# Date 2008-01-16 Time 05:25:53 PST -0800 (1200489953.22 s)
#phil __OFF__

Command line arguments: "../735.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4884
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 735

-------------------------------------------------------------------------------
  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: (70.6012, 45.7567, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 1.95386
Completeness in resolution range: 0.920969
Completeness with d_max=infinity: 0.918335

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1289
                             d_min =   1.9539

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: (70.6012, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 1.95386
Completeness in resolution range: 0.920969
Completeness with d_max=infinity: 0.918335

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1294 -  4.1826 [2228/2254]  2005   223  10.0%
  bin  2:  4.1826 -  3.3315 [2154/2174]  1941   213   9.9%
  bin  3:  3.3315 -  2.9138 [2116/2135]  1904   212  10.0%
  bin  4:  2.9138 -  2.6489 [2099/2129]  1881   218  10.4%
  bin  5:  2.6489 -  2.4599 [2102/2121]  1893   209   9.9%
  bin  6:  2.4599 -  2.3154 [2070/2095]  1863   207  10.0%
  bin  7:  2.3154 -  2.1998 [2080/2108]  1873   207  10.0%
  bin  8:  2.1998 -  2.1043 [2047/2083]  1837   210  10.3%
  bin  9:  2.1043 -  2.0235 [2009/2087]  1822   187   9.3%
  bin 10:  2.0235 -  1.9539 [ 684/2084]   611    73  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_735/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 35
        2.32 -     2.97: 1780
        2.97 -     3.61: 4572
        3.61 -     4.26: 9167
        4.26 -     4.90: 12782
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.847 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28331 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_735/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_735/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 = 70.60125 45.75675 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4718   r_free= 0.4743   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.289435                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.6659 0.99   1447  160 0.3902 0.3819      6.6127      6.5832|
|  2:  4.6659 -  3.7216 0.99   1396  157 0.4158 0.4133      6.8328      6.8074|
|  3:  3.7216 -  3.2565 0.99   1371  152 0.4426 0.4289      6.6784      6.6685|
|  4:  3.2565 -  2.9612 0.99   1366  152 0.4757 0.5047      6.5367      6.5409|
|  5:  2.9612 -  2.7503 0.99   1349  151 0.5032 0.4821      6.3633      6.3829|
|  6:  2.7503 -  2.5890 0.99   1361  148 0.5019 0.5254      6.2675      6.2114|
|  7:  2.5890 -  2.4599 0.99   1334  155 0.4973 0.5312      6.2263       6.174|
|  8:  2.4599 -  2.3533 0.98   1323  148 0.5223 0.5072      6.1695      6.1539|
|  9:  2.3533 -  2.2630 0.98   1328  141 0.5101 0.5490      6.1193      6.2103|
| 10:  2.2630 -  2.1851 1.00   1347  148 0.5153 0.5474       6.069      6.0843|
| 11:  2.1851 -  2.1170 0.98   1322  150 0.5035 0.4683      6.0127      6.0289|
| 12:  2.1170 -  2.0566 0.98   1316  142 0.5113 0.4944      5.9324      5.9268|
| 13:  2.0566 -  2.0026 0.83   1107  127 0.5130 0.5101      5.8842      5.7926|
| 14:  2.0026 -  1.9539 0.20    263   28 0.5261 0.4936       5.844      5.8928|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.6659  1447   160  0.71  33.14   0.81     0.77      70693.06|
|  2:  4.6659 -  3.7216  1396   157  0.68  37.10   0.89     0.79     119133.23|
|  3:  3.7216 -  3.2565  1371   152  0.53  49.16   0.91     0.72     131090.61|
|  4:  3.2565 -  2.9612  1366   152  0.42  58.48   0.88     0.60     123097.01|
|  5:  2.9612 -  2.7503  1349   151  0.36  62.55   0.87     0.53      90468.66|
|  6:  2.7503 -  2.5890  1361   148  0.34  64.43   0.89     0.50      76320.42|
|  7:  2.5890 -  2.4599  1334   155  0.35  63.99   0.91     0.49      66509.34|
|  8:  2.4599 -  2.3533  1323   148  0.32  66.31   0.89     0.47      61864.17|
|  9:  2.3533 -  2.2630  1328   141  0.29  68.10   0.92     0.44      59287.96|
| 10:  2.2630 -  2.1851  1347   148  0.29  68.14   0.91     0.44      52686.05|
| 11:  2.1851 -  2.1170  1322   150  0.28  69.08   0.97     0.44      50486.53|
| 12:  2.1170 -  2.0566  1316   142  0.31  67.12   0.92     0.49      43674.94|
| 13:  2.0566 -  2.0026  1107   127  0.31  66.66   0.95     0.53      37898.70|
| 14:  2.0026 -  1.9539   263    28  0.40  60.47   1.01     0.58      28611.64|
|alpha:            min =        0.44 max =            0.79 mean =         0.56|
|beta:             min =    28611.64 max =       131090.61 mean =     75800.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.99 mean =        59.20|
|phase err.(test): min =        0.00 max =           89.93 mean =        59.70|
|-----------------------------------------------------------------------------|

============================== 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 = 21.710543             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.626   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.292103              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.634   (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 |  1.681 -  2.003:       16 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       74 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1706 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1910 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2662 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4740 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4427 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5810 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6972 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.547 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.795)------------------------------------------|
|    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 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4718   r_free= 0.4743   ksol= 0.00   Bsol= 0.00   scale= 0.883    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.289435                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4617   r_free= 0.4677   ksol= 0.34   Bsol= 50.00   scale= 0.917   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,1.68,2.49,0.00,0.00,0.00); trace/3= 0.36                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.284198                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.090657             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.474   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.512695              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.363   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4617      final r-factor (work) = 0.3692          |
| start r-factor (free) = 0.4677      final r-factor (free) = 0.4194          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.8445 = 17.09 * 0.50 * 6.2791 + 1.00 * 0.1875                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.0139 = 17.09 * 0.50 * 6.1844 + 1.00 * 0.1663                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3692      final r-factor (work) = 0.3390          |
| start r-factor (free) = 0.4194      final r-factor (free) = 0.4286          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3613 = 1.51 * 1.00 * 6.1844 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2474 = 1.51 * 1.00 * 6.0990 + 1.00 * 0.0215                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.795)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.08   18.54    None  None   None       |
|    all(noH): 2823   0      0.00    80.08   18.54    None  None   None       |
|    Sol.    : 438    0      0.00    80.08   35.80    None  None   None       |
|    Mac.    : 2385   0      0.00    69.96   15.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.008:  661   |   5:    40.041 -  48.049:  117        |
|      1:     8.008 -  16.016:  815   |   6:    48.049 -  56.057:   78        |
|      2:    16.016 -  24.025:  565   |   7:    56.057 -  64.065:   39        |
|      3:    24.025 -  32.033:  340   |   8:    64.065 -  72.073:   12        |
|      4:    32.033 -  40.041:  191   |   9:    72.073 -  80.082:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3390 r_free = 0.4286             target_work(ml) = 6.105         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3385 r_free = 0.4292             target_work(ml) = 6.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3385   r_free= 0.4292   ksol= 0.34   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,1.68,2.49,0.00,0.00,0.00); trace/3= 0.36                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.105246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3376   r_free= 0.4274   ksol= 0.36   Bsol= 79.66   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,0.24,1.25,0.00,0.00,0.00); trace/3= 0.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.106274                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.742984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.419  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.697998              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.959  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3376      final r-factor (work) = 0.2966          |
| start r-factor (free) = 0.4274      final r-factor (free) = 0.3794          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7839 = 7.74 * 0.50 * 6.1005 + 1.00 * 0.1657                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5645 = 7.74 * 0.50 * 6.0676 + 1.00 * 0.0738                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2966      final r-factor (work) = 0.2857          |
| start r-factor (free) = 0.3794      final r-factor (free) = 0.3698          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2555 = 0.70 * 1.00 * 6.0676 + 1.00 * 0.0203                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1953 = 0.70 * 1.00 * 5.9907 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.795)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.04   18.37    None  None   None       |
|    all(noH): 2823   0      0.00    83.04   18.37    None  None   None       |
|    Sol.    : 438    0      0.00    83.04   35.81    None  None   None       |
|    Mac.    : 2385   0      0.00    69.64   15.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.304:  698   |   5:    41.519 -  49.823:  114        |
|      1:     8.304 -  16.608:  876   |   6:    49.823 -  58.127:   59        |
|      2:    16.608 -  24.912:  544   |   7:    58.127 -  66.431:   30        |
|      3:    24.912 -  33.215:  312   |   8:    66.431 -  74.735:   12        |
|      4:    33.215 -  41.519:  175   |   9:    74.735 -  83.039:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2857 r_free = 0.3698             target_work(ml) = 5.981         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2857 r_free = 0.3700             target_work(ml) = 5.981         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2857   r_free= 0.3700   ksol= 0.36   Bsol= 79.66   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,0.24,1.25,0.00,0.00,0.00); trace/3= 0.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.981425                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2861   r_free= 0.3698   ksol= 0.35   Bsol= 81.71   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-0.12,1.06,-0.00,0.00,0.00); trace/3= 0.02                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.981682                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.653102              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.796  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.037281              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.858  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2861      final r-factor (work) = 0.2429          |
| start r-factor (free) = 0.3698      final r-factor (free) = 0.3205          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0127 = 4.65 * 0.50 * 5.9913 + 1.00 * 0.0738                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8435 = 4.65 * 0.50 * 5.9201 + 1.00 * 0.0701                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2429      final r-factor (work) = 0.2268          |
| start r-factor (free) = 0.3205      final r-factor (free) = 0.3101          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1546 = 1.04 * 1.00 * 5.9201 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0469 = 1.04 * 1.00 * 5.8134 + 1.00 * 0.0168                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.795)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.55   19.06    None  None   None       |
|    all(noH): 2823   0      0.00    96.55   19.06    None  None   None       |
|    Sol.    : 438    0      0.00    96.55   43.70    None  None   None       |
|    Mac.    : 2385   0      0.00    96.27   14.53    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:     0.000 -   9.655:  950   |   5:    48.274 -  57.929:   93        |
|      1:     9.655 -  19.310:  920   |   6:    57.929 -  67.584:   66        |
|      2:    19.310 -  28.965:  394   |   7:    67.584 -  77.239:   31        |
|      3:    28.965 -  38.620:  197   |   8:    77.239 -  86.894:   17        |
|      4:    38.620 -  48.274:  146   |   9:    86.894 -  96.549:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2268 r_free = 0.3101             target_work(ml) = 5.797         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2268 r_free = 0.3101             target_work(ml) = 5.797         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2268   r_free= 0.3101   ksol= 0.35   Bsol= 81.71   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-0.12,1.06,-0.00,0.00,0.00); trace/3= 0.02                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.796645                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2269   r_free= 0.3099   ksol= 0.34   Bsol= 81.32   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.20,-0.98,0.66,-0.00,0.00,0.00); trace/3= -0.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.796300                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.980993              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.830  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.272448              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.462  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2269      final r-factor (work) = 0.1802          |
| start r-factor (free) = 0.3099      final r-factor (free) = 0.2410          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5491 = 4.98 * 0.50 * 5.8137 + 1.00 * 0.0701                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2857 = 4.98 * 0.50 * 5.7085 + 1.00 * 0.0687                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1802      final r-factor (work) = 0.1632          |
| start r-factor (free) = 0.2410      final r-factor (free) = 0.2163          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5719 = 0.27 * 1.00 * 5.7085 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5158 = 0.27 * 1.00 * 5.5253 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.795)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.72   17.85    None  None   None       |
|    all(noH): 2823   0      0.00    95.72   17.85    None  None   None       |
|    Sol.    : 438    0      4.64    93.79   43.60    None  None   None       |
|    Mac.    : 2385   0      0.00    95.72   13.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.572: 1001   |   5:    47.861 -  57.433:  100        |
|      1:     9.572 -  19.144: 1068   |   6:    57.433 -  67.005:   67        |
|      2:    19.144 -  28.716:  262   |   7:    67.005 -  76.577:   21        |
|      3:    28.716 -  38.289:  159   |   8:    76.577 -  86.149:   18        |
|      4:    38.289 -  47.861:  120   |   9:    86.149 -  95.721:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1632 r_free = 0.2163             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1629 r_free = 0.2155             target_work(ml) = 5.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1629   r_free= 0.2155   ksol= 0.34   Bsol= 81.32   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.20,-0.98,0.66,-0.00,0.00,0.00); trace/3= -0.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.468310                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1625   r_free= 0.2148   ksol= 0.32   Bsol= 60.31   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-1.94,0.10,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.464509                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.370141              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.728  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.434535              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.988  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1625      final r-factor (work) = 0.1424          |
| start r-factor (free) = 0.2148      final r-factor (free) = 0.1919          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6172 = 2.37 * 0.50 * 5.5258 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4675 = 2.37 * 0.50 * 5.4120 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1424      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.1919      final r-factor (free) = 0.1888          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1861 = 2.43 * 1.00 * 5.4120 + 1.00 * 0.0104                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.0585 = 2.43 * 1.00 * 5.3275 + 1.00 * 1.0886                              |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.795)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.78   17.72    None  None   None       |
|    all(noH): 2823   0      0.00    96.78   17.72    None  None   None       |
|    Sol.    : 438    0      0.00    94.75   44.82    None  None   None       |
|    Mac.    : 2385   0      0.00    96.78   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.678: 1086   |   5:    48.390 -  58.068:  103        |
|      1:     9.678 -  19.356: 1022   |   6:    58.068 -  67.746:   80        |
|      2:    19.356 -  29.034:  238   |   7:    67.746 -  77.424:   23        |
|      3:    29.034 -  38.712:  134   |   8:    77.424 -  87.103:   19        |
|      4:    38.712 -  48.390:  111   |   9:    87.103 -  96.781:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1369 r_free = 0.1888             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1367 r_free = 0.1887             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1887   ksol= 0.32   Bsol= 60.31   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-1.94,0.10,-0.00,0.00,0.00); trace/3= -1.19                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.321434                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.6659 0.99   1447  160 0.0996 0.1380      5.4087      5.6482|
|  2:  4.6659 -  3.7216 0.99   1396  157 0.0929 0.1280      5.5177      5.7741|
|  3:  3.7216 -  3.2565 0.99   1371  152 0.1289 0.1782      5.6263      5.9282|
|  4:  3.2565 -  2.9612 0.99   1366  152 0.1626 0.2074      5.6635      5.8021|
|  5:  2.9612 -  2.7503 0.99   1349  151 0.1681 0.2211      5.5325      5.7728|
|  6:  2.7503 -  2.5890 0.99   1361  148 0.1616 0.2270      5.4025      5.6064|
|  7:  2.5890 -  2.4599 0.99   1334  155 0.1554 0.2030      5.3487      5.5076|
|  8:  2.4599 -  2.3533 0.98   1323  148 0.1544 0.2203      5.2836      5.5736|
|  9:  2.3533 -  2.2630 0.98   1328  141 0.1531 0.2139      5.2381      5.4618|
| 10:  2.2630 -  2.1851 1.00   1347  148 0.1373 0.1770       5.105      5.2868|
| 11:  2.1851 -  2.1170 0.98   1322  150 0.1366 0.2175      5.0872      5.4651|
| 12:  2.1170 -  2.0566 0.98   1316  142 0.1386 0.2147      5.0138      5.2886|
| 13:  2.0566 -  2.0026 0.83   1107  127 0.1342 0.1921      4.9383      5.1137|
| 14:  2.0026 -  1.9539 0.20    263   28 0.1251 0.1932      4.8415      5.1562|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.6659  1447   160  0.93   9.90   0.97     0.94       7932.82|
|  2:  4.6659 -  3.7216  1396   157  0.95   8.99   1.03     1.01      10696.29|
|  3:  3.7216 -  3.2565  1371   152  0.91  14.27   1.05     1.05      13948.03|
|  4:  3.2565 -  2.9612  1366   152  0.88  18.60   1.02     0.99      15676.91|
|  5:  2.9612 -  2.7503  1349   151  0.86  20.11   1.00     0.97      12776.57|
|  6:  2.7503 -  2.5890  1361   148  0.86  20.61   0.99     0.95      10219.42|
|  7:  2.5890 -  2.4599  1334   155  0.87  19.98   1.00     0.96       9260.10|
|  8:  2.4599 -  2.3533  1323   148  0.86  20.29   1.01     0.97       8273.21|
|  9:  2.3533 -  2.2630  1328   141  0.86  20.77   1.00     0.94       7538.80|
| 10:  2.2630 -  2.1851  1347   148  0.87  19.12   1.01     0.97       6044.20|
| 11:  2.1851 -  2.1170  1322   150  0.87  19.81   1.00     0.93       5956.25|
| 12:  2.1170 -  2.0566  1316   142  0.87  19.39   1.01     0.99       5315.06|
| 13:  2.0566 -  2.0026  1107   127  0.87  20.23   0.99     0.97       4716.77|
| 14:  2.0026 -  1.9539   263    28  0.91  16.30   0.99     0.95       3569.22|
|alpha:            min =        0.93 max =            1.05 mean =         0.97|
|beta:             min =     3569.22 max =        15676.91 mean =      9107.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.94 mean =        17.71|
|phase err.(test): min =        0.00 max =           89.81 mean =        16.87|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1883   ksol= 0.32   Bsol= 60.32   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.18,-0.01,-0.00,-0.00,-0.00); trace/3= -1.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.321182                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1883   ksol= 0.32   Bsol= 60.32   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.18,-0.01,-0.00,-0.00,-0.00); trace/3= -1.34                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.321182                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.6659 0.99   1447  160 0.1005 0.1362      5.4035      5.6339|
|  2:  4.6659 -  3.7216 0.99   1396  157 0.0935 0.1280      5.5192      5.7753|
|  3:  3.7216 -  3.2565 0.99   1371  152 0.1293 0.1788      5.6293       5.931|
|  4:  3.2565 -  2.9612 0.99   1366  152 0.1629 0.2078      5.6652      5.8036|
|  5:  2.9612 -  2.7503 0.99   1349  151 0.1681 0.2212      5.5332      5.7718|
|  6:  2.7503 -  2.5890 0.99   1361  148 0.1615 0.2275      5.4022      5.6067|
|  7:  2.5890 -  2.4599 0.99   1334  155 0.1555 0.2024      5.3483      5.5067|
|  8:  2.4599 -  2.3533 0.98   1323  148 0.1543 0.2202      5.2822      5.5726|
|  9:  2.3533 -  2.2630 0.98   1328  141 0.1531 0.2135      5.2372      5.4607|
| 10:  2.2630 -  2.1851 1.00   1347  148 0.1372 0.1771      5.1043      5.2878|
| 11:  2.1851 -  2.1170 0.98   1322  150 0.1365 0.2179      5.0869      5.4659|
| 12:  2.1170 -  2.0566 0.98   1316  142 0.1385 0.2145      5.0139      5.2881|
| 13:  2.0566 -  2.0026 0.83   1107  127 0.1342 0.1917      4.9376      5.1124|
| 14:  2.0026 -  1.9539 0.20    263   28 0.1254 0.1927      4.8402      5.1524|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.6659  1447   160  0.93   9.73   0.96     0.94       7753.39|
|  2:  4.6659 -  3.7216  1396   157  0.95   8.93   1.02     1.01      10614.76|
|  3:  3.7216 -  3.2565  1371   152  0.91  14.30   1.04     1.04      14004.70|
|  4:  3.2565 -  2.9612  1366   152  0.88  18.63   1.02     0.98      15731.04|
|  5:  2.9612 -  2.7503  1349   151  0.86  20.11   0.99     0.97      12804.49|
|  6:  2.7503 -  2.5890  1361   148  0.86  20.59   0.99     0.94      10212.69|
|  7:  2.5890 -  2.4599  1334   155  0.87  19.98   1.00     0.95       9251.61|
|  8:  2.4599 -  2.3533  1323   148  0.86  20.25   1.00     0.96       8244.88|
|  9:  2.3533 -  2.2630  1328   141  0.86  20.75   1.00     0.93       7526.05|
| 10:  2.2630 -  2.1851  1347   148  0.87  19.11   1.00     0.97       6036.88|
| 11:  2.1851 -  2.1170  1322   150  0.87  19.82   0.99     0.93       5965.81|
| 12:  2.1170 -  2.0566  1316   142  0.87  19.39   1.00     0.98       5315.52|
| 13:  2.0566 -  2.0026  1107   127  0.87  20.21   0.99     0.96       4707.31|
| 14:  2.0026 -  1.9539   263    28  0.91  16.22   0.98     0.95       3549.74|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3549.74 max =        15731.04 mean =      9092.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.93 mean =        17.69|
|phase err.(test): min =        0.00 max =           89.70 mean =        16.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.795)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.78   17.73    None  None   None       |
|    all(noH): 2823   0      0.00    96.78   17.73    None  None   None       |
|    Sol.    : 438    0      0.00    94.75   44.82    None  None   None       |
|    Mac.    : 2385   0      0.00    96.78   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.681: 1086   |   5:    48.393 -  58.071:  103        |
|      1:     9.681 -  19.359: 1022   |   6:    58.071 -  67.749:   80        |
|      2:    19.359 -  29.037:  238   |   7:    67.749 -  77.427:   23        |
|      3:    29.037 -  38.715:  134   |   8:    77.427 -  87.106:   19        |
|      4:    38.715 -  48.393:  111   |   9:    87.106 -  96.784:    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)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.589 - 5.848
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 348
   mapped sites are within: 0.755 - 5.848

peak=    7.744 closest distance to " O   HOH Z 390 " =    1.256
peak=    7.394 closest distance to " O   HOH Z 103 " =    0.969
peak=    6.945 closest distance to " O   HOH Z 385 " =    1.708
peak=    6.865 closest distance to " O  BHOH Z  74 " =    1.109
peak=    6.695 closest distance to " O   HOH Z 245 " =    1.412
peak=    6.671 closest distance to " O   HOH Z 381 " =    1.024
peak=    5.711 closest distance to " O   HOH Z  77 " =    1.218
peak=    5.461 closest distance to " O   HOH Z 222 " =    1.686
peak=    5.386 closest distance to " O   HOH Z  65 " =    1.751
peak=    5.292 closest distance to " O   HOH Z 130 " =    0.853
peak=    5.278 closest distance to " O   HOH Z 431 " =    1.656
peak=    5.222 closest distance to " O   HOH Z 278 " =    1.560
peak=    5.208 closest distance to " O   HOH Z 287 " =    2.126
peak=    5.188 closest distance to " CG  PRO A  90 " =    1.424
peak=    5.174 closest distance to " O   HOH Z 417 " =    2.695
peak=    5.090 closest distance to " O   HOH Z 142 " =    2.094
peak=    5.069 closest distance to " O   HOH Z   7 " =    1.975
peak=    5.016 closest distance to " O   HOH Z 126 " =    2.056
peak=    4.909 closest distance to " O   HOH Z  69 " =    2.061
peak=    4.893 closest distance to " O   HOH Z 419 " =    2.525
peak=    4.883 closest distance to " O   HOH Z 293 " =    1.569
peak=    4.781 closest distance to " O   HOH Z 105 " =    1.323
peak=    4.715 closest distance to " CB  SER A 216 " =    1.065
peak=    4.708 closest distance to " NE2 GLN A  11 " =    1.304
peak=    4.703 closest distance to " O   HOH Z 422 " =    1.164
peak=    4.682 closest distance to " O   HOH Z  46 " =    1.220
peak=    4.681 closest distance to " O   HOH Z  29 " =    1.470
peak=    4.670 closest distance to " CG  PRO A  54 " =    1.494
peak=    4.669 closest distance to " CB  PRO A  54 " =    1.254
peak=    4.638 closest distance to " O   HOH Z 403 " =    1.734
peak=    4.634 closest distance to " O   HOH Z  63 " =    1.666
peak=    4.577 closest distance to " O   HOH Z 427 " =    2.122
peak=    4.572 closest distance to " O   HOH Z  39 " =    1.265
peak=    4.542 closest distance to " O   HOH Z  66 " =    1.137
peak=    4.507 closest distance to " CG2 ILE A 120 " =    0.997
peak=    4.506 closest distance to " O   HOH Z 359 " =    1.553
peak=    4.487 closest distance to " CB  GLN A 223 " =    1.604
peak=    4.486 closest distance to " C   GLN A  73 " =    1.010
peak=    4.430 closest distance to " CB  ASN A 148 " =    1.315
peak=    4.421 closest distance to " O   HOH Z 375 " =    1.220
peak=    4.414 closest distance to " O   HOH Z 380 " =    2.300
peak=    4.400 closest distance to " O   HOH Z 139 " =    1.393
peak=    4.399 closest distance to " O   HOH Z 418 " =    1.286
peak=    4.395 closest distance to " O   HOH Z 423 " =    2.177
peak=    4.367 closest distance to " O   HOH Z 295 " =    1.198
peak=    4.364 closest distance to " O   HOH Z 393 " =    1.259
peak=    4.345 closest distance to " NZ BLYS A 290 " =    1.016
peak=    4.341 closest distance to " CB  ALA A 114 " =    1.018
peak=    4.339 closest distance to " N   GLN A 278 " =    1.109
peak=    4.318 closest distance to " CZ3 TRP A 266 " =    1.145
peak=    4.296 closest distance to " O   HOH Z 232 " =    2.265
peak=    4.290 closest distance to " O   HOH Z 127 " =    1.052
peak=    4.247 closest distance to " O   HOH Z 145 " =    1.908
peak=    4.229 closest distance to " O   HOH Z 135 " =    1.526
peak=    4.221 closest distance to " O   HOH Z 316 " =    3.039
peak=    4.216 closest distance to " CB  ARG A 275 " =    1.095
peak=    4.202 closest distance to " O   VAL A  72 " =    0.994
peak=    4.198 closest distance to " O   HOH Z  97 " =    1.353
peak=    4.191 closest distance to " ND2BASN A 224 " =    0.963
peak=    4.188 closest distance to " O   HOH Z 158 " =    1.454
peak=    4.156 closest distance to " NH1AARG A 145 " =    1.163
peak=    4.154 closest distance to " O   HOH Z   9 " =    1.950
peak=    4.145 closest distance to " O   HOH Z  30 " =    1.857
peak=    4.126 closest distance to " O   HOH Z 298 " =    2.097
peak=    4.124 closest distance to " O   HOH Z 361 " =    1.539
peak=    4.111 closest distance to " O   HOH Z 126 " =    1.459
peak=    4.054 closest distance to " O   HOH Z 425 " =    1.247
peak=    4.033 closest distance to " CA  ALA A  51 " =    1.056
peak=    4.007 closest distance to " O   PRO A 198 " =    1.351
peak=    4.005 closest distance to " O   HOH Z 365 " =    2.538
peak=    4.002 closest distance to " CB  SER A  63 " =    1.387
peak=    3.994 closest distance to " CB  LYS A 290 " =    0.916
peak=    3.991 closest distance to " O   HOH Z  43 " =    1.301
peak=    3.988 closest distance to " CD  GLN A  77 " =    1.386
peak=    3.982 closest distance to " CE3 TRP A 274 " =    1.459
peak=    3.977 closest distance to " O   HOH Z  91 " =    2.495
peak=    3.976 closest distance to " CG  GLN A  58 " =    1.141
peak=    3.970 closest distance to " O   HOH Z 424 " =    1.118
peak=    3.968 closest distance to " CE  LYS A 119 " =    1.274
peak=    3.964 closest distance to " O   HOH Z 225 " =    1.806
peak=    3.958 closest distance to " O   HOH Z 133 " =    1.069
peak=    3.939 closest distance to " CA  TYR A  30 " =    1.157
peak=    3.928 closest distance to " CB  ASP A 124 " =    0.916
peak=    3.928 closest distance to " CB  GLU A 128 " =    1.041
peak=    3.911 closest distance to " O   HOH Z  61 " =    1.704
peak=    3.907 closest distance to " O   HOH Z 371 " =    1.857
peak=    3.903 closest distance to " ND2 ASN A  60 " =    2.913
peak=    3.884 closest distance to " O   HOH Z 276 " =    1.398
peak=    3.880 closest distance to " O   HOH Z 392 " =    1.410
peak=    3.880 closest distance to " O   HOH Z 124 " =    1.345
peak=    3.875 closest distance to " O   HOH Z 414 " =    1.532
peak=    3.871 closest distance to " CB  PRO A  90 " =    1.107
peak=    3.865 closest distance to " O   HOH Z 400 " =    0.760
peak=    3.863 closest distance to " O   HOH Z  27 " =    1.024
peak=    3.856 closest distance to " NH2 ARG A  56 " =    2.007
peak=    3.838 closest distance to " O   ASN A 142 " =    0.968
peak=    3.830 closest distance to " O   HOH Z 119 " =    1.480
peak=    3.826 closest distance to " CB  LEU A 300 " =    0.934
peak=    3.825 closest distance to " CG2 THR A 221 " =    1.251
peak=    3.820 closest distance to " CG2 VAL A 257 " =    0.901
peak=    3.817 closest distance to " O   HOH Z 415 " =    0.966
peak=    3.816 closest distance to " O   HOH Z 368 " =    3.597
peak=    3.802 closest distance to " O   HOH Z 427 " =    1.263
peak=    3.798 closest distance to " CE2 PHE A  16 " =    0.843
peak=    3.796 closest distance to " CG  TRP A 179 " =    2.159
peak=    3.787 closest distance to " O   HOH Z   7 " =    2.923
peak=    3.786 closest distance to " O   HOH Z  11 " =    1.260
peak=    3.776 closest distance to " CG2BVAL A  41 " =    1.102
peak=    3.763 closest distance to " O   HOH Z 211 " =    1.365
peak=    3.759 closest distance to " CD  ARG A 195 " =    3.593
peak=    3.757 closest distance to " CB  GLU A 152 " =    1.174
peak=    3.757 closest distance to " CE3 TRP A 150 " =    1.112
peak=    3.752 closest distance to " O   HOH Z 368 " =    1.713
peak=    3.747 closest distance to " CB  SER A 210 " =    1.009
peak=    3.731 closest distance to " CG  PRO A 198 " =    1.282
peak=    3.724 closest distance to " O   TYR A 116 " =    1.252
peak=    3.722 closest distance to " CB  GLU A 277 " =    3.592
peak=    3.722 closest distance to " O   HOH Z 244 " =    1.462
peak=    3.710 closest distance to " CB  SER A  99 " =    0.907
peak=    3.703 closest distance to " ND2 ASN A 249 " =    0.769
peak=    3.698 closest distance to " NZ  LYS A 117 " =    3.167
peak=    3.695 closest distance to " CA  VAL A 125 " =    1.131
peak=    3.692 closest distance to " CA  PHE A 283 " =    1.295
peak=    3.690 closest distance to " O   HOH Z  57 " =    1.157
peak=    3.685 closest distance to " O   HOH Z 394 " =    1.859
peak=    3.682 closest distance to " O   HOH Z  40 " =    2.191
peak=    3.678 closest distance to " CB  SER A   3 " =    1.381
peak=    3.676 closest distance to " N   TYR A  15 " =    1.151
peak=    3.669 closest distance to " O   HOH Z 193 " =    1.727
peak=    3.666 closest distance to " O   HOH Z 410 " =    1.418
peak=    3.666 closest distance to " CB  TRP A 179 " =    1.480
peak=    3.664 closest distance to " CB  TYR A 116 " =    1.338
peak=    3.663 closest distance to " O   HOH Z 280 " =    1.418
peak=    3.660 closest distance to " OD1 ASP A 171 " =    1.373
peak=    3.658 closest distance to " NH2AARG A 190 " =    1.811
peak=    3.657 closest distance to " CB  MET A  40 " =    0.831
peak=    3.653 closest distance to " O   HOH Z 416 " =    1.285
peak=    3.651 closest distance to " O   HOH Z 156 " =    3.399
peak=    3.649 closest distance to " OD1 ASP A 238 " =    1.030
peak=    3.645 closest distance to " OG ASER A 212 " =    1.379
peak=    3.638 closest distance to " NZ  LYS A 119 " =    2.285
peak=    3.631 closest distance to " CE  MET A  93 " =    1.429
peak=    3.625 closest distance to " CB  SER A 276 " =    1.195
peak=    3.625 closest distance to " O   HOH Z 143 " =    1.303
peak=    3.621 closest distance to " O   HOH Z 296 " =    1.195
peak=    3.615 closest distance to " O   HOH Z  78 " =    1.826
peak=    3.608 closest distance to " O   HOH Z 373 " =    1.544
peak=    3.606 closest distance to " O   HOH Z 153 " =    3.680
peak=    3.602 closest distance to " CG2 ILE A  20 " =    1.615
peak=    3.602 closest distance to " CG  LYS A  76 " =    1.752
peak=    3.596 closest distance to " CB  PRO A 213 " =    1.286
peak=    3.593 closest distance to " O   HOH Z 358 " =    1.305
peak=    3.591 closest distance to " O   HOH Z  92 " =    1.221
peak=    3.587 closest distance to " O   HOH Z  68 " =    1.790
peak=    3.582 closest distance to " O   HOH Z 201 " =    1.988
peak=    3.578 closest distance to " NZ  LYS A 119 " =    1.993
peak=    3.575 closest distance to " O   HOH Z  59 " =    1.890
peak=    3.575 closest distance to " N   CYS A 260 " =    0.964
peak=    3.573 closest distance to " OG1 THR A 157 " =    1.055
peak=    3.569 closest distance to " NZ  LYS A 166 " =    1.006
peak=    3.563 closest distance to " O   HOH Z 259 " =    2.243
peak=    3.559 closest distance to " O   HOH Z 104 " =    1.764
peak=    3.551 closest distance to " O   HOH Z  67 " =    1.276
peak=    3.542 closest distance to " O   HOH Z 389 " =    1.876
peak=    3.527 closest distance to " OE1 GLU A   2 " =    2.229
peak=    3.522 closest distance to " OG  SER A 276 " =    1.025
peak=    3.521 closest distance to " O   HOH Z 424 " =    3.087
peak=    3.520 closest distance to " O   HOH Z 214 " =    2.354
peak=    3.518 closest distance to " CB  TRP A 150 " =    0.900
peak=    3.508 closest distance to " CG  ARG A 159 " =    0.801
peak=    3.506 closest distance to " N   ALA A   1 " =    1.570
peak=    3.504 closest distance to " NE2 HIS A 207 " =    1.048
peak=    3.501 closest distance to " O   HOH Z 180 " =    2.347
peak=    3.501 closest distance to " CE3 TRP A  85 " =    0.929
peak=    3.496 closest distance to " O   HOH Z 146 " =    1.563
peak=    3.493 closest distance to " O   HOH Z  44 " =    2.073
peak=    3.491 closest distance to " O   HOH Z   6 " =    1.804
peak=    3.491 closest distance to " CB  ASP A 140 " =    1.079
peak=    3.489 closest distance to " O   HOH Z 411 " =    3.489
peak=    3.488 closest distance to " O   THR A 294 " =    1.115
peak=    3.486 closest distance to " O   HOH Z  58 " =    1.917
peak=    3.485 closest distance to " CB  TRP A 266 " =    0.988
peak=    3.484 closest distance to " O   HOH Z 363 " =    1.139
peak=    3.484 closest distance to " CA  TYR A 116 " =    1.502
peak=    3.479 closest distance to " CD  LYS A 166 " =    1.587
peak=    3.459 closest distance to " CB  PHE A 130 " =    1.007
peak=    3.458 closest distance to " O   HOH Z 116 " =    1.214
peak=    3.457 closest distance to " CA  ARG A 195 " =    1.341
peak=    3.454 closest distance to " O   HOH Z 357 " =    2.074
peak=    3.453 closest distance to " CA  LEU A 282 " =    1.063
peak=    3.452 closest distance to " CA  ALA A   7 " =    1.048
peak=    3.451 closest distance to " CG  LEU A 167 " =    1.339
peak=    3.449 closest distance to " O   HOH Z  88 " =    3.417
peak=    3.447 closest distance to " O   HOH Z 147 " =    1.481
peak=    3.438 closest distance to " O   HOH Z 437 " =    2.044
peak=    3.437 closest distance to " O   HOH Z 426 " =    1.093
peak=    3.434 closest distance to " O   HOH Z 422 " =    2.224
peak=    3.428 closest distance to " O   HOH Z 434 " =    1.574
peak=    3.428 closest distance to " O   HOH Z 218 " =    1.857
peak=    3.427 closest distance to " CG2 THR A 279 " =    0.931
peak=    3.424 closest distance to " CB  ARG A 219 " =    0.842
peak=    3.410 closest distance to " O   HOH Z 258 " =    2.120
peak=    3.409 closest distance to " O   HOH Z 147 " =    1.085
peak=    3.405 closest distance to " NZ  LYS A 117 " =    1.216
peak=    3.395 closest distance to " O   HOH Z 385 " =    2.602
peak=    3.386 closest distance to " CA  ILE A 234 " =    1.202
peak=    3.386 closest distance to " CB  VAL A 296 " =    1.512
peak=    3.386 closest distance to " CB  THR A  31 " =    1.526
peak=    3.383 closest distance to " O   HOH Z 117 " =    0.801
peak=    3.382 closest distance to " CA  ALA A 180 " =    1.312
peak=    3.381 closest distance to " O   HOH Z 219 " =    3.920
peak=    3.380 closest distance to " N   ALA A 165 " =    1.355
peak=    3.373 closest distance to " O   HOH Z 215 " =    1.700
peak=    3.371 closest distance to " CB  GLN A 183 " =    1.230
peak=    3.371 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.370 closest distance to " O   HOH Z 272 " =    1.861
peak=    3.369 closest distance to " O   HOH Z  47 " =    2.095
peak=    3.367 closest distance to " OG  SER A  26 " =    1.495
peak=    3.364 closest distance to " O   HOH Z 119 " =    4.188
peak=    3.364 closest distance to " O   HOH Z 120 " =    0.755
peak=    3.360 closest distance to " ND1 HIS A  86 " =    1.860
peak=    3.353 closest distance to " NE1 TRP A 274 " =    1.035
peak=    3.349 closest distance to " CB  SER A  62 " =    0.802
peak=    3.346 closest distance to " CA  ALA A 233 " =    1.881
peak=    3.342 closest distance to " CB  ARG A  79 " =    0.907
peak=    3.341 closest distance to " O   HOH Z 327 " =    1.838
peak=    3.338 closest distance to " OG BSER A  99 " =    2.298
peak=    3.335 closest distance to " O   HOH Z 132 " =    0.895
peak=    3.330 closest distance to " O   TRP A  70 " =    1.248
peak=    3.328 closest distance to " CA  SER A  87 " =    1.100
peak=    3.326 closest distance to " CB  ASP A 171 " =    0.879
peak=    3.326 closest distance to " CG2 ILE A 239 " =    1.029
peak=    3.324 closest distance to " CA  LEU A  83 " =    1.678
peak=    3.308 closest distance to " CG  GLN A  89 " =    1.588
peak=    3.308 closest distance to " CG  PRO A 243 " =    1.109
peak=    3.307 closest distance to " CZ  PHE A  38 " =    1.250
peak=    3.307 closest distance to " O   HOH Z 405 " =    1.713
peak=    3.303 closest distance to " O   HOH Z  40 " =    1.762
peak=    3.302 closest distance to " O   HOH Z 128 " =    1.950
peak=    3.302 closest distance to " CA  SER A  95 " =    0.941
peak=    3.300 closest distance to " O   HOH Z 189 " =    2.776
peak=    3.298 closest distance to " CB  ALA A  43 " =    0.890
peak=    3.295 closest distance to " O   HOH Z  76 " =    1.280
peak=    3.290 closest distance to " O   HOH Z  51 " =    1.859
peak=    3.289 closest distance to " OG BSER A 164 " =    2.299
peak=    3.288 closest distance to " O   HOH Z  26 " =    1.504
peak=    3.287 closest distance to " O   HOH Z 171 " =    1.549
peak=    3.286 closest distance to " CB  VAL A 202 " =    1.622
peak=    3.285 closest distance to " N   ARG A 156 " =    1.190
peak=    3.284 closest distance to " O   HOH Z 240 " =    2.020
peak=    3.283 closest distance to " CG1 VAL A 296 " =    1.224
peak=    3.281 closest distance to " O   HOH Z 352 " =    1.637
peak=    3.279 closest distance to " CA  GLY A 136 " =    1.038
peak=    3.277 closest distance to " O   HOH Z 248 " =    1.647
peak=    3.275 closest distance to " CB  ASN A 187 " =    0.911
peak=    3.275 closest distance to " CG1 ILE A 120 " =    1.369
peak=    3.272 closest distance to " NH2AARG A 145 " =    1.139
peak=    3.268 closest distance to " O   HOH Z 145 " =    1.934
peak=    3.261 closest distance to " O   HOH Z 207 " =    2.402
peak=    3.260 closest distance to " O   HOH Z 158 " =    2.734
peak=    3.257 closest distance to " O   HOH Z 287 " =    2.068
peak=    3.257 closest distance to " CG2 VAL A 202 " =    1.632
peak=    3.256 closest distance to " O   HOH Z 106 " =    4.001
peak=    3.254 closest distance to " CA  ALA A 129 " =    1.322
peak=    3.254 closest distance to " O   HOH Z 260 " =    2.451
peak=    3.254 closest distance to " O   HOH Z 273 " =    1.148
peak=    3.251 closest distance to " CD  ARG A  66 " =    2.182
peak=    3.250 closest distance to " CZ  PHE A 218 " =    1.179
peak=    3.247 closest distance to " CE AMET A  47 " =    1.334
peak=    3.243 closest distance to " CB  SER A 141 " =    1.158
peak=    3.242 closest distance to " O   HOH Z 222 " =    2.365
peak=    3.241 closest distance to " CD2 LEU A   5 " =    1.279
peak=    3.236 closest distance to " CB  ALA A  10 " =    0.979
peak=    3.230 closest distance to " CB  ARG A 138 " =    0.944
peak=    3.228 closest distance to " CA  ARG A  36 " =    1.136
peak=    3.228 closest distance to " O   HOH Z 230 " =    1.455
peak=    3.225 closest distance to " O   HOH Z 430 " =    1.982
peak=    3.222 closest distance to " CD2 HIS A  86 " =    0.879
peak=    3.222 closest distance to " OD1 ASN A 217 " =    1.154
peak=    3.221 closest distance to " CB  ALA A 291 " =    1.036
peak=    3.220 closest distance to " CA  MET A 105 " =    0.884
peak=    3.220 closest distance to " ND2 ASN A 176 " =    0.761
peak=    3.215 closest distance to " CA  ARG A 159 " =    1.285
peak=    3.215 closest distance to " CZ  PHE A  16 " =    0.928
peak=    3.214 closest distance to " O   HOH Z 302 " =    1.575
peak=    3.210 closest distance to " CB  GLU A 277 " =    1.051
peak=    3.210 closest distance to " NE1 TRP A  85 " =    1.190
peak=    3.209 closest distance to " CB  GLU A 175 " =    1.032
peak=    3.206 closest distance to " CA  VAL A 121 " =    0.989
peak=    3.204 closest distance to " O   HOH Z 104 " =    1.940
peak=    3.203 closest distance to " N   SER A  97 " =    0.843
peak=    3.202 closest distance to " CA  SER A  12 " =    1.647
peak=    3.200 closest distance to " N   GLN A  73 " =    0.927
peak=    3.197 closest distance to " O   HIS A 115 " =    0.989
peak=    3.197 closest distance to " OE2 GLU A  53 " =    2.044
peak=    3.196 closest distance to " O   HOH Z 330 " =    1.140
peak=    3.196 closest distance to " CA  GLU A 152 " =    1.188
peak=    3.192 closest distance to " O   GLY A 302 " =    2.416
peak=    3.187 closest distance to " O   HOH Z  33 " =    1.684
peak=    3.186 closest distance to " NH2 ARG A 269 " =    1.044
peak=    3.184 closest distance to " O   PHE A  61 " =    1.399
peak=    3.183 closest distance to " O   HOH Z 172 " =    1.950
peak=    3.182 closest distance to " CG  GLU A 277 " =    1.950
peak=    3.181 closest distance to " O   HOH Z 340 " =    1.951
peak=    3.179 closest distance to " N   ARG A  66 " =    0.983
peak=    3.173 closest distance to " O   HOH Z  21 " =    1.537
peak=    3.173 closest distance to " CB  ASN A 215 " =    1.210
peak=    3.172 closest distance to " CB  ASN A 142 " =    0.954
peak=    3.170 closest distance to " CD2 LEU A  25 " =    1.218
peak=    3.167 closest distance to " O   GLN A  55 " =    1.647
peak=    3.167 closest distance to " O   HOH Z 362 " =    1.784
peak=    3.166 closest distance to " CB  LEU A 237 " =    0.865
peak=    3.166 closest distance to " N   GLU A 152 " =    1.426
peak=    3.165 closest distance to " CB  VAL A 265 " =    1.334
peak=    3.162 closest distance to " OG ASER A 212 " =    1.498
peak=    3.155 closest distance to " O   HOH Z 365 " =    1.472
peak=    3.151 closest distance to " O   HOH Z  28 " =    0.917
peak=    3.140 closest distance to " N   TRP A  70 " =    0.974
peak=    3.139 closest distance to " N   GLU A   2 " =    1.317
peak=    3.137 closest distance to " CG  ARG A 156 " =    1.212
peak=    3.133 closest distance to " CD2 TRP A 179 " =    1.521
peak=    3.131 closest distance to " O   HOH Z 217 " =    1.258
peak=    3.131 closest distance to " CB  VAL A 268 " =    0.879
peak=    3.130 closest distance to " O   HOH Z 399 " =    0.916
peak=    3.130 closest distance to " CD  ARG A  79 " =    0.972
peak=    3.128 closest distance to " O   HOH Z 406 " =    1.467
peak=    3.122 closest distance to " CG AARG A 275 " =    1.346
peak=    3.117 closest distance to " O   HOH Z 189 " =    3.052
peak=    3.113 closest distance to " O   HOH Z   2 " =    1.571
peak=    3.107 closest distance to " CG  LYS A 119 " =    1.071
peak=    3.107 closest distance to " O   HOH Z 425 " =    2.025
peak=    3.103 closest distance to " O   HOH Z 280 " =    1.612
peak=    3.101 closest distance to " CD  GLN A  58 " =    5.848
peak=    3.098 closest distance to " NH2 ARG A  66 " =    5.178
peak=    3.095 closest distance to " O   HOH Z 171 " =    2.201
peak=    3.085 closest distance to " CA  ALA A 160 " =    0.981
peak=    3.079 closest distance to " CB  ARG A 190 " =    1.376
peak=    3.070 closest distance to " NE2 GLN A 278 " =    3.604
peak=    3.062 closest distance to " OG BSER A 212 " =    2.730
peak=    3.051 closest distance to " O   HOH Z  22 " =    1.458
peak=    3.045 closest distance to " CB  GLN A  88 " =    1.421
peak=    3.034 closest distance to " O   HOH Z 265 " =    2.123
peak=    3.015 closest distance to " O   HOH Z 212 " =    1.632
peak=    3.007 closest distance to " CA  PRO A  54 " =    1.312

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.369 - 5.581
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 206
   mapped sites are within: 0.775 - 5.581

peak=   -4.615 closest distance to " O   HOH Z 231 " =    0.847
peak=   -4.555 closest distance to " O   HOH Z  60 " =    1.497
peak=   -4.426 closest distance to " O   ALA A  10 " =    1.536
peak=   -4.304 closest distance to " O   HOH Z  39 " =    0.779
peak=   -4.233 closest distance to " O   PRO A 198 " =    1.107
peak=   -4.193 closest distance to " O   HOH Z 242 " =    1.423
peak=   -4.179 closest distance to " OD1 ASP A 191 " =    1.948
peak=   -4.171 closest distance to " OG  SER A  97 " =    2.047
peak=   -4.118 closest distance to " CD  ARG A  14 " =    3.165
peak=   -4.111 closest distance to " O   HOH Z  28 " =    1.070
peak=   -4.095 closest distance to " OG1 THR A 157 " =    1.672
peak=   -4.084 closest distance to " CG  MET A 105 " =    1.024
peak=   -4.051 closest distance to " CD  LYS A 166 " =    2.552
peak=   -4.040 closest distance to " CG2 ILE A  49 " =    2.742
peak=   -4.034 closest distance to " O   HOH Z 313 " =    1.134
peak=   -4.020 closest distance to " O   HOH Z 385 " =    1.171
peak=   -4.014 closest distance to " O   HOH Z  69 " =    1.267
peak=   -4.003 closest distance to " CB  ALA A 291 " =    2.249
peak=   -3.982 closest distance to " O   HOH Z  24 " =    0.848
peak=   -3.958 closest distance to " OE1 GLU A  44 " =    1.965
peak=   -3.879 closest distance to " CD1 TRP A 179 " =    1.249
peak=   -3.876 closest distance to " O   HOH Z 216 " =    1.435
peak=   -3.864 closest distance to " CB  GLN A  55 " =    1.256
peak=   -3.864 closest distance to " CB  PRO A 243 " =    2.522
peak=   -3.854 closest distance to " OG  SER A  32 " =    0.966
peak=   -3.844 closest distance to " O   HOH Z 100 " =    1.116
peak=   -3.817 closest distance to " O   HOH Z 275 " =    1.698
peak=   -3.801 closest distance to " O   SER A  22 " =    2.682
peak=   -3.793 closest distance to " O   HOH Z 111 " =    1.623
peak=   -3.784 closest distance to " CB  ALA A 131 " =    1.899
peak=   -3.774 closest distance to " ND2 ASN A 209 " =    1.846
peak=   -3.757 closest distance to " O   GLY A 203 " =    2.555
peak=   -3.756 closest distance to " O   HOH Z 163 " =    1.818
peak=   -3.726 closest distance to " CB  ALA A   9 " =    2.468
peak=   -3.724 closest distance to " CB  ALA A 160 " =    2.060
peak=   -3.708 closest distance to " CZ  PHE A  59 " =    1.571
peak=   -3.691 closest distance to " CD2 TYR A 293 " =    1.822
peak=   -3.678 closest distance to " O   HOH Z 198 " =    1.565
peak=   -3.677 closest distance to " O   HOH Z 298 " =    2.612
peak=   -3.662 closest distance to " O   HOH Z 185 " =    2.083
peak=   -3.654 closest distance to " N   ALA A  43 " =    2.714
peak=   -3.654 closest distance to " CE3 TRP A 179 " =    1.372
peak=   -3.654 closest distance to " O   HOH Z 200 " =    3.444
peak=   -3.650 closest distance to " CB  PRO A  54 " =    2.365
peak=   -3.641 closest distance to " CD2 HIS A 207 " =    1.510
peak=   -3.636 closest distance to " O   HOH Z 381 " =    1.433
peak=   -3.612 closest distance to " CZ2 TRP A 274 " =    1.033
peak=   -3.611 closest distance to " O   HOH Z 425 " =    0.793
peak=   -3.595 closest distance to " O   HOH Z 266 " =    5.141
peak=   -3.589 closest distance to " O   HOH Z  49 " =    1.160
peak=   -3.570 closest distance to " O   HOH Z 211 " =    0.792
peak=   -3.569 closest distance to " CG1 VAL A 265 " =    2.453
peak=   -3.568 closest distance to " CA  GLY A 241 " =    2.205
peak=   -3.568 closest distance to " CB  ASP A 171 " =    2.286
peak=   -3.558 closest distance to " O   HOH Z   5 " =    1.117
peak=   -3.557 closest distance to " N   GLN A  58 " =    1.339
peak=   -3.555 closest distance to " O   HOH Z 143 " =    1.040
peak=   -3.553 closest distance to " CG1BVAL A  41 " =    2.749
peak=   -3.548 closest distance to " O   HOH Z 356 " =    3.865
peak=   -3.544 closest distance to " O   ASP A 253 " =    1.699
peak=   -3.541 closest distance to " NE2 GLN A  55 " =    0.991
peak=   -3.539 closest distance to " O   HOH Z 415 " =    1.014
peak=   -3.537 closest distance to " O   HOH Z 404 " =    1.429
peak=   -3.535 closest distance to " CA  ASP A  27 " =    2.506
peak=   -3.526 closest distance to " ND2 ASN A 285 " =    2.179
peak=   -3.523 closest distance to " C   VAL A  72 " =    0.954
peak=   -3.500 closest distance to " OG  SER A 245 " =    1.534
peak=   -3.494 closest distance to " O   PRO A 163 " =    1.359
peak=   -3.493 closest distance to " O   HOH Z  26 " =    0.833
peak=   -3.488 closest distance to " O   HOH Z  22 " =    2.590
peak=   -3.487 closest distance to " O   HOH Z 324 " =    0.858
peak=   -3.486 closest distance to " O   GLN A 240 " =    3.171
peak=   -3.479 closest distance to " O   ASP A  27 " =    1.885
peak=   -3.476 closest distance to " O   HOH Z 351 " =    1.648
peak=   -3.472 closest distance to " CA  GLY A 133 " =    1.898
peak=   -3.471 closest distance to " O   HOH Z 435 " =    3.277
peak=   -3.471 closest distance to " CA  ASN A 110 " =    0.904
peak=   -3.467 closest distance to " CZ  TYR A 169 " =    1.925
peak=   -3.466 closest distance to " CA  GLY A  35 " =    2.037
peak=   -3.458 closest distance to " O   HOH Z 128 " =    2.563
peak=   -3.458 closest distance to " CD  ARG A 156 " =    1.992
peak=   -3.456 closest distance to " O   HOH Z 389 " =    2.397
peak=   -3.452 closest distance to " OG  SER A  63 " =    1.419
peak=   -3.448 closest distance to " N   ASP A 270 " =    1.249
peak=   -3.448 closest distance to " O   ALA A 100 " =    1.507
peak=   -3.434 closest distance to " O   HOH Z 181 " =    1.626
peak=   -3.432 closest distance to " CD2 TYR A 116 " =    2.174
peak=   -3.431 closest distance to " O   HOH Z 251 " =    0.918
peak=   -3.428 closest distance to " N   ALA A   1 " =    1.612
peak=   -3.428 closest distance to " C   HIS A 207 " =    1.212
peak=   -3.423 closest distance to " NE2 GLN A 223 " =    1.649
peak=   -3.414 closest distance to " CD2 PHE A  61 " =    2.065
peak=   -3.414 closest distance to " CB  ALA A  43 " =    2.467
peak=   -3.410 closest distance to " CE2 TYR A  30 " =    2.548
peak=   -3.403 closest distance to " CD  PRO A 213 " =    2.197
peak=   -3.396 closest distance to " O   PHE A 218 " =    1.630
peak=   -3.395 closest distance to " O   HOH Z 126 " =    1.847
peak=   -3.389 closest distance to " N   ARG A 159 " =    2.044
peak=   -3.387 closest distance to " O   ALA A   1 " =    1.603
peak=   -3.385 closest distance to " OD2 ASP A 272 " =    1.589
peak=   -3.379 closest distance to " CD  GLU A 277 " =    1.021
peak=   -3.378 closest distance to " O   HOH Z 348 " =    1.890
peak=   -3.371 closest distance to " O   GLY A  80 " =    2.495
peak=   -3.369 closest distance to " O   LYS A  76 " =    1.889
peak=   -3.364 closest distance to " O   HOH Z 389 " =    1.075
peak=   -3.363 closest distance to " CE3 TRP A 274 " =    2.438
peak=   -3.362 closest distance to " CB  LYS A 289 " =    2.932
peak=   -3.350 closest distance to " O   HOH Z 276 " =    1.114
peak=   -3.347 closest distance to " O   HOH Z 275 " =    1.511
peak=   -3.343 closest distance to " O   HOH Z 412 " =    3.981
peak=   -3.341 closest distance to " O   HOH Z 129 " =    3.729
peak=   -3.339 closest distance to " O   ILE A  49 " =    1.557
peak=   -3.336 closest distance to " CB  TRP A  85 " =    2.087
peak=   -3.334 closest distance to " OE1 GLU A 277 " =    2.352
peak=   -3.333 closest distance to " CG  TRP A 266 " =    1.874
peak=   -3.323 closest distance to " C   PHE A  59 " =    1.086
peak=   -3.322 closest distance to " CB  ASN A  45 " =    2.074
peak=   -3.315 closest distance to " NH2 ARG A 219 " =    2.029
peak=   -3.311 closest distance to " O   HOH Z 285 " =    1.460
peak=   -3.309 closest distance to " O   HOH Z 323 " =    2.097
peak=   -3.306 closest distance to " O   HOH Z 212 " =    0.917
peak=   -3.305 closest distance to " O   ALA A  84 " =    1.596
peak=   -3.303 closest distance to " CB  ALA A 158 " =    1.712
peak=   -3.299 closest distance to " O   HOH Z 142 " =    0.775
peak=   -3.298 closest distance to " NZ  LYS A 289 " =    1.715
peak=   -3.289 closest distance to " CA  GLY A  98 " =    1.836
peak=   -3.289 closest distance to " OG  SER A  87 " =    1.908
peak=   -3.287 closest distance to " CA  GLY A 203 " =    2.466
peak=   -3.282 closest distance to " O   HOH Z 105 " =    1.028
peak=   -3.279 closest distance to " CB  TYR A  68 " =    1.075
peak=   -3.278 closest distance to " CG  ARG A 219 " =    2.375
peak=   -3.274 closest distance to " O   ALA A 137 " =    0.910
peak=   -3.273 closest distance to " OE1 GLN A  11 " =    0.816
peak=   -3.271 closest distance to " CA  GLY A 133 " =    2.232
peak=   -3.269 closest distance to " NZ  LYS A 166 " =    1.572
peak=   -3.264 closest distance to " CB  ALA A 227 " =    2.352
peak=   -3.262 closest distance to " OG BSER A 134 " =    1.631
peak=   -3.259 closest distance to " CG  GLN A  88 " =    0.997
peak=   -3.253 closest distance to " CB  ALA A   7 " =    1.884
peak=   -3.253 closest distance to " CZ  ARG A  36 " =    1.350
peak=   -3.251 closest distance to " O   GLU A 152 " =    1.538
peak=   -3.251 closest distance to " CZ  PHE A 130 " =    1.074
peak=   -3.242 closest distance to " O   HOH Z 139 " =    2.922
peak=   -3.241 closest distance to " O   ARG A 145 " =    1.310
peak=   -3.236 closest distance to " OD2 ASP A 171 " =    1.408
peak=   -3.232 closest distance to " O   HOH Z 131 " =    3.849
peak=   -3.230 closest distance to " O   HOH Z  88 " =    2.096
peak=   -3.229 closest distance to " CE BMET A  47 " =    1.354
peak=   -3.227 closest distance to " CG  ASN A  39 " =    1.675
peak=   -3.222 closest distance to " O   HOH Z 234 " =    4.600
peak=   -3.221 closest distance to " CD2 LEU A  25 " =    2.238
peak=   -3.220 closest distance to " CZ  ARG A 259 " =    1.013
peak=   -3.219 closest distance to " O   HOH Z 362 " =    3.949
peak=   -3.218 closest distance to " O   HOH Z 231 " =    1.905
peak=   -3.209 closest distance to " O   HOH Z 155 " =    0.947
peak=   -3.203 closest distance to " O   HOH Z 426 " =    1.808
peak=   -3.201 closest distance to " N   GLU A 277 " =    1.318
peak=   -3.193 closest distance to " ND2 ASN A 187 " =    1.605
peak=   -3.190 closest distance to " O   HOH Z 385 " =    1.596
peak=   -3.188 closest distance to " CE1 TYR A  15 " =    2.337
peak=   -3.181 closest distance to " O   HOH Z  37 " =    1.397
peak=   -3.173 closest distance to " N   PRO A 163 " =    1.685
peak=   -3.170 closest distance to " CG2 THR A  52 " =    3.175
peak=   -3.166 closest distance to " NE2 GLN A 194 " =    1.832
peak=   -3.162 closest distance to " CG  GLU A 128 " =    1.758
peak=   -3.160 closest distance to " O   HOH Z 414 " =    1.779
peak=   -3.158 closest distance to " CD2 LEU A 297 " =    2.179
peak=   -3.156 closest distance to " OD1 ASN A 249 " =    1.732
peak=   -3.154 closest distance to " CB  TYR A  15 " =    2.182
peak=   -3.152 closest distance to " C   GLU A   2 " =    1.843
peak=   -3.152 closest distance to " O   VAL A 125 " =    2.238
peak=   -3.149 closest distance to " OE1 GLN A  88 " =    1.006
peak=   -3.146 closest distance to " CE  MET A  93 " =    2.060
peak=   -3.145 closest distance to " O   HOH Z 188 " =    1.003
peak=   -3.138 closest distance to " O   HOH Z 165 " =    2.320
peak=   -3.138 closest distance to " O   HOH Z  73 " =    2.313
peak=   -3.133 closest distance to " O   HOH Z 244 " =    1.671
peak=   -3.131 closest distance to " OH  TYR A 247 " =    1.488
peak=   -3.128 closest distance to " O   HOH Z 428 " =    2.260
peak=   -3.126 closest distance to " O   HOH Z 337 " =    1.561
peak=   -3.120 closest distance to " CG1 VAL A 126 " =    2.569
peak=   -3.119 closest distance to " CG1 VAL A 125 " =    2.321
peak=   -3.116 closest distance to " OE2 GLU A 175 " =    1.282
peak=   -3.114 closest distance to " CB  CYS A 201 " =    2.003
peak=   -3.114 closest distance to " C   ILE A 239 " =    2.140
peak=   -3.114 closest distance to " CB  SER A  62 " =    2.357
peak=   -3.109 closest distance to " CD  GLU A 236 " =    1.111
peak=   -3.107 closest distance to " CB  ALA A 100 " =    1.991
peak=   -3.105 closest distance to " CG2 VAL A 202 " =    1.931
peak=   -3.099 closest distance to " N   LYS A 166 " =    1.901
peak=   -3.097 closest distance to " ND2 ASN A  39 " =    1.825
peak=   -3.094 closest distance to " CA  ILE A 120 " =    1.150
peak=   -3.092 closest distance to " CG  LEU A  83 " =    2.168
peak=   -3.092 closest distance to " NH2 ARG A  66 " =    5.581
peak=   -3.086 closest distance to " O   HOH Z 181 " =    2.034
peak=   -3.086 closest distance to " OE1 GLN A  58 " =    5.380
peak=   -3.080 closest distance to " CG  LEU A 281 " =    1.793
peak=   -3.079 closest distance to " O   ASP A 162 " =    2.006
peak=   -3.069 closest distance to " O   SER A  87 " =    2.044
peak=   -3.062 closest distance to " N   ALA A   1 " =    1.477
peak=   -3.062 closest distance to " CB  HIS A  81 " =    1.150
peak=   -3.037 closest distance to " O   HOH Z 218 " =    3.920
peak=   -3.012 closest distance to " CE BMET A  47 " =    1.705

================= 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    :  0.4718 0.4743   6.289435e+00   6.280484e+00
   1_bss:  0.4617 0.4677   6.284198e+00   6.273869e+00
   1_xyz:  0.3692 0.4194   6.138250e+00   6.211321e+00
   1_adp:  0.3390 0.4286   6.105118e+00   6.221846e+00
   1_occ:  0.3385 0.4292   6.105246e+00   6.222331e+00
   2_bss:  0.3376 0.4274   6.106274e+00   6.222788e+00
   2_xyz:  0.2966 0.3794   6.000262e+00   6.147616e+00
   2_adp:  0.2857 0.3698   5.981149e+00   6.132830e+00
   2_occ:  0.2857 0.3700   5.981425e+00   6.133454e+00
   3_bss:  0.2861 0.3698   5.981682e+00   6.133305e+00
   3_xyz:  0.2429 0.3205   5.841644e+00   6.020274e+00
   3_adp:  0.2268 0.3101   5.797202e+00   5.993198e+00
   3_occ:  0.2268 0.3101   5.796645e+00   5.992844e+00
   4_bss:  0.2269 0.3099   5.796300e+00   5.992291e+00
   4_xyz:  0.1802 0.2410   5.564014e+00   5.785604e+00
   4_adp:  0.1632 0.2163   5.470405e+00   5.688844e+00
   4_occ:  0.1629 0.2155   5.468310e+00   5.686022e+00
   5_bss:  0.1625 0.2148   5.464509e+00   5.680989e+00
   5_xyz:  0.1424 0.1919   5.347103e+00   5.573254e+00
   5_adp:  0.1369 0.1888   5.321727e+00   5.559297e+00
   5_occ:  0.1367 0.1887   5.321434e+00   5.559157e+00
   5_bss:  0.1372 0.1883   5.321182e+00   5.558108e+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:  0.343  50.001  -3.105   1.677   2.495   0.000   0.000   0.000
   1_xyz:  0.343  50.001  -3.105   1.677   2.495   0.000   0.000   0.000
   1_adp:  0.343  50.001  -3.105   1.677   2.495   0.000   0.000   0.000
   1_occ:  0.343  50.001  -3.105   1.677   2.495   0.000   0.000   0.000
   2_bss:  0.363  79.656  -1.220   0.235   1.251   0.000   0.000   0.000
   2_xyz:  0.363  79.656  -1.220   0.235   1.251   0.000   0.000   0.000
   2_adp:  0.363  79.656  -1.220   0.235   1.251   0.000   0.000   0.000
   2_occ:  0.363  79.656  -1.220   0.235   1.251   0.000   0.000   0.000
   3_bss:  0.353  81.709  -0.886  -0.120   1.065  -0.000   0.000   0.000
   3_xyz:  0.353  81.709  -0.886  -0.120   1.065  -0.000   0.000   0.000
   3_adp:  0.353  81.709  -0.886  -0.120   1.065  -0.000   0.000   0.000
   3_occ:  0.353  81.709  -0.886  -0.120   1.065  -0.000   0.000   0.000
   4_bss:  0.344  81.323  -1.203  -0.982   0.662  -0.000   0.000   0.000
   4_xyz:  0.344  81.323  -1.203  -0.982   0.662  -0.000   0.000   0.000
   4_adp:  0.344  81.323  -1.203  -0.982   0.662  -0.000   0.000   0.000
   4_occ:  0.344  81.323  -1.203  -0.982   0.662  -0.000   0.000   0.000
   5_bss:  0.323  60.313  -1.720  -1.945   0.100  -0.000   0.000   0.000
   5_xyz:  0.323  60.313  -1.720  -1.945   0.100  -0.000   0.000   0.000
   5_adp:  0.323  60.313  -1.720  -1.945   0.100  -0.000   0.000   0.000
   5_occ:  0.323  60.313  -1.720  -1.945   0.100  -0.000   0.000   0.000
   5_bss:  0.323  60.316  -1.828  -2.183  -0.006  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.253 0.4033  0.5567    75806.927
   1_bss:  58.208 0.4158  0.5867    73636.909
   1_xyz:  48.838 0.5343  0.7342    54569.817
   1_adp:  49.873 0.5209  0.7211    56726.781
   1_occ:  50.033 0.5188  0.7172    56876.882
   2_bss:  49.796 0.5217  0.7165    56617.885
   2_xyz:  42.191 0.6146  0.8275    41785.305
   2_adp:  40.728 0.6326  0.8384    39891.008
   2_occ:  40.776 0.6320  0.8378    39986.333
   3_bss:  40.740 0.6324  0.8358    39889.574
   3_xyz:  33.868 0.7131  0.9221    28298.905
   3_adp:  32.262 0.7317  0.9239    26053.549
   3_occ:  32.242 0.7319  0.9238    26011.030
   4_bss:  32.186 0.7324  0.9074    25932.826
   4_xyz:  24.253 0.8176  0.9761    15054.025
   4_adp:  21.243 0.8491  0.9888    12299.726
   4_occ:  21.158 0.8499  0.9889    12207.135
   5_bss:  21.029 0.8509  0.9659    12009.434
   5_xyz:  18.050 0.8797  0.9788     9373.629
   5_adp:  17.635 0.8839  0.9720     9119.633
   5_occ:  17.628 0.8839  0.9719     9108.715
   5_bss:  17.605 0.8841  0.9673     9093.331
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8747e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8747e-01
   1_xyz:   1.713  0.013  0.118 16.705  0.008  4.110   1.6631e-01
   1_adp:   1.713  0.013  0.118 16.705  0.008  4.110   1.6631e-01
   1_occ:   1.713  0.013  0.118 16.705  0.008  4.110   1.6631e-01
   2_bss:   1.713  0.013  0.118 16.705  0.008  4.110   1.6631e-01
   2_xyz:   1.137  0.007  0.083 15.033  0.004  4.109   7.3757e-02
   2_adp:   1.137  0.007  0.083 15.033  0.004  4.109   7.3757e-02
   2_occ:   1.137  0.007  0.083 15.033  0.004  4.109   7.3757e-02
   3_bss:   1.137  0.007  0.083 15.033  0.004  4.109   7.3757e-02
   3_xyz:   1.131  0.007  0.077 14.622  0.004  4.117   7.0059e-02
   3_adp:   1.131  0.007  0.077 14.622  0.004  4.117   7.0059e-02
   3_occ:   1.131  0.007  0.077 14.622  0.004  4.117   7.0059e-02
   4_bss:   1.131  0.007  0.077 14.622  0.004  4.117   7.0059e-02
   4_xyz:   1.093  0.008  0.081 14.746  0.004  4.111   6.8733e-02
   4_adp:   1.093  0.008  0.081 14.746  0.004  4.111   6.8733e-02
   4_occ:   1.093  0.008  0.081 14.746  0.004  4.111   6.8733e-02
   5_bss:   1.093  0.008  0.081 14.746  0.004  4.111   6.8733e-02
   5_xyz:   0.940  0.006  0.068 14.563  0.003  4.110   5.3924e-02
   5_adp:   0.940  0.006  0.068 14.563  0.003  4.110   5.3924e-02
   5_occ:   0.940  0.006  0.068 14.563  0.003  4.110   5.3924e-02
   5_bss:   0.940  0.006  0.068 14.563  0.003  4.110   5.3924e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4166e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4166e-01
   1_xyz:  10.307  0.065  0.406 80.102  0.050  1.993   1.0597e-01
   1_adp:  10.307  0.065  0.406 80.102  0.050  1.993   1.0597e-01
   1_occ:  10.307  0.065  0.406 80.102  0.050  1.993   1.0597e-01
   2_bss:  10.307  0.065  0.406 80.102  0.050  1.993   1.0597e-01
   2_xyz:   9.404  0.064  0.310 79.639  0.034  2.237   6.9549e-02
   2_adp:   9.404  0.064  0.310 79.639  0.034  2.237   6.9549e-02
   2_occ:   9.404  0.064  0.310 79.639  0.034  2.237   6.9549e-02
   3_bss:   9.404  0.064  0.310 79.639  0.034  2.237   6.9549e-02
   3_xyz:   6.758  0.037  0.301 81.331  0.042  2.232   4.8655e-02
   3_adp:   6.758  0.037  0.301 81.331  0.042  2.232   4.8655e-02
   3_occ:   6.758  0.037  0.301 81.331  0.042  2.232   4.8655e-02
   4_bss:   6.758  0.037  0.301 81.331  0.042  2.232   4.8655e-02
   4_xyz:   7.233  0.057  0.280 84.315  0.032  2.234   5.7743e-02
   4_adp:   7.233  0.057  0.280 84.315  0.032  2.234   5.7743e-02
   4_occ:   7.233  0.057  0.280 84.315  0.032  2.234   5.7743e-02
   5_bss:   7.233  0.057  0.280 84.315  0.032  2.234   5.7743e-02
   5_xyz:   6.565  0.041  0.236 80.333  0.035  2.383   4.1461e-02
   5_adp:   6.565  0.041  0.236 80.333  0.035  2.383   4.1461e-02
   5_occ:   6.565  0.041  0.236 80.333  0.035  2.383   4.1461e-02
   5_bss:   6.565  0.041  0.236 80.333  0.035  2.383   4.1461e-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:  80.08   0.00  18.54  69.96   0.00  15.36  80.08   0.00  35.80
   1_occ:  80.08   0.00  18.54  69.96   0.00  15.36  80.08   0.00  35.80
   2_bss:  80.08   0.00  18.54  69.96   0.00  15.36  80.08   0.00  35.80
   2_xyz:  80.08   0.00  18.54  69.96   0.00  15.36  80.08   0.00  35.80
   2_adp:  83.04   0.00  18.37  69.64   0.00  15.17  83.04   0.00  35.81
   2_occ:  83.04   0.00  18.37  69.64   0.00  15.17  83.04   0.00  35.81
   3_bss:  83.04   0.00  18.37  69.64   0.00  15.17  83.04   0.00  35.81
   3_xyz:  83.04   0.00  18.37  69.64   0.00  15.17  83.04   0.00  35.81
   3_adp:  96.55   0.00  19.06  96.27   0.00  14.53  96.55   0.00  43.70
   3_occ:  96.55   0.00  19.06  96.27   0.00  14.53  96.55   0.00  43.70
   4_bss:  96.55   0.00  19.06  96.27   0.00  14.53  96.55   0.00  43.70
   4_xyz:  96.55   0.00  19.06  96.27   0.00  14.53  96.55   0.00  43.70
   4_adp:  95.72   0.00  17.85  95.72   0.00  13.13  93.79   4.64  43.60
   4_occ:  95.72   0.00  17.85  95.72   0.00  13.13  93.79   4.64  43.60
   5_bss:  95.72   0.00  17.85  95.72   0.00  13.13  93.79   4.64  43.60
   5_xyz:  95.72   0.00  17.85  95.72   0.00  13.13  93.79   4.64  43.60
   5_adp:  96.78   0.00  17.72  96.78   0.00  12.75  94.75   0.00  44.82
   5_occ:  96.78   0.00  17.72  96.78   0.00  12.75  94.75   0.00  44.82
   5_bss:  96.78   0.00  17.73  96.78   0.00  12.75  94.75   0.00  44.82
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.801    0.033    0.439
   1_adp:    1.801    0.033    0.439
   1_occ:    1.801    0.033    0.439
   2_bss:    1.801    0.033    0.439
   2_xyz:    1.535    0.028    0.519
   2_adp:    1.535    0.028    0.519
   2_occ:    1.535    0.028    0.519
   3_bss:    1.535    0.028    0.519
   3_xyz:    1.614    0.047    0.664
   3_adp:    1.614    0.047    0.664
   3_occ:    1.614    0.047    0.664
   4_bss:    1.614    0.047    0.664
   4_xyz:    1.630    0.076    0.811
   4_adp:    1.630    0.076    0.811
   4_occ:    1.630    0.076    0.811
   5_bss:    1.630    0.076    0.811
   5_xyz:    1.645    0.075    0.842
   5_adp:    1.645    0.075    0.842
   5_occ:    1.645    0.075    0.842
   5_bss:    1.645    0.075    0.842
------------------------------------------------------------------------

CPU time actual refinement: 367.61


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_735/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_735/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_735/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_735/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_735/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 367.46 
  Macro-tasks:
    bulk solvent and scale       = 53.70  
    individual site refinement   = 149.35 
    weights calculation          = 29.77  
    collect and process          = 6.30   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 239.21 
  Micro-tasks:
    mask                            = 3.13   
    f_calc                          = 116.42 
    alpha_beta                      = 8.27   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 124.60 
    fmodel                         = 8.58   
    r_factors                      = 0.30   
    phase_errors                   = 10.13  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 272.89 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.159 micro seconds
Total CPU time: 6.35 minutes
from_scatterers_fft:    648 calls, 116.01 s
gradients_fft:          593 calls, 111.41 s

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

# Date 2008-01-16 Time 05:32:12 PST -0800 (1200490332.77 s)
Start R-work = 0.4718, R-free = 0.4743 (no bulk solvent and anisotropic scale)
Final R-work = 0.1563, R-free = 0.2035 (no bulk solvent and anisotropic scale)

Start R-work = 0.4617, R-free = 0.4677
Final R-work = 0.1372, R-free = 0.1883