000
   2_occ:  0.333  61.261  -0.808   1.521   0.437   0.000   0.000   0.000
   3_bss:  0.328  65.089  -1.161   0.257  -0.702   0.000  -0.000  -0.000
   3_xyz:  0.328  65.089  -1.161   0.257  -0.702   0.000  -0.000  -0.000
   3_adp:  0.328  65.089  -1.161   0.257  -0.702   0.000  -0.000  -0.000
   3_occ:  0.328  65.089  -1.161   0.257  -0.702   0.000  -0.000  -0.000
   4_bss:  0.329  65.089  -1.815  -0.759  -1.460  -0.000  -0.000  -0.000
   4_xyz:  0.329  65.089  -1.815  -0.759  -1.460  -0.000  -0.000  -0.000
   4_adp:  0.329  65.089  -1.815  -0.759  -1.460  -0.000  -0.000  -0.000
   4_occ:  0.329  65.089  -1.815  -0.759  -1.460  -0.000  -0.000  -0.000
   5_bss:  0.323  59.748  -1.942  -1.140  -1.660  -0.000  -0.000  -0.000
   5_xyz:  0.323  59.748  -1.942  -1.140  -1.660  -0.000  -0.000  -0.000
   5_adp:  0.323  59.748  -1.942  -1.140  -1.660  -0.000  -0.000  -0.000
   5_occ:  0.323  59.748  -1.942  -1.140  -1.660  -0.000  -0.000  -0.000
   5_bss:  0.317  51.265  -1.951  -1.312  -1.696  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.265 0.3890  0.5238    72633.655
   1_bss:  59.084 0.4026  0.5608    69352.858
   1_xyz:  45.696 0.5725  0.7928    46774.825
   1_adp:  45.930 0.5691  0.7879    46981.342
   1_occ:  45.888 0.5696  0.7868    46837.329
   2_bss:  45.614 0.5730  0.7795    46457.091
   2_xyz:  33.339 0.7186  0.9380    26548.609
   2_adp:  31.318 0.7420  0.9470    24077.249
   2_occ:  31.317 0.7420  0.9469    24062.624
   3_bss:  31.121 0.7440  0.9185    23794.661
   3_xyz:  24.869 0.8112  0.9692    15735.654
   3_adp:  22.242 0.8392  0.9802    13466.509
   3_occ:  22.228 0.8394  0.9803    13460.201
   4_bss:  22.229 0.8395  0.9535    13497.773
   4_xyz:  18.472 0.8755  0.9758     9586.364
   4_adp:  17.981 0.8806  0.9740     9353.037
   4_occ:  17.984 0.8806  0.9739     9361.420
   5_bss:  18.013 0.8804  0.9659     9405.156
   5_xyz:  16.977 0.8898  0.9692     8518.626
   5_adp:  16.310 0.8960  0.9678     8102.215
   5_occ:  16.319 0.8959  0.9677     8121.576
   5_bss:  16.299 0.8960  0.9626     8092.019
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9813e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9813e-01
   1_xyz:   1.693  0.014  0.102 16.525  0.007  4.113   1.6625e-01
   1_adp:   1.693  0.014  0.102 16.525  0.007  4.113   1.6625e-01
   1_occ:   1.693  0.014  0.102 16.525  0.007  4.113   1.6625e-01
   2_bss:   1.693  0.014  0.102 16.525  0.007  4.113   1.6625e-01
   2_xyz:   1.369  0.009  0.089 15.009  0.006  4.108   9.5283e-02
   2_adp:   1.369  0.009  0.089 15.009  0.006  4.108   9.5283e-02
   2_occ:   1.369  0.009  0.089 15.009  0.006  4.108   9.5283e-02
   3_bss:   1.369  0.009  0.089 15.009  0.006  4.108   9.5283e-02
   3_xyz:   0.959  0.006  0.063 14.487  0.003  4.118   5.7204e-02
   3_adp:   0.959  0.006  0.063 14.487  0.003  4.118   5.7204e-02
   3_occ:   0.959  0.006  0.063 14.487  0.003  4.118   5.7204e-02
   4_bss:   0.959  0.006  0.063 14.487  0.003  4.118   5.7204e-02
   4_xyz:   0.999  0.007  0.070 14.352  0.004  4.127   5.8285e-02
   4_adp:   0.999  0.007  0.070 14.352  0.004  4.127   5.8285e-02
   4_occ:   0.999  0.007  0.070 14.352  0.004  4.127   5.8285e-02
   5_bss:   0.999  0.007  0.070 14.352  0.004  4.127   5.8285e-02
   5_xyz:   0.937  0.006  0.067 14.229  0.003  4.114   5.2013e-02
   5_adp:   0.937  0.006  0.067 14.229  0.003  4.114   5.2013e-02
   5_occ:   0.937  0.006  0.067 14.229  0.003  4.114   5.2013e-02
   5_bss:   0.937  0.006  0.067 14.229  0.003  4.114   5.2013e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.440   2.4324e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.440   2.4324e-01
   1_xyz:  10.279  0.141  0.400 88.560  0.029  1.923   1.7023e-01
   1_adp:  10.279  0.141  0.400 88.560  0.029  1.923   1.7023e-01
   1_occ:  10.279  0.141  0.400 88.560  0.029  1.923   1.7023e-01
   2_bss:  10.279  0.141  0.400 88.560  0.029  1.923   1.7023e-01
   2_xyz:   8.192  0.048  0.308 77.294  0.057  2.159   1.0030e-01
   2_adp:   8.192  0.048  0.308 77.294  0.057  2.159   1.0030e-01
   2_occ:   8.192  0.048  0.308 77.294  0.057  2.159   1.0030e-01
   3_bss:   8.192  0.048  0.308 77.294  0.057  2.159   1.0030e-01
   3_xyz:   7.779  0.061  0.219 82.599  0.027  2.257   5.3411e-02
   3_adp:   7.779  0.061  0.219 82.599  0.027  2.257   5.3411e-02
   3_occ:   7.779  0.061  0.219 82.599  0.027  2.257   5.3411e-02
   4_bss:   7.779  0.061  0.219 82.599  0.027  2.257   5.3411e-02
   4_xyz:   7.706  0.042  0.242 83.904  0.028  2.338   4.4008e-02
   4_adp:   7.706  0.042  0.242 83.904  0.028  2.338   4.4008e-02
   4_occ:   7.706  0.042  0.242 83.904  0.028  2.338   4.4008e-02
   5_bss:   7.706  0.042  0.242 83.904  0.028  2.338   4.4008e-02
   5_xyz:   7.646  0.048  0.222 80.925  0.032  2.395   3.3147e-02
   5_adp:   7.646  0.048  0.222 80.925  0.032  2.395   3.3147e-02
   5_occ:   7.646  0.048  0.222 80.925  0.032  2.395   3.3147e-02
   5_bss:   7.646  0.048  0.222 80.925  0.032  2.395   3.3147e-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: 121.16   0.00  17.76 121.16   0.00  14.05  71.90   0.00  37.93
   1_occ: 121.16   0.00  17.76 121.16   0.00  14.05  71.90   0.00  37.93
   2_bss: 121.16   0.00  17.76 121.16   0.00  14.05  71.90   0.00  37.93
   2_xyz: 121.16   0.00  17.76 121.16   0.00  14.05  71.90   0.00  37.93
   2_adp: 111.71   0.00  19.39 100.67   0.00  14.55 111.71   3.48  45.74
   2_occ: 111.71   0.00  19.39 100.67   0.00  14.55 111.71   3.48  45.74
   3_bss: 111.71   0.00  19.39 100.67   0.00  14.55 111.71   3.48  45.74
   3_xyz: 111.71   0.00  19.39 100.67   0.00  14.55 111.71   3.48  45.74
   3_adp: 102.68   0.00  18.27  99.83   0.00  13.52 102.68   5.53  44.15
   3_occ: 102.68   0.00  18.27  99.83   0.00  13.52 102.68   5.53  44.15
   4_bss: 102.68   0.00  18.27  99.83   0.00  13.52 102.68   5.53  44.15
   4_xyz: 102.68   0.00  18.27  99.83   0.00  13.52 102.68   5.53  44.15
   4_adp: 101.42   0.00  18.14 100.87   0.00  13.27 101.42   5.55  44.64
   4_occ: 101.42   0.00  18.14 100.87   0.00  13.27 101.42   5.55  44.64
   5_bss: 101.42   0.00  18.14 100.87   0.00  13.27 101.42   5.55  44.64
   5_xyz: 101.42   0.00  18.14 100.87   0.00  13.27 101.42   5.55  44.64
   5_adp:  90.04   2.26  16.81  88.97   2.26  12.61  90.04   5.12  39.66
   5_occ:  90.04   2.26  16.81  88.97   2.26  12.61  90.04   5.12  39.66
   5_bss:  89.95   2.17  16.72  88.89   2.17  12.53  89.95   5.03  39.58
------------------------------------------------------------------------
 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:    2.299    0.037    0.453
   1_adp:    2.299    0.037    0.453
   1_occ:    2.299    0.037    0.453
   2_bss:    2.299    0.037    0.453
   2_xyz:    2.152    0.042    0.639
   2_adp:    2.152    0.042    0.639
   2_occ:    2.152    0.042    0.639
   3_bss:    2.152    0.042    0.639
   3_xyz:    2.113    0.034    0.737
   3_adp:    2.113    0.034    0.737
   3_occ:    2.113    0.034    0.737
   4_bss:    2.113    0.034    0.737
   4_xyz:    2.000    0.070    0.802
   4_adp:    2.000    0.070    0.802
   4_occ:    2.000    0.070    0.802
   5_bss:    2.000    0.070    0.802
   5_xyz:    1.840    0.060    0.836
   5_adp:    1.840    0.060    0.836
   5_occ:    1.840    0.060    0.836
   5_bss:    1.840    0.060    0.836
------------------------------------------------------------------------

CPU time actual refinement: 305.60


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1067/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_1067/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1067/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1067/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1067/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 305.47 
  Macro-tasks:
    bulk solvent and scale       = 37.07  
    individual site refinement   = 124.31 
    weights calculation          = 25.77  
    collect and process          = 5.45   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 192.72 
  Micro-tasks:
    mask                            = 2.10   
    f_calc                          = 100.25 
    alpha_beta                      = 7.15   
    target                          = 1.02   
    gradients_wrt_atomic_parameters = 106.22 
    fmodel                         = 6.13   
    r_factors                      = 0.16   
    phase_errors                   = 8.52   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 231.82 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.355 micro seconds
Total CPU time: 5.28 minutes
from_scatterers_fft:    643 calls, 99.95 s
gradients_fft:          588 calls, 95.19 s

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

# Date 2008-01-16 Time 06:20:55 PST -0800 (1200493255.98 s)
Start R-work = 0.4778, R-free = 0.4713 (no bulk solvent and anisotropic scale)
Final R-work = 0.1521, R-free = 0.1956 (no bulk solvent and anisotropic scale)

Start R-work = 0.4707, R-free = 0.4660
Final R-work = 0.1313, R-free = 0.1746