# Date 2008-01-16 Time 04:47:45 PST -0800 (1200487665.24 s)
#phil __OFF__

Command line arguments: "../461.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12526
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 461

-------------------------------------------------------------------------------
  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: (69.5475, 47.6339, 88.5498, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (69.5475, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98087
Completeness in resolution range: 0.931125
Completeness with d_max=infinity: 0.928301

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9810
                             d_min =   1.9809

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: (69.5475, 47.6339, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.98087
Completeness in resolution range: 0.931125
Completeness with d_max=infinity: 0.928301

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2385 [2214/2242]  1991   223  10.1%
  bin  2:  4.2385 -  3.3769 [2110/2133]  1896   214  10.1%
  bin  3:  3.3769 -  2.9537 [2088/2110]  1885   203   9.7%
  bin  4:  2.9537 -  2.6854 [2087/2106]  1877   210  10.1%
  bin  5:  2.6854 -  2.4938 [2052/2081]  1837   215  10.5%
  bin  6:  2.4938 -  2.3474 [2048/2090]  1847   201   9.8%
  bin  7:  2.3474 -  2.2302 [2042/2078]  1849   193   9.5%
  bin  8:  2.2302 -  2.1334 [2041/2079]  1826   215  10.5%
  bin  9:  2.1334 -  2.0515 [2024/2055]  1829   195   9.6%
  bin 10:  2.0515 -  1.9809 [ 883/2064]   793    90  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_461/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.41 -     2.11: 12
        2.11 -     2.81: 770
        2.81 -     3.51: 4397
        3.51 -     4.20: 9182
        4.20 -     4.90: 13543
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.413 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.588 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.714 3.040 -x+1,y+1/2,-z+1/2
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.732 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.797 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27899 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_461/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_461/model_refine_001.geo

CPU time processing inputs: 8.81


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.63395 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4533   r_free= 0.4494   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.260667                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7273 0.99   1437  158 0.3501 0.3559      6.5221       6.485|
|  2:  4.7273 -  3.7719 0.99   1386  154 0.3836 0.4189      6.7644      6.8659|
|  3:  3.7719 -  3.3009 0.99   1347  151 0.4311 0.3750      6.6488      6.5803|
|  4:  3.3009 -  3.0018 0.99   1349  144 0.4392 0.4304      6.4767      6.4606|
|  5:  3.0018 -  2.7881 0.99   1326  154 0.4812 0.4522      6.3398      6.3536|
|  6:  2.7881 -  2.6246 0.98   1333  146 0.4857 0.5113      6.2571      6.1721|
|  7:  2.6246 -  2.4938 0.99   1308  158 0.4799 0.4698      6.2092      6.1251|
|  8:  2.4938 -  2.3857 0.99   1341  136 0.5021 0.4741      6.1561      6.1292|
|  9:  2.3857 -  2.2942 0.98   1320  145 0.5047 0.4945      6.1056      6.1792|
| 10:  2.2942 -  2.2153 0.98   1298  144 0.5172 0.5137      6.0842      6.0769|
| 11:  2.2153 -  2.1462 0.98   1303  155 0.5078 0.4948      6.0104      5.9979|
| 12:  2.1462 -  2.0850 0.99   1311  144 0.5169 0.5283      5.9427      5.9578|
| 13:  2.0850 -  2.0303 0.91   1231  121 0.5247 0.5511      5.8761      5.8433|
| 14:  2.0303 -  1.9809 0.26    340   49 0.4703 0.4644       5.876      5.7481|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7273  1437   158  0.74  30.84   0.83     0.75      58997.68|
|  2:  4.7273 -  3.7719  1386   154  0.73  32.60   0.91     0.82      92885.88|
|  3:  3.7719 -  3.3009  1347   151  0.64  40.44   0.89     0.80      97284.70|
|  4:  3.3009 -  3.0018  1349   144  0.56  46.90   0.91     0.73      85406.57|
|  5:  3.0018 -  2.7881  1326   154  0.50  51.97   0.88     0.66      66804.35|
|  6:  2.7881 -  2.6246  1333   146  0.46  55.44   0.89     0.61      61557.58|
|  7:  2.6246 -  2.4938  1308   158  0.46  55.05   0.92     0.61      55075.42|
|  8:  2.4938 -  2.3857  1341   136  0.45  56.01   0.90     0.62      49718.72|
|  9:  2.3857 -  2.2942  1320   145  0.45  55.93   0.91     0.65      45902.57|
| 10:  2.2942 -  2.2153  1298   144  0.43  57.62   0.91     0.61      42694.05|
| 11:  2.2153 -  2.1462  1303   155  0.37  62.54   0.91     0.56      44821.20|
| 12:  2.1462 -  2.0850  1311   144  0.31  67.06   0.92     0.48      43306.89|
| 13:  2.0850 -  2.0303  1231   121  0.27  69.85   0.89     0.43      40024.66|
| 14:  2.0303 -  1.9809   340    49  0.32  65.98   1.01     0.41      30557.88|
|alpha:            min =        0.41 max =            0.82 mean =         0.64|
|beta:             min =    30557.88 max =        97284.70 mean =     60123.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.39|
|phase err.(test): min =        0.00 max =           89.91 mean =        52.59|
|-----------------------------------------------------------------------------|

============================== 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 = 11.621039             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.045   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.799294              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.073   (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 |  1.413 -  1.762:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.762 -  2.110:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.110 -  2.459:       22 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.459 -  2.808:      748 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.808 -  3.157:     2040 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.157 -  3.505:     2357 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.505 -  3.854:     4531 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.854 -  4.203:     4651 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.203 -  4.551:     6116 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7427 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.413 |       0.396 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4533   r_free= 0.4494   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.260667                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4435   r_free= 0.4366   ksol= 0.31   Bsol= 50.00   scale= 0.940   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,1.58,4.64,0.00,0.00,0.00); trace/3= 1.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.252273                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.600697              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.706   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.963315              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.788   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4435      final r-factor (work) = 0.3026          |
| start r-factor (free) = 0.4366      final r-factor (free) = 0.3266          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.1764 = 9.60 * 0.50 * 6.2489 + 1.00 * 0.1793                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.3015 = 9.60 * 0.50 * 6.0757 + 1.00 * 0.1363                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3026      final r-factor (work) = 0.2736          |
| start r-factor (free) = 0.3266      final r-factor (free) = 0.3361          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8587 = 0.96 * 1.00 * 6.0757 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7001 = 0.96 * 1.00 * 5.8999 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.65   18.36    None  None   None       |
|    all(noH): 2823   0      0.00    99.65   18.36    None  None   None       |
|    Sol.    : 438    0      1.11    99.65   41.50    None  None   None       |
|    Mac.    : 2385   0      0.00    86.37   14.11    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 -   9.965:  989   |   5:    49.823 -  59.788:   77        |
|      1:     9.965 -  19.929:  972   |   6:    59.788 -  69.752:   50        |
|      2:    19.929 -  29.894:  363   |   7:    69.752 -  79.717:   22        |
|      3:    29.894 -  39.858:  204   |   8:    79.717 -  89.681:   12        |
|      4:    39.858 -  49.823:  129   |   9:    89.681 -  99.646:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2736 r_free = 0.3361             target_work(ml) = 5.910         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2733 r_free = 0.3362             target_work(ml) = 5.910         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2733   r_free= 0.3362   ksol= 0.31   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,1.58,4.64,0.00,0.00,0.00); trace/3= 1.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.909954                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2702   r_free= 0.3352   ksol= 0.33   Bsol= 72.52   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-0.09,1.55,-0.00,0.00,0.00); trace/3= -0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.906215                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.866129              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.456   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.279290              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.440  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2702      final r-factor (work) = 0.2005          |
| start r-factor (free) = 0.3352      final r-factor (free) = 0.2560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4918 = 4.87 * 0.50 * 5.9002 + 1.00 * 0.1363                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1862 = 4.87 * 0.50 * 5.8010 + 1.00 * 0.0719                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2005      final r-factor (work) = 0.1898          |
| start r-factor (free) = 0.2560      final r-factor (free) = 0.2385          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6367 = 0.28 * 1.00 * 5.8010 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6330 = 0.28 * 1.00 * 5.6223 + 1.00 * 0.0627                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.26   17.93    None  None   None       |
|    all(noH): 2823   0      0.00    99.26   17.93    None  None   None       |
|    Sol.    : 438    0      4.67    99.26   41.43    None  None   None       |
|    Mac.    : 2385   0      0.00    84.88   13.62    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 -   9.926: 1005   |   5:    49.629 -  59.555:   80        |
|      1:     9.926 -  19.852: 1043   |   6:    59.555 -  69.481:   45        |
|      2:    19.852 -  29.778:  309   |   7:    69.481 -  79.407:   23        |
|      3:    29.778 -  39.703:  176   |   8:    79.407 -  89.333:    7        |
|      4:    39.703 -  49.629:  131   |   9:    89.333 -  99.259:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1898 r_free = 0.2385             target_work(ml) = 5.593         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1895 r_free = 0.2385             target_work(ml) = 5.593         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1895   r_free= 0.2385   ksol= 0.33   Bsol= 72.52   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-0.09,1.55,-0.00,0.00,0.00); trace/3= -0.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.592651                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1897   r_free= 0.2376   ksol= 0.34   Bsol= 71.78   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.07,0.36,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.592274                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.817206              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.931   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.657386              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.242   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1897      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2376      final r-factor (free) = 0.1952          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9944 = 2.82 * 0.50 * 5.6243 + 1.00 * 0.0720                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8069 = 2.82 * 0.50 * 5.4988 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1518      final r-factor (work) = 0.1402          |
| start r-factor (free) = 0.1952      final r-factor (free) = 0.1907          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1329 = 1.66 * 1.00 * 5.4988 + 1.00 * 0.0192                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8981 = 1.66 * 1.00 * 5.3607 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.40    103.96  18.35    None  None   None       |
|    all(noH): 2823   0      0.40    103.96  18.35    None  None   None       |
|    Sol.    : 438    0      5.73    103.96  45.80    None  None   None       |
|    Mac.    : 2385   0      0.40    91.86   13.31    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:     0.402 -  10.758: 1201   |   5:    52.183 -  62.540:   93        |
|      1:    10.758 -  21.115:  975   |   6:    62.540 -  72.896:   63        |
|      2:    21.115 -  31.471:  209   |   7:    72.896 -  83.252:   32        |
|      3:    31.471 -  41.827:  119   |   8:    83.252 -  93.608:   13        |
|      4:    41.827 -  52.183:  114   |   9:    93.608 - 103.964:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1402 r_free = 0.1907             target_work(ml) = 5.347         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1402 r_free = 0.1907             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1402   r_free= 0.1907   ksol= 0.34   Bsol= 71.78   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-1.07,0.36,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.346435                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1404   r_free= 0.1908   ksol= 0.34   Bsol= 82.45   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-1.49,-0.12,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.347353                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.637813              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.704  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.529555              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.894  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1404      final r-factor (work) = 0.1270          |
| start r-factor (free) = 0.1908      final r-factor (free) = 0.1763          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1337 = 2.64 * 0.50 * 5.3623 + 1.00 * 0.0613                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0601 = 2.64 * 0.50 * 5.3042 + 1.00 * 0.0644                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1763      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8222 = 0.53 * 1.00 * 5.3042 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7953 = 0.53 * 1.00 * 5.2556 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.90  17.82    None  None   None       |
|    all(noH): 2823   0      0.00    104.90  17.82    None  None   None       |
|    Sol.    : 438    0      5.13    104.90  44.67    None  None   None       |
|    Mac.    : 2385   0      0.00    92.75   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.490: 1212   |   5:    52.450 -  62.940:   88        |
|      1:    10.490 -  20.980:  986   |   6:    62.940 -  73.430:   59        |
|      2:    20.980 -  31.470:  205   |   7:    73.430 -  83.920:   24        |
|      3:    31.470 -  41.960:  116   |   8:    83.920 -  94.409:   15        |
|      4:    41.960 -  52.450:  115   |   9:    94.409 - 104.899:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1248 r_free = 0.1727             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1247 r_free = 0.1726             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1247   r_free= 0.1726   ksol= 0.34   Bsol= 82.45   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-1.49,-0.12,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.243829                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1723   ksol= 0.33   Bsol= 72.11   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-1.30,0.13,-0.00,0.00,0.00); trace/3= -1.20                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.243904                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.388418              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.040  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.495054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.606  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9703 = 3.39 * 0.50 * 5.2567 + 1.00 * 0.0644                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9314 = 3.39 * 0.50 * 5.2218 + 1.00 * 0.0846                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.0409 = 2.50 * 1.00 * 5.2218 + 1.00 * 0.0121                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9982 = 2.50 * 1.00 * 5.2044 + 1.00 * 0.0130                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.61  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    110.61  17.62    None  None   None       |
|    Sol.    : 438    0      3.84    110.61  44.56    None  None   None       |
|    Mac.    : 2385   0      0.00    98.44   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.061: 1362   |   5:    55.303 -  66.364:   78        |
|      1:    11.061 -  22.121:  881   |   6:    66.364 -  77.425:   48        |
|      2:    22.121 -  33.182:  193   |   7:    77.425 -  88.485:   22        |
|      3:    33.182 -  44.243:  121   |   8:    88.485 -  99.546:   14        |
|      4:    44.243 -  55.303:  103   |   9:    99.546 - 110.607:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1690             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1690             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1690   ksol= 0.33   Bsol= 72.11   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-1.30,0.13,-0.00,0.00,0.00); trace/3= -1.20                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206699                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7273 0.99   1437  158 0.0963 0.1304      5.3883      5.5712|
|  2:  4.7273 -  3.7719 0.99   1386  154 0.0818 0.1062      5.4204        5.63|
|  3:  3.7719 -  3.3009 0.99   1347  151 0.1122 0.1566      5.5132      5.8604|
|  4:  3.3009 -  3.0018 0.99   1349  144 0.1314 0.1766      5.5054      5.6947|
|  5:  3.0018 -  2.7881 0.99   1326  154 0.1416 0.1792      5.3968      5.5814|
|  6:  2.7881 -  2.6246 0.98   1333  146 0.1334 0.2185      5.2866      5.5786|
|  7:  2.6246 -  2.4938 0.99   1308  158 0.1343 0.1816      5.2429      5.4397|
|  8:  2.4938 -  2.3857 0.99   1341  136 0.1267 0.1866      5.1734      5.3926|
|  9:  2.3857 -  2.2942 0.98   1320  145 0.1252 0.2047      5.1031      5.4138|
| 10:  2.2942 -  2.2153 0.98   1298  144 0.1202 0.1763      5.0193      5.1955|
| 11:  2.2153 -  2.1462 0.98   1303  155 0.1216 0.2048       4.967      5.3508|
| 12:  2.1462 -  2.0850 0.99   1311  144 0.1152 0.1673      4.9043      5.1524|
| 13:  2.0850 -  2.0303 0.91   1231  121 0.1120 0.1789       4.814      5.0497|
| 14:  2.0303 -  1.9809 0.26    340   49 0.0986 0.1872      4.7294      5.0229|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7273  1437   158  0.94   9.45   0.97     0.94       7571.59|
|  2:  4.7273 -  3.7719  1386   154  0.95   8.37   1.01     0.99       9330.22|
|  3:  3.7719 -  3.3009  1347   151  0.93  11.97   1.03     1.02      11200.90|
|  4:  3.3009 -  3.0018  1349   144  0.91  15.08   1.01     0.99      11610.91|
|  5:  3.0018 -  2.7881  1326   154  0.89  17.60   1.00     0.97       9907.41|
|  6:  2.7881 -  2.6246  1333   146  0.88  18.20   0.98     0.95       8482.92|
|  7:  2.6246 -  2.4938  1308   158  0.89  17.47   0.99     0.95       7512.00|
|  8:  2.4938 -  2.3857  1341   136  0.89  17.84   0.99     0.94       6918.81|
|  9:  2.3857 -  2.2942  1320   145  0.89  17.85   0.98     0.93       5944.02|
| 10:  2.2942 -  2.2153  1298   144  0.89  17.43   0.98     0.93       5154.21|
| 11:  2.2153 -  2.1462  1303   155  0.89  17.13   0.98     0.94       4694.55|
| 12:  2.1462 -  2.0850  1311   144  0.89  17.05   0.99     0.99       4348.08|
| 13:  2.0850 -  2.0303  1231   121  0.89  17.26   0.98     0.96       3718.76|
| 14:  2.0303 -  1.9809   340    49  0.91  14.98   0.95     0.90       2951.78|
|alpha:            min =        0.90 max =            1.02 mean =         0.96|
|beta:             min =     2951.78 max =        11610.91 mean =      7376.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.50|
|phase err.(test): min =        0.00 max =           89.84 mean =        14.97|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1688   ksol= 0.33   Bsol= 69.53   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-1.15,0.25,-0.00,0.00,0.00); trace/3= -1.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206864                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1688   ksol= 0.33   Bsol= 69.53   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-1.15,0.25,-0.00,0.00,0.00); trace/3= -1.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.206864                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7273 0.99   1437  158 0.0962 0.1303      5.3876      5.5709|
|  2:  4.7273 -  3.7719 0.99   1386  154 0.0817 0.1061      5.4201      5.6289|
|  3:  3.7719 -  3.3009 0.99   1347  151 0.1122 0.1568      5.5131      5.8614|
|  4:  3.3009 -  3.0018 0.99   1349  144 0.1315 0.1766      5.5061      5.6954|
|  5:  3.0018 -  2.7881 0.99   1326  154 0.1417 0.1794      5.3974      5.5819|
|  6:  2.7881 -  2.6246 0.98   1333  146 0.1334 0.2187       5.287      5.5795|
|  7:  2.6246 -  2.4938 0.99   1308  158 0.1343 0.1818      5.2435      5.4401|
|  8:  2.4938 -  2.3857 0.99   1341  136 0.1267 0.1866       5.174      5.3931|
|  9:  2.3857 -  2.2942 0.98   1320  145 0.1251 0.2046      5.1033      5.4138|
| 10:  2.2942 -  2.2153 0.98   1298  144 0.1202 0.1761      5.0194      5.1955|
| 11:  2.2153 -  2.1462 0.98   1303  155 0.1216 0.2046      4.9668      5.3505|
| 12:  2.1462 -  2.0850 0.99   1311  144 0.1152 0.1674      4.9043      5.1528|
| 13:  2.0850 -  2.0303 0.91   1231  121 0.1120 0.1789       4.814      5.0491|
| 14:  2.0303 -  1.9809 0.26    340   49 0.0985 0.1870       4.731      5.0234|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9814 -  4.7273  1437   158  0.94   9.45   0.97     0.94       7565.84|
|  2:  4.7273 -  3.7719  1386   154  0.95   8.36   1.01     0.99       9321.91|
|  3:  3.7719 -  3.3009  1347   151  0.93  11.97   1.03     1.03      11195.66|
|  4:  3.3009 -  3.0018  1349   144  0.91  15.09   1.01     1.00      11624.91|
|  5:  3.0018 -  2.7881  1326   154  0.89  17.61   1.00     0.97       9923.50|
|  6:  2.7881 -  2.6246  1333   146  0.88  18.22   0.98     0.96       8494.05|
|  7:  2.6246 -  2.4938  1308   158  0.89  17.49   0.99     0.96       7523.18|
|  8:  2.4938 -  2.3857  1341   136  0.89  17.85   1.00     0.95       6926.37|
|  9:  2.3857 -  2.2942  1320   145  0.89  17.86   0.99     0.94       5947.00|
| 10:  2.2942 -  2.2153  1298   144  0.89  17.43   0.99     0.94       5152.25|
| 11:  2.2153 -  2.1462  1303   155  0.89  17.12   0.99     0.94       4689.41|
| 12:  2.1462 -  2.0850  1311   144  0.89  17.05   1.00     1.00       4347.44|
| 13:  2.0850 -  2.0303  1231   121  0.89  17.27   0.99     0.97       3717.84|
| 14:  2.0303 -  1.9809   340    49  0.91  15.01   0.96     0.91       2953.45|
|alpha:            min =        0.91 max =            1.03 mean =         0.97|
|beta:             min =     2953.45 max =        11624.91 mean =      7379.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.63 mean =        15.50|
|phase err.(test): min =        0.00 max =           89.90 mean =        14.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.139)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.61  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    110.61  17.62    None  None   None       |
|    Sol.    : 438    0      3.84    110.61  44.56    None  None   None       |
|    Mac.    : 2385   0      0.00    98.44   12.67    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 -  11.064: 1362   |   5:    55.306 -  66.367:   78        |
|      1:    11.064 -  22.124:  881   |   6:    66.367 -  77.428:   48        |
|      2:    22.124 -  33.185:  193   |   7:    77.428 -  88.488:   22        |
|      3:    33.185 -  44.246:  121   |   8:    88.488 -  99.549:   14        |
|      4:    44.246 -  55.306:  103   |   9:    99.549 - 110.609:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.438 - 5.656
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 305
   mapped sites are within: 0.735 - 5.656

peak=    7.287 closest distance to " O  BHOH Z  74 " =    1.140
peak=    5.955 closest distance to " O   HOH Z 210 " =    1.229
peak=    5.310 closest distance to " CG  PRO A  54 " =    1.380
peak=    5.219 closest distance to " O   HOH Z  49 " =    1.422
peak=    5.156 closest distance to " O   HOH Z 403 " =    1.826
peak=    5.007 closest distance to " O   HOH Z 113 " =    1.841
peak=    4.758 closest distance to " O   HOH Z 369 " =    2.090
peak=    4.750 closest distance to " CB  GLN A 223 " =    1.470
peak=    4.720 closest distance to " O   HOH Z  76 " =    1.161
peak=    4.713 closest distance to " O   HOH Z 117 " =    1.172
peak=    4.661 closest distance to " CB  ARG A 190 " =    1.632
peak=    4.641 closest distance to " O   HOH Z 248 " =    1.412
peak=    4.619 closest distance to " O   HOH Z  65 " =    0.946
peak=    4.618 closest distance to " CD2 TRP A 179 " =    1.323
peak=    4.589 closest distance to " O   HOH Z 287 " =    1.733
peak=    4.513 closest distance to " CB  ARG A 275 " =    0.939
peak=    4.507 closest distance to " CB  GLN A 183 " =    1.270
peak=    4.489 closest distance to " O   PRO A 198 " =    1.528
peak=    4.453 closest distance to " CZ3 TRP A 266 " =    1.106
peak=    4.451 closest distance to " CG  PRO A 280 " =    0.808
peak=    4.436 closest distance to " CB  GLU A 277 " =    3.772
peak=    4.403 closest distance to " CA  TYR A  30 " =    0.958
peak=    4.397 closest distance to " CB  SER A  63 " =    1.078
peak=    4.396 closest distance to " CG  GLN A  58 " =    1.062
peak=    4.383 closest distance to " CG  PRO A  90 " =    1.222
peak=    4.363 closest distance to " CA  ARG A  36 " =    1.084
peak=    4.330 closest distance to " O   HOH Z 368 " =    2.193
peak=    4.252 closest distance to " O   HOH Z 232 " =    2.402
peak=    4.243 closest distance to " CZ  PHE A 218 " =    1.167
peak=    4.234 closest distance to " O   HOH Z 255 " =    0.985
peak=    4.202 closest distance to " O   HOH Z 214 " =    1.429
peak=    4.201 closest distance to " CA  ARG A 195 " =    1.274
peak=    4.189 closest distance to " O   HOH Z 298 " =    1.873
peak=    4.182 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.148 closest distance to " O   SER A  87 " =    2.328
peak=    4.140 closest distance to " CB  ARG A  79 " =    1.503
peak=    4.135 closest distance to " O   HOH Z 361 " =    3.576
peak=    4.050 closest distance to " O   HOH Z  63 " =    1.813
peak=    4.041 closest distance to " O   HOH Z 412 " =    3.824
peak=    4.031 closest distance to " CG  ARG A  66 " =    2.607
peak=    4.026 closest distance to " CA  ALA A  51 " =    1.009
peak=    4.012 closest distance to " O   HOH Z 142 " =    1.525
peak=    4.007 closest distance to " NZ  LYS A 117 " =    2.891
peak=    4.000 closest distance to " CB  GLU A 152 " =    1.146
peak=    3.991 closest distance to " O   HOH Z 346 " =    1.620
peak=    3.974 closest distance to " CZ  PHE A  38 " =    1.170
peak=    3.966 closest distance to " O   HOH Z 126 " =    1.606
peak=    3.958 closest distance to " CB  TRP A 179 " =    1.413
peak=    3.957 closest distance to " CA  ALA A 160 " =    0.904
peak=    3.943 closest distance to " NE2 GLN A  11 " =    1.130
peak=    3.912 closest distance to " CB  ASN A 148 " =    1.472
peak=    3.894 closest distance to " O   HOH Z 251 " =    1.576
peak=    3.892 closest distance to " O   HOH Z 183 " =    1.772
peak=    3.891 closest distance to " O   HOH Z 188 " =    2.705
peak=    3.871 closest distance to " OG BSER A 164 " =    2.249
peak=    3.864 closest distance to " O   HOH Z 234 " =    3.666
peak=    3.862 closest distance to " O   HOH Z 402 " =    1.468
peak=    3.859 closest distance to " CG2AVAL A 121 " =    2.167
peak=    3.853 closest distance to " ND2 ASN A 187 " =    1.497
peak=    3.849 closest distance to " O   HOH Z 406 " =    1.615
peak=    3.837 closest distance to " NH1AARG A 145 " =    1.437
peak=    3.823 closest distance to " O   HOH Z 193 " =    1.837
peak=    3.807 closest distance to " O   HOH Z  43 " =    1.734
peak=    3.787 closest distance to " O   HOH Z 193 " =    1.271
peak=    3.784 closest distance to " O   HOH Z  19 " =    1.668
peak=    3.782 closest distance to " CB  PRO A  54 " =    0.929
peak=    3.777 closest distance to " O   HOH Z 261 " =    2.397
peak=    3.771 closest distance to " CD1 LEU A  96 " =    0.813
peak=    3.769 closest distance to " O   HOH Z 365 " =    2.700
peak=    3.764 closest distance to " O   HOH Z 199 " =    1.514
peak=    3.762 closest distance to " O   HOH Z 102 " =    1.306
peak=    3.747 closest distance to " CG  PRO A 243 " =    1.038
peak=    3.738 closest distance to " CD  LYS A 166 " =    1.397
peak=    3.733 closest distance to " O   HOH Z  40 " =    1.838
peak=    3.722 closest distance to " O   HOH Z  80 " =    1.944
peak=    3.717 closest distance to " CA  MET A 105 " =    1.107
peak=    3.699 closest distance to " O   HOH Z 203 " =    1.676
peak=    3.692 closest distance to " O   HOH Z 425 " =    1.389
peak=    3.688 closest distance to " O   HOH Z 359 " =    1.752
peak=    3.687 closest distance to " CD  LYS A  76 " =    1.798
peak=    3.687 closest distance to " CB  VAL A 202 " =    1.545
peak=    3.684 closest distance to " O   HOH Z 393 " =    3.101
peak=    3.678 closest distance to " CA  VAL A 125 " =    1.220
peak=    3.676 closest distance to " O   HOH Z 290 " =    1.112
peak=    3.673 closest distance to " O   HOH Z 423 " =    1.852
peak=    3.671 closest distance to " O  BHOH Z 338 " =    2.220
peak=    3.670 closest distance to " O   HOH Z 280 " =    2.982
peak=    3.670 closest distance to " CG  PRO A 198 " =    1.308
peak=    3.668 closest distance to " O   TYR A 116 " =    1.378
peak=    3.666 closest distance to " CD  ARG A 159 " =    0.775
peak=    3.656 closest distance to " CA  TYR A 116 " =    1.272
peak=    3.654 closest distance to " O   HOH Z  35 " =    2.449
peak=    3.645 closest distance to " CA  ALA A 100 " =    0.979
peak=    3.644 closest distance to " CB  PRO A  90 " =    1.148
peak=    3.641 closest distance to " O   HOH Z 265 " =    2.012
peak=    3.638 closest distance to " O   HOH Z 361 " =    2.555
peak=    3.623 closest distance to " CG2 VAL A 197 " =    1.111
peak=    3.620 closest distance to " CE  LYS A 119 " =    1.140
peak=    3.619 closest distance to " O   HOH Z 132 " =    2.824
peak=    3.608 closest distance to " CG1 ILE A  20 " =    1.305
peak=    3.592 closest distance to " O   HOH Z 299 " =    4.490
peak=    3.583 closest distance to " O   HOH Z  78 " =    1.661
peak=    3.581 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.573 closest distance to " O   ALA A 165 " =    1.441
peak=    3.572 closest distance to " O   HOH Z 313 " =    1.930
peak=    3.570 closest distance to " CB  GLU A 128 " =    1.095
peak=    3.569 closest distance to " O   HOH Z 214 " =    3.227
peak=    3.565 closest distance to " CB  ARG A  79 " =    0.984
peak=    3.562 closest distance to " N   ARG A 156 " =    1.477
peak=    3.561 closest distance to " O   HOH Z 180 " =    2.157
peak=    3.556 closest distance to " O   HOH Z 316 " =    3.117
peak=    3.553 closest distance to " O   HOH Z 303 " =    2.336
peak=    3.544 closest distance to " O   HOH Z 353 " =    2.779
peak=    3.543 closest distance to " O   HOH Z  88 " =    3.385
peak=    3.540 closest distance to " O   HOH Z 345 " =    1.634
peak=    3.540 closest distance to " O   HOH Z 371 " =    3.051
peak=    3.536 closest distance to " CB  SER A 141 " =    1.184
peak=    3.535 closest distance to " CA  GLU A 152 " =    0.841
peak=    3.530 closest distance to " CG2 THR A 221 " =    1.198
peak=    3.527 closest distance to " O   HOH Z 214 " =    2.543
peak=    3.523 closest distance to " CB  SER A  62 " =    1.006
peak=    3.515 closest distance to " O   HOH Z 357 " =    2.108
peak=    3.513 closest distance to " O   HOH Z 427 " =    3.035
peak=    3.511 closest distance to " O   HOH Z 126 " =    1.873
peak=    3.506 closest distance to " CG2AVAL A  72 " =    1.884
peak=    3.504 closest distance to " O   HOH Z 383 " =    2.090
peak=    3.490 closest distance to " O   HOH Z 417 " =    3.078
peak=    3.487 closest distance to " O   HOH Z 247 " =    1.406
peak=    3.483 closest distance to " O   HOH Z   1 " =    2.396
peak=    3.480 closest distance to " O   HOH Z 380 " =    2.040
peak=    3.479 closest distance to " O   HOH Z 433 " =    1.462
peak=    3.475 closest distance to " CB  TYR A 169 " =    0.883
peak=    3.470 closest distance to " O   HOH Z 331 " =    1.130
peak=    3.468 closest distance to " O   HOH Z 411 " =    3.457
peak=    3.465 closest distance to " CB  PHE A 204 " =    0.868
peak=    3.464 closest distance to " O   HOH Z 368 " =    4.249
peak=    3.463 closest distance to " OH  TYR A 116 " =    1.126
peak=    3.462 closest distance to " CD1 ILE A 199 " =    1.274
peak=    3.462 closest distance to " CB  THR A  52 " =    0.790
peak=    3.459 closest distance to " CG AARG A 275 " =    1.310
peak=    3.458 closest distance to " O   HOH Z 227 " =    1.532
peak=    3.452 closest distance to " O   HOH Z 148 " =    3.492
peak=    3.450 closest distance to " N   ASN A  39 " =    1.324
peak=    3.449 closest distance to " O   HOH Z 325 " =    2.146
peak=    3.449 closest distance to " CB  ASN A 285 " =    0.977
peak=    3.447 closest distance to " O   HOH Z  47 " =    2.211
peak=    3.446 closest distance to " CA  ALA A 295 " =    0.982
peak=    3.436 closest distance to " CG2 ILE A  20 " =    1.291
peak=    3.436 closest distance to " O   HOH Z 131 " =    2.523
peak=    3.431 closest distance to " CB  THR A  31 " =    1.577
peak=    3.430 closest distance to " O   HOH Z 285 " =    2.333
peak=    3.428 closest distance to " O   HOH Z 250 " =    1.313
peak=    3.426 closest distance to " O   THR A 220 " =    1.157
peak=    3.424 closest distance to " O   THR A 182 " =    1.545
peak=    3.423 closest distance to " O   HOH Z 273 " =    1.112
peak=    3.423 closest distance to " CG  GLN A  11 " =    1.450
peak=    3.421 closest distance to " CA  ASP A 162 " =    1.081
peak=    3.419 closest distance to " O   HOH Z 209 " =    2.233
peak=    3.418 closest distance to " O   HOH Z  20 " =    1.258
peak=    3.417 closest distance to " O   HOH Z 298 " =    2.323
peak=    3.414 closest distance to " O   HOH Z 366 " =    2.429
peak=    3.413 closest distance to " O   HOH Z 117 " =    1.980
peak=    3.410 closest distance to " O   HOH Z 258 " =    1.993
peak=    3.410 closest distance to " CG  MET A 185 " =    1.143
peak=    3.409 closest distance to " CD  PRO A  54 " =    1.007
peak=    3.407 closest distance to " CB  LYS A 117 " =    1.149
peak=    3.407 closest distance to " O   HOH Z  15 " =    2.149
peak=    3.405 closest distance to " O   HOH Z 291 " =    1.378
peak=    3.404 closest distance to " N   TYR A 116 " =    1.612
peak=    3.402 closest distance to " O   HOH Z 132 " =    2.779
peak=    3.400 closest distance to " OG  SER A 245 " =    1.591
peak=    3.400 closest distance to " CG1 ILE A  33 " =    1.182
peak=    3.396 closest distance to " N   CYS A 260 " =    0.945
peak=    3.393 closest distance to " O   ALA A 158 " =    1.150
peak=    3.391 closest distance to " O   HOH Z 271 " =    2.502
peak=    3.388 closest distance to " O   HOH Z 420 " =    5.656
peak=    3.382 closest distance to " CB  SER A  26 " =    1.849
peak=    3.381 closest distance to " CB  ASN A 142 " =    1.117
peak=    3.381 closest distance to " O   HOH Z 285 " =    2.090
peak=    3.378 closest distance to " OG  SER A 135 " =    1.273
peak=    3.377 closest distance to " CG  ARG A 138 " =    1.358
peak=    3.376 closest distance to " NH2AARG A 275 " =    3.316
peak=    3.372 closest distance to " CG2 ILE A 120 " =    1.319
peak=    3.368 closest distance to " O   HOH Z 278 " =    0.789
peak=    3.367 closest distance to " O   HOH Z 132 " =    1.027
peak=    3.366 closest distance to " O   HOH Z 126 " =    1.569
peak=    3.363 closest distance to " CE  LYS A  76 " =    0.901
peak=    3.360 closest distance to " O   HOH Z 392 " =    2.380
peak=    3.358 closest distance to " O   HOH Z 391 " =    3.006
peak=    3.358 closest distance to " CB  VAL A 265 " =    1.242
peak=    3.355 closest distance to " CB  MET A  40 " =    1.032
peak=    3.354 closest distance to " O   HOH Z 134 " =    1.231
peak=    3.352 closest distance to " O   HOH Z 170 " =    2.240
peak=    3.348 closest distance to " O   HOH Z 394 " =    1.559
peak=    3.342 closest distance to " CD2 LEU A  83 " =    1.434
peak=    3.342 closest distance to " OE1 GLN A  55 " =    1.465
peak=    3.341 closest distance to " O   HOH Z 147 " =    1.670
peak=    3.341 closest distance to " CE1 HIS A  81 " =    1.637
peak=    3.339 closest distance to " O   HOH Z  62 " =    2.229
peak=    3.339 closest distance to " CB  LEU A  83 " =    0.784
peak=    3.339 closest distance to " O   HOH Z  54 " =    1.037
peak=    3.338 closest distance to " OG  SER A  28 " =    1.584
peak=    3.337 closest distance to " ND2 ASN A 249 " =    0.909
peak=    3.332 closest distance to " NE2 GLN A  77 " =    3.115
peak=    3.330 closest distance to " O   LEU A 228 " =    1.879
peak=    3.327 closest distance to " O   HOH Z 189 " =    2.672
peak=    3.327 closest distance to " O   HOH Z  63 " =    2.202
peak=    3.327 closest distance to " O   HOH Z 128 " =    1.459
peak=    3.324 closest distance to " CG1 ILE A  49 " =    1.555
peak=    3.318 closest distance to " O   HOH Z 213 " =    1.920
peak=    3.317 closest distance to " OG BSER A 134 " =    2.832
peak=    3.317 closest distance to " CA  ALA A 158 " =    1.323
peak=    3.313 closest distance to " OD2 ASP A  50 " =    2.940
peak=    3.304 closest distance to " NH2BARG A 145 " =    2.237
peak=    3.299 closest distance to " CE1 HIS A  81 " =    1.767
peak=    3.295 closest distance to " CB  ASP A 124 " =    0.735
peak=    3.291 closest distance to " CD  ARG A  66 " =    2.631
peak=    3.290 closest distance to " O   HOH Z 394 " =    3.861
peak=    3.289 closest distance to " O   HOH Z  97 " =    2.138
peak=    3.288 closest distance to " CG2 ILE A 234 " =    1.065
peak=    3.288 closest distance to " CA  SER A  32 " =    1.626
peak=    3.284 closest distance to " CA  ASP A 140 " =    1.662
peak=    3.282 closest distance to " CB  ASN A 215 " =    1.259
peak=    3.277 closest distance to " O   HOH Z 141 " =    1.640
peak=    3.276 closest distance to " CB  PRO A 198 " =    1.238
peak=    3.272 closest distance to " CG1 VAL A 153 " =    1.124
peak=    3.272 closest distance to " O   HOH Z  85 " =    1.234
peak=    3.270 closest distance to " CB  TRP A 266 " =    1.070
peak=    3.269 closest distance to " CA  LEU A 101 " =    1.377
peak=    3.266 closest distance to " CB  GLU A  46 " =    1.005
peak=    3.263 closest distance to " CG  MET A 188 " =    0.891
peak=    3.260 closest distance to " CB  SER A   3 " =    1.511
peak=    3.260 closest distance to " CB  ARG A 138 " =    0.836
peak=    3.256 closest distance to " O   HOH Z  21 " =    1.868
peak=    3.252 closest distance to " O   HOH Z 371 " =    1.534
peak=    3.251 closest distance to " OG  SER A  22 " =    2.680
peak=    3.249 closest distance to " NE2 GLN A  58 " =    4.974
peak=    3.245 closest distance to " CA  GLY A  35 " =    0.912
peak=    3.243 closest distance to " O   HOH Z 389 " =    1.880
peak=    3.236 closest distance to " CB  ALA A  43 " =    0.796
peak=    3.232 closest distance to " OG BSER A  99 " =    2.338
peak=    3.232 closest distance to " CA  GLY A 267 " =    1.152
peak=    3.231 closest distance to " O   HOH Z 411 " =    1.670
peak=    3.227 closest distance to " CA  ARG A 102 " =    1.044
peak=    3.225 closest distance to " CA  ALA A 291 " =    0.767
peak=    3.222 closest distance to " CZ3 TRP A  85 " =    0.874
peak=    3.220 closest distance to " CA  GLY A   6 " =    0.872
peak=    3.219 closest distance to " CA  ALA A 154 " =    1.109
peak=    3.219 closest distance to " O   HOH Z 185 " =    1.718
peak=    3.217 closest distance to " CA  MET A 188 " =    1.006
peak=    3.212 closest distance to " CG1BVAL A  72 " =    3.166
peak=    3.210 closest distance to " O   HOH Z 305 " =    3.538
peak=    3.205 closest distance to " O   CYS A 168 " =    1.204
peak=    3.201 closest distance to " O   HOH Z 395 " =    3.112
peak=    3.198 closest distance to " CB  GLN A  88 " =    1.153
peak=    3.191 closest distance to " OG  SER A  22 " =    2.473
peak=    3.181 closest distance to " CB  ASN A 148 " =    2.020
peak=    3.179 closest distance to " CE3 TRP A 150 " =    1.124
peak=    3.179 closest distance to " O   ASP A 191 " =    1.585
peak=    3.177 closest distance to " O   HOH Z 213 " =    2.758
peak=    3.177 closest distance to " CG BARG A 275 " =    1.513
peak=    3.176 closest distance to " CA  SER A  87 " =    0.998
peak=    3.176 closest distance to " N   ALA A   1 " =    2.173
peak=    3.173 closest distance to " CB  ALA A  10 " =    1.154
peak=    3.171 closest distance to " O   HOH Z 327 " =    2.678
peak=    3.171 closest distance to " CG  ARG A 219 " =    1.147
peak=    3.165 closest distance to " O   HOH Z 173 " =    1.977
peak=    3.165 closest distance to " O   HOH Z 345 " =    3.682
peak=    3.158 closest distance to " O   HOH Z 162 " =    1.678
peak=    3.158 closest distance to " CE1 PHE A 218 " =    1.166
peak=    3.155 closest distance to " CB  ALA A 248 " =    1.485
peak=    3.154 closest distance to " O   HOH Z 258 " =    1.803
peak=    3.153 closest distance to " OD1 ASN A  69 " =    2.510
peak=    3.152 closest distance to " O   HOH Z 188 " =    1.416
peak=    3.151 closest distance to " O   HOH Z 327 " =    1.486
peak=    3.150 closest distance to " CB  ASP A 140 " =    1.160
peak=    3.149 closest distance to " OE1 GLN A 223 " =    2.381
peak=    3.140 closest distance to " O   ASP A 124 " =    1.734
peak=    3.138 closest distance to " CB  SER A 271 " =    1.312
peak=    3.133 closest distance to " OD1 ASN A 217 " =    1.660
peak=    3.131 closest distance to " OE2 GLU A  53 " =    2.016
peak=    3.130 closest distance to " CE1 TYR A  30 " =    1.054
peak=    3.127 closest distance to " O   HOH Z  83 " =    1.557
peak=    3.124 closest distance to " O   HOH Z 150 " =    1.087
peak=    3.123 closest distance to " CA  LEU A  83 " =    1.209
peak=    3.117 closest distance to " O   HOH Z 298 " =    4.199
peak=    3.112 closest distance to " CG  MET A 185 " =    1.016
peak=    3.111 closest distance to " CA  LYS A 117 " =    1.251
peak=    3.107 closest distance to " N   TYR A 247 " =    1.349
peak=    3.107 closest distance to " O   HOH Z  48 " =    1.711
peak=    3.106 closest distance to " CB  ARG A 156 " =    1.201
peak=    3.103 closest distance to " CG  LEU A 167 " =    1.228
peak=    3.102 closest distance to " CG  GLU A  37 " =    1.004
peak=    3.096 closest distance to " O   HOH Z 183 " =    1.844
peak=    3.091 closest distance to " CB  ASP A 191 " =    1.193
peak=    3.081 closest distance to " O   HOH Z 336 " =    1.847
peak=    3.065 closest distance to " CB  ALA A   1 " =    4.984
peak=    3.057 closest distance to " CA  GLY A 211 " =    1.388
peak=    3.051 closest distance to " O   HOH Z 162 " =    1.546
peak=    3.044 closest distance to " N   TRP A 150 " =    1.095
peak=    3.034 closest distance to " CA  ALA A 248 " =    1.208
peak=    3.027 closest distance to " CA  GLY A 133 " =    3.712

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.785 - 5.978
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 205
   mapped sites are within: 0.785 - 5.978

peak=   -4.956 closest distance to " CD  ARG A  14 " =    3.476
peak=   -4.723 closest distance to " O   PRO A 198 " =    1.402
peak=   -4.602 closest distance to " CG2 ILE A  49 " =    2.806
peak=   -4.570 closest distance to " O   VAL A  67 " =    2.915
peak=   -4.493 closest distance to " CG  GLN A  58 " =    1.020
peak=   -4.436 closest distance to " O   HOH Z 377 " =    2.075
peak=   -4.407 closest distance to " CE2 PHE A  61 " =    2.731
peak=   -4.336 closest distance to " CG1 VAL A 250 " =    2.716
peak=   -4.250 closest distance to " CD2 TYR A 293 " =    1.905
peak=   -4.244 closest distance to " CB  PRO A 243 " =    2.731
peak=   -4.242 closest distance to " O   HOH Z 193 " =    0.906
peak=   -4.230 closest distance to " O   HOH Z 266 " =    5.650
peak=   -4.230 closest distance to " CE  MET A 105 " =    2.858
peak=   -4.106 closest distance to " CG2 ILE A  20 " =    3.002
peak=   -4.091 closest distance to " O   HOH Z 278 " =    1.054
peak=   -4.069 closest distance to " O   HOH Z 166 " =    1.655
peak=   -4.056 closest distance to " O  BHOH Z  74 " =    0.785
peak=   -4.054 closest distance to " CD  ARG A 156 " =    2.204
peak=   -4.018 closest distance to " CD1 LEU A 101 " =    2.389
peak=   -3.992 closest distance to " CD  GLN A 223 " =    1.549
peak=   -3.981 closest distance to " OG  SER A  97 " =    2.156
peak=   -3.967 closest distance to " CB  ALA A  43 " =    2.590
peak=   -3.958 closest distance to " C   HIS A 108 " =    1.102
peak=   -3.929 closest distance to " CG  PRO A 243 " =    1.714
peak=   -3.916 closest distance to " O   HOH Z  10 " =    1.607
peak=   -3.898 closest distance to " N   ALA A  43 " =    2.723
peak=   -3.897 closest distance to " O   HOH Z 211 " =    1.180
peak=   -3.896 closest distance to " O   HOH Z 196 " =    2.155
peak=   -3.892 closest distance to " CE3 TRP A 150 " =    2.296
peak=   -3.883 closest distance to " CD2 PHE A  61 " =    2.192
peak=   -3.866 closest distance to " OXT GLY A 302 " =    3.067
peak=   -3.858 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.857 closest distance to " O   PRO A 163 " =    2.116
peak=   -3.849 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -3.839 closest distance to " CA  GLY A 241 " =    2.398
peak=   -3.832 closest distance to " CD1 PHE A  59 " =    2.065
peak=   -3.824 closest distance to " O   HOH Z 150 " =    2.050
peak=   -3.803 closest distance to " O   HOH Z 198 " =    1.480
peak=   -3.798 closest distance to " CG  GLN A  11 " =    1.548
peak=   -3.790 closest distance to " O   HOH Z  52 " =    1.160
peak=   -3.781 closest distance to " O   HOH Z 106 " =    1.907
peak=   -3.779 closest distance to " CA  GLY A 241 " =    3.234
peak=   -3.766 closest distance to " O   HOH Z 374 " =    2.022
peak=   -3.764 closest distance to " O   HOH Z  68 " =    1.682
peak=   -3.761 closest distance to " ND2BASN A 224 " =    1.902
peak=   -3.734 closest distance to " O   HOH Z  13 " =    1.951
peak=   -3.729 closest distance to " CB  ASP A 132 " =    2.348
peak=   -3.691 closest distance to " CG1AVAL A  41 " =    2.632
peak=   -3.678 closest distance to " O   HOH Z 283 " =    2.506
peak=   -3.675 closest distance to " CD1 LEU A 222 " =    2.571
peak=   -3.668 closest distance to " CG2 VAL A 189 " =    2.097
peak=   -3.667 closest distance to " O   ALA A 256 " =    1.727
peak=   -3.662 closest distance to " O   HOH Z 366 " =    1.650
peak=   -3.649 closest distance to " O   ALA A  34 " =    2.542
peak=   -3.648 closest distance to " O   HOH Z   6 " =    1.520
peak=   -3.646 closest distance to " ND2 ASN A  45 " =    1.899
peak=   -3.641 closest distance to " CB  HIS A  86 " =    1.178
peak=   -3.640 closest distance to " OD1 ASP A 171 " =    1.645
peak=   -3.635 closest distance to " CD1 LEU A  25 " =    2.529
peak=   -3.624 closest distance to " O   HOH Z 216 " =    0.945
peak=   -3.618 closest distance to " NE2 GLN A 278 " =    1.476
peak=   -3.610 closest distance to " O   TRP A  92 " =    1.962
peak=   -3.609 closest distance to " OE1 GLN A 223 " =    2.249
peak=   -3.603 closest distance to " O   SER A 210 " =    1.825
peak=   -3.601 closest distance to " CE2 TYR A  30 " =    2.770
peak=   -3.601 closest distance to " O   HOH Z 149 " =    1.988
peak=   -3.592 closest distance to " OG BSER A 134 " =    1.330
peak=   -3.589 closest distance to " O   HOH Z 348 " =    2.233
peak=   -3.589 closest distance to " CG  GLU A  53 " =    1.582
peak=   -3.583 closest distance to " O   HOH Z 421 " =    3.987
peak=   -3.568 closest distance to " O   HOH Z 128 " =    2.721
peak=   -3.555 closest distance to " O   HOH Z 252 " =    3.738
peak=   -3.550 closest distance to " O   HOH Z 191 " =    5.978
peak=   -3.549 closest distance to " CH2 TRP A 179 " =    1.263
peak=   -3.536 closest distance to " O   HOH Z 156 " =    3.531
peak=   -3.525 closest distance to " CH2 TRP A 150 " =    1.219
peak=   -3.513 closest distance to " O   TYR A 186 " =    1.876
peak=   -3.508 closest distance to " CZ  PHE A  38 " =    2.293
peak=   -3.507 closest distance to " O   HOH Z 154 " =    1.509
peak=   -3.505 closest distance to " CD  GLN A  88 " =    0.900
peak=   -3.501 closest distance to " NE2 GLN A  88 " =    1.906
peak=   -3.496 closest distance to " O   HOH Z 165 " =    1.967
peak=   -3.491 closest distance to " CG  GLN A 103 " =    2.527
peak=   -3.490 closest distance to " CA  GLY A 241 " =    3.011
peak=   -3.489 closest distance to " CE BMET A  47 " =    1.663
peak=   -3.484 closest distance to " O   HOH Z  64 " =    1.361
peak=   -3.479 closest distance to " OE1 GLN A 223 " =    2.162
peak=   -3.476 closest distance to " O   HOH Z 174 " =    2.364
peak=   -3.461 closest distance to " C   ASN A 285 " =    2.292
peak=   -3.458 closest distance to " O   HOH Z   6 " =    1.784
peak=   -3.456 closest distance to " CA  GLY A 203 " =    2.385
peak=   -3.455 closest distance to " O   HOH Z 285 " =    1.606
peak=   -3.455 closest distance to " CG2 THR A 182 " =    2.226
peak=   -3.447 closest distance to " CZ  TYR A 169 " =    1.900
peak=   -3.447 closest distance to " C   LEU A 143 " =    1.140
peak=   -3.444 closest distance to " O   HOH Z 131 " =    4.219
peak=   -3.440 closest distance to " O   HOH Z  88 " =    2.071
peak=   -3.439 closest distance to " NE2 GLN A  88 " =    1.165
peak=   -3.434 closest distance to " CG1 VAL A 112 " =    2.577
peak=   -3.433 closest distance to " O   HOH Z 244 " =    1.420
peak=   -3.430 closest distance to " O   GLN A 240 " =    2.694
peak=   -3.429 closest distance to " O   HOH Z 166 " =    1.593
peak=   -3.415 closest distance to " O   HOH Z 264 " =    1.816
peak=   -3.415 closest distance to " CG  ARG A 269 " =    2.242
peak=   -3.412 closest distance to " OE2 GLU A 152 " =    1.446
peak=   -3.411 closest distance to " CB  ALA A 184 " =    2.375
peak=   -3.403 closest distance to " NE2 HIS A 108 " =    1.909
peak=   -3.394 closest distance to " CD2 HIS A 207 " =    2.178
peak=   -3.377 closest distance to " O   HOH Z 418 " =    1.314
peak=   -3.370 closest distance to " O   HOH Z 171 " =    2.479
peak=   -3.368 closest distance to " CD2 LEU A 282 " =    2.124
peak=   -3.368 closest distance to " O   HOH Z 424 " =    2.991
peak=   -3.364 closest distance to " O   SER A 276 " =    1.703
peak=   -3.362 closest distance to " O   HOH Z 113 " =    1.690
peak=   -3.362 closest distance to " O   HOH Z 393 " =    1.316
peak=   -3.348 closest distance to " CB  ALA A  10 " =    2.245
peak=   -3.338 closest distance to " CD2 PHE A 192 " =    2.113
peak=   -3.338 closest distance to " O   TRP A  70 " =    1.588
peak=   -3.337 closest distance to " O   HOH Z 133 " =    1.364
peak=   -3.335 closest distance to " OD1 ASP A 191 " =    1.608
peak=   -3.334 closest distance to " O   HOH Z 221 " =    1.238
peak=   -3.331 closest distance to " O   ALA A  10 " =    1.914
peak=   -3.319 closest distance to " CB  ALA A 129 " =    2.356
peak=   -3.316 closest distance to " CB  TRP A  85 " =    2.478
peak=   -3.315 closest distance to " O   HOH Z 275 " =    1.457
peak=   -3.315 closest distance to " CD2 TYR A 247 " =    2.458
peak=   -3.314 closest distance to " O   HOH Z 407 " =    3.005
peak=   -3.312 closest distance to " N   THR A  52 " =    1.714
peak=   -3.308 closest distance to " OD2 ASP A 191 " =    1.491
peak=   -3.307 closest distance to " O   HOH Z 351 " =    1.745
peak=   -3.306 closest distance to " CG  ASN A 148 " =    2.418
peak=   -3.304 closest distance to " CB  ASP A 171 " =    2.452
peak=   -3.295 closest distance to " O   HOH Z 340 " =    1.890
peak=   -3.293 closest distance to " CZ  ARG A 156 " =    2.744
peak=   -3.289 closest distance to " O   HOH Z 102 " =    1.526
peak=   -3.288 closest distance to " O   HOH Z  78 " =    1.980
peak=   -3.283 closest distance to " CD  LYS A 289 " =    2.317
peak=   -3.282 closest distance to " O   HOH Z 148 " =    3.844
peak=   -3.281 closest distance to " NH2 ARG A  79 " =    2.306
peak=   -3.280 closest distance to " CB  ALA A 291 " =    2.396
peak=   -3.275 closest distance to " O   HOH Z 345 " =    2.925
peak=   -3.266 closest distance to " O   VAL A 257 " =    1.378
peak=   -3.264 closest distance to " O   HOH Z  19 " =    2.344
peak=   -3.264 closest distance to " O   ALA A 161 " =    1.854
peak=   -3.262 closest distance to " O   HOH Z 357 " =    2.223
peak=   -3.261 closest distance to " O   HOH Z   9 " =    2.431
peak=   -3.261 closest distance to " O   HOH Z 215 " =    1.117
peak=   -3.261 closest distance to " O   ILE A 263 " =    2.249
peak=   -3.255 closest distance to " CD1 TRP A  70 " =    1.086
peak=   -3.254 closest distance to " O   HOH Z 185 " =    2.358
peak=   -3.254 closest distance to " O   GLU A 152 " =    1.436
peak=   -3.250 closest distance to " O   HOH Z 281 " =    2.515
peak=   -3.249 closest distance to " CB  ALA A 161 " =    2.580
peak=   -3.249 closest distance to " CG  PHE A 283 " =    2.603
peak=   -3.248 closest distance to " O   HOH Z 287 " =    1.932
peak=   -3.246 closest distance to " C   SER A 206 " =    1.505
peak=   -3.243 closest distance to " O   HOH Z  43 " =    1.556
peak=   -3.233 closest distance to " CB  ALA A   9 " =    2.511
peak=   -3.230 closest distance to " ND2 ASN A 249 " =    2.187
peak=   -3.219 closest distance to " CG1 VAL A 265 " =    2.699
peak=   -3.218 closest distance to " CD  ARG A 195 " =    5.128
peak=   -3.218 closest distance to " CG  GLN A  58 " =    1.311
peak=   -3.217 closest distance to " O   VAL A 189 " =    1.784
peak=   -3.216 closest distance to " O   HOH Z  37 " =    1.902
peak=   -3.215 closest distance to " CB  SER A  62 " =    5.601
peak=   -3.212 closest distance to " CB  PHE A  16 " =    2.431
peak=   -3.211 closest distance to " O   ILE A 106 " =    1.819
peak=   -3.211 closest distance to " CD  ARG A  79 " =    1.208
peak=   -3.205 closest distance to " CD2 PHE A 225 " =    1.308
peak=   -3.202 closest distance to " CB  GLU A 277 " =    1.344
peak=   -3.201 closest distance to " O   HOH Z 259 " =    4.045
peak=   -3.193 closest distance to " C   ALA A   8 " =    1.705
peak=   -3.192 closest distance to " O   HOH Z 389 " =    1.761
peak=   -3.182 closest distance to " O   HOH Z  55 " =    1.918
peak=   -3.181 closest distance to " O   HOH Z 234 " =    4.394
peak=   -3.176 closest distance to " CD  PRO A 243 " =    2.042
peak=   -3.174 closest distance to " NH2 ARG A  66 " =    1.144
peak=   -3.171 closest distance to " O   HOH Z 145 " =    3.103
peak=   -3.169 closest distance to " O   HOH Z  63 " =    1.358
peak=   -3.163 closest distance to " OE1 GLN A  88 " =    0.908
peak=   -3.162 closest distance to " OD2 ASP A 270 " =    1.148
peak=   -3.154 closest distance to " CA  ASP A  65 " =    1.392
peak=   -3.154 closest distance to " CE1 HIS A  81 " =    1.612
peak=   -3.152 closest distance to " CG  LEU A  83 " =    2.103
peak=   -3.151 closest distance to " CB  ASN A  45 " =    2.072
peak=   -3.147 closest distance to " CZ3 TRP A 274 " =    2.332
peak=   -3.147 closest distance to " OD1 ASN A 148 " =    1.382
peak=   -3.144 closest distance to " O   HOH Z 174 " =    3.595
peak=   -3.137 closest distance to " O   GLY A  80 " =    2.613
peak=   -3.133 closest distance to " O   HOH Z  38 " =    1.921
peak=   -3.128 closest distance to " CG1 VAL A  78 " =    2.639
peak=   -3.126 closest distance to " CG1BVAL A  41 " =    2.816
peak=   -3.125 closest distance to " O   SER A   3 " =    1.115
peak=   -3.119 closest distance to " O   HOH Z  52 " =    2.132
peak=   -3.119 closest distance to " CB  ALA A 248 " =    2.257
peak=   -3.116 closest distance to " N   ALA A 226 " =    1.936
peak=   -3.112 closest distance to " OE1 GLN A 183 " =    1.551
peak=   -3.110 closest distance to " CG  ASP A 286 " =    1.567
peak=   -3.109 closest distance to " CA  PRO A 243 " =    2.389
peak=   -3.100 closest distance to " O   HOH Z 265 " =    2.465
peak=   -3.099 closest distance to " OD1 ASN A 187 " =    1.631
peak=   -3.094 closest distance to " NE2 GLN A 223 " =    1.216
peak=   -3.074 closest distance to " OG BSER A 134 " =    1.894
peak=   -3.064 closest distance to " CA  GLY A 133 " =    2.063
peak=   -3.058 closest distance to " OD2 ASP A 171 " =    1.808

================= 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    :  0.4533 0.4494   6.260667e+00   6.245128e+00
   1_bss:  0.4435 0.4366   6.252273e+00   6.233363e+00
   1_xyz:  0.3026 0.3266   5.959470e+00   6.038537e+00
   1_adp:  0.2736 0.3361   5.909753e+00   6.056434e+00
   1_occ:  0.2733 0.3362   5.909954e+00   6.057641e+00
   2_bss:  0.2702 0.3352   5.906215e+00   6.056588e+00
   2_xyz:  0.2005 0.2560   5.645375e+00   5.836538e+00
   2_adp:  0.1898 0.2385   5.593025e+00   5.779320e+00
   2_occ:  0.1895 0.2385   5.592651e+00   5.779379e+00
   3_bss:  0.1897 0.2376   5.592274e+00   5.777497e+00
   3_xyz:  0.1518 0.1952   5.399098e+00   5.600786e+00
   3_adp:  0.1402 0.1907   5.346793e+00   5.567316e+00
   3_occ:  0.1402 0.1907   5.346435e+00   5.567014e+00
   4_bss:  0.1404 0.1908   5.347353e+00   5.567129e+00
   4_xyz:  0.1270 0.1763   5.262578e+00   5.494271e+00
   4_adp:  0.1248 0.1727   5.244218e+00   5.472737e+00
   4_occ:  0.1247 0.1726   5.243829e+00   5.472343e+00
   5_bss:  0.1245 0.1723   5.243904e+00   5.472357e+00
   5_xyz:  0.1180 0.1686   5.208640e+00   5.450373e+00
   5_adp:  0.1171 0.1690   5.206797e+00   5.452194e+00
   5_occ:  0.1170 0.1690   5.206699e+00   5.452118e+00
   5_bss:  0.1170 0.1688   5.206864e+00   5.452299e+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:  0.306  50.000  -2.908   1.584   4.645   0.000   0.000   0.000
   1_xyz:  0.306  50.000  -2.908   1.584   4.645   0.000   0.000   0.000
   1_adp:  0.306  50.000  -2.908   1.584   4.645   0.000   0.000   0.000
   1_occ:  0.306  50.000  -2.908   1.584   4.645   0.000   0.000   0.000
   2_bss:  0.333  72.517  -2.399  -0.090   1.546  -0.000   0.000   0.000
   2_xyz:  0.333  72.517  -2.399  -0.090   1.546  -0.000   0.000   0.000
   2_adp:  0.333  72.517  -2.399  -0.090   1.546  -0.000   0.000   0.000
   2_occ:  0.333  72.517  -2.399  -0.090   1.546  -0.000   0.000   0.000
   3_bss:  0.337  71.784  -2.697  -1.072   0.360  -0.000   0.000   0.000
   3_xyz:  0.337  71.784  -2.697  -1.072   0.360  -0.000   0.000   0.000
   3_adp:  0.337  71.784  -2.697  -1.072   0.360  -0.000   0.000   0.000
   3_occ:  0.337  71.784  -2.697  -1.072   0.360  -0.000   0.000   0.000
   4_bss:  0.338  82.448  -2.830  -1.488  -0.116  -0.000  -0.000  -0.000
   4_xyz:  0.338  82.448  -2.830  -1.488  -0.116  -0.000  -0.000  -0.000
   4_adp:  0.338  82.448  -2.830  -1.488  -0.116  -0.000  -0.000  -0.000
   4_occ:  0.338  82.448  -2.830  -1.488  -0.116  -0.000  -0.000  -0.000
   5_bss:  0.331  72.107  -2.432  -1.297   0.131  -0.000   0.000   0.000
   5_xyz:  0.331  72.107  -2.432  -1.297   0.131  -0.000   0.000   0.000
   5_adp:  0.331  72.107  -2.432  -1.297   0.131  -0.000   0.000   0.000
   5_occ:  0.331  72.107  -2.432  -1.297   0.131  -0.000   0.000   0.000
   5_bss:  0.328  69.529  -2.207  -1.150   0.246  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.408 0.4906  0.6403    60118.052
   1_bss:  50.845 0.5090  0.6932    56706.670
   1_xyz:  35.112 0.7003  0.9135    29734.518
   1_adp:  36.326 0.6854  0.8966    31369.291
   1_occ:  36.404 0.6845  0.8953    31500.427
   2_bss:  35.950 0.6899  0.8627    31128.722
   2_xyz:  25.963 0.8005  0.9608    17142.166
   2_adp:  23.728 0.8248  0.9720    15016.408
   2_occ:  23.737 0.8247  0.9718    15028.080
   3_bss:  23.633 0.8257  0.9458    14932.565
   3_xyz:  18.810 0.8729  0.9762    10002.930
   3_adp:  18.018 0.8803  0.9708     9436.350
   3_occ:  18.005 0.8804  0.9709     9430.548
   4_bss:  17.982 0.8807  0.9595     9429.312
   4_xyz:  16.430 0.8944  0.9644     8017.842
   4_adp:  15.894 0.8994  0.9571     7695.015
   4_occ:  15.883 0.8995  0.9572     7689.898
   5_bss:  15.890 0.8995  0.9666     7688.924
   5_xyz:  15.437 0.9033  0.9699     7346.633
   5_adp:  15.448 0.9033  0.9608     7376.331
   5_occ:  15.444 0.9034  0.9607     7375.958
   5_bss:  15.451 0.9033  0.9662     7378.583
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.7929e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.7929e-01
   1_xyz:   1.620  0.012  0.099 15.788  0.007  4.116   1.3625e-01
   1_adp:   1.620  0.012  0.099 15.788  0.007  4.116   1.3625e-01
   1_occ:   1.620  0.012  0.099 15.788  0.007  4.116   1.3625e-01
   2_bss:   1.620  0.012  0.099 15.788  0.007  4.116   1.3625e-01
   2_xyz:   1.117  0.008  0.078 14.636  0.005  4.130   7.1942e-02
   2_adp:   1.117  0.008  0.078 14.636  0.005  4.130   7.1942e-02
   2_occ:   1.117  0.008  0.078 14.636  0.005  4.130   7.1942e-02
   3_bss:   1.117  0.008  0.078 14.636  0.005  4.130   7.1942e-02
   3_xyz:   1.035  0.008  0.073 14.438  0.004  4.129   6.1261e-02
   3_adp:   1.035  0.008  0.073 14.438  0.004  4.129   6.1261e-02
   3_occ:   1.035  0.008  0.073 14.438  0.004  4.129   6.1261e-02
   4_bss:   1.035  0.008  0.073 14.438  0.004  4.129   6.1261e-02
   4_xyz:   1.067  0.009  0.079 14.505  0.004  4.138   6.4353e-02
   4_adp:   1.067  0.009  0.079 14.505  0.004  4.138   6.4353e-02
   4_occ:   1.067  0.009  0.079 14.505  0.004  4.138   6.4353e-02
   5_bss:   1.067  0.009  0.079 14.505  0.004  4.138   6.4353e-02
   5_xyz:   1.217  0.012  0.091 14.572  0.004  4.114   8.4569e-02
   5_adp:   1.217  0.012  0.091 14.572  0.004  4.114   8.4569e-02
   5_occ:   1.217  0.012  0.091 14.572  0.004  4.114   8.4569e-02
   5_bss:   1.217  0.012  0.091 14.572  0.004  4.114   8.4569e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.413   2.4443e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.413   2.4443e-01
   1_xyz:  10.701  0.078  0.347 85.956  0.049  1.890   1.2762e-01
   1_adp:  10.701  0.078  0.347 85.956  0.049  1.890   1.2762e-01
   1_occ:  10.701  0.078  0.347 85.956  0.049  1.890   1.2762e-01
   2_bss:  10.701  0.078  0.347 85.956  0.049  1.890   1.2762e-01
   2_xyz:   7.235  0.047  0.297 81.524  0.056  2.268   1.1993e-01
   2_adp:   7.235  0.047  0.297 81.524  0.056  2.268   1.1993e-01
   2_occ:   7.235  0.047  0.297 81.524  0.056  2.268   1.1993e-01
   3_bss:   7.235  0.047  0.297 81.524  0.056  2.268   1.1993e-01
   3_xyz:   7.640  0.058  0.231 81.824  0.036  2.291   4.3721e-02
   3_adp:   7.640  0.058  0.231 81.824  0.036  2.291   4.3721e-02
   3_occ:   7.640  0.058  0.231 81.824  0.036  2.291   4.3721e-02
   4_bss:   7.640  0.058  0.231 81.824  0.036  2.291   4.3721e-02
   4_xyz:   7.834  0.050  0.261 83.041  0.035  2.282   4.6861e-02
   4_adp:   7.834  0.050  0.261 83.041  0.035  2.282   4.6861e-02
   4_occ:   7.834  0.050  0.261 83.041  0.035  2.282   4.6861e-02
   5_bss:   7.834  0.050  0.261 83.041  0.035  2.282   4.6861e-02
   5_xyz:   8.765  0.059  0.337 82.224  0.031  2.267   6.0480e-02
   5_adp:   8.765  0.059  0.337 82.224  0.031  2.267   6.0480e-02
   5_occ:   8.765  0.059  0.337 82.224  0.031  2.267   6.0480e-02
   5_bss:   8.765  0.059  0.337 82.224  0.031  2.267   6.0480e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  99.65   0.00  18.36  86.37   0.00  14.11  99.65   1.11  41.50
   1_occ:  99.65   0.00  18.36  86.37   0.00  14.11  99.65   1.11  41.50
   2_bss:  99.65   0.00  18.36  86.37   0.00  14.11  99.65   1.11  41.50
   2_xyz:  99.65   0.00  18.36  86.37   0.00  14.11  99.65   1.11  41.50
   2_adp:  99.26   0.00  17.93  84.88   0.00  13.62  99.26   4.67  41.43
   2_occ:  99.26   0.00  17.93  84.88   0.00  13.62  99.26   4.67  41.43
   3_bss:  99.26   0.00  17.93  84.88   0.00  13.62  99.26   4.67  41.43
   3_xyz:  99.26   0.00  17.93  84.88   0.00  13.62  99.26   4.67  41.43
   3_adp: 103.96   0.40  18.35  91.86   0.40  13.31 103.96   5.73  45.80
   3_occ: 103.96   0.40  18.35  91.86   0.40  13.31 103.96   5.73  45.80
   4_bss: 103.96   0.40  18.35  91.86   0.40  13.31 103.96   5.73  45.80
   4_xyz: 103.96   0.40  18.35  91.86   0.40  13.31 103.96   5.73  45.80
   4_adp: 104.90   0.00  17.82  92.75   0.00  12.89 104.90   5.13  44.67
   4_occ: 104.90   0.00  17.82  92.75   0.00  12.89 104.90   5.13  44.67
   5_bss: 104.90   0.00  17.82  92.75   0.00  12.89 104.90   5.13  44.67
   5_xyz: 104.90   0.00  17.82  92.75   0.00  12.89 104.90   5.13  44.67
   5_adp: 110.61   0.00  17.62  98.44   0.00  12.67 110.61   3.84  44.56
   5_occ: 110.61   0.00  17.62  98.44   0.00  12.67 110.61   3.84  44.56
   5_bss: 110.61   0.00  17.62  98.44   0.00  12.67 110.61   3.84  44.56
------------------------------------------------------------------------
 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:    1.843    0.023    0.474
   1_adp:    1.843    0.023    0.474
   1_occ:    1.843    0.023    0.474
   2_bss:    1.843    0.023    0.474
   2_xyz:    1.776    0.053    0.559
   2_adp:    1.776    0.053    0.559
   2_occ:    1.776    0.053    0.559
   3_bss:    1.776    0.053    0.559
   3_xyz:    1.685    0.036    0.664
   3_adp:    1.685    0.036    0.664
   3_occ:    1.685    0.036    0.664
   4_bss:    1.685    0.036    0.664
   4_xyz:    1.764    0.048    0.695
   4_adp:    1.764    0.048    0.695
   4_occ:    1.764    0.048    0.695
   5_bss:    1.764    0.048    0.695
   5_xyz:    1.816    0.040    0.706
   5_adp:    1.816    0.040    0.706
   5_occ:    1.816    0.040    0.706
   5_bss:    1.816    0.040    0.706
------------------------------------------------------------------------

CPU time actual refinement: 334.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_461/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_461/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_461/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_461/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_461/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.73 
  Macro-tasks:
    bulk solvent and scale       = 48.91  
    individual site refinement   = 129.25 
    weights calculation          = 29.44  
    collect and process          = 6.29   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 213.98 
  Micro-tasks:
    mask                            = 1.70   
    f_calc                          = 105.93 
    alpha_beta                      = 8.68   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 107.74 
    fmodel                         = 7.80   
    r_factors                      = 0.15   
    phase_errors                   = 11.78  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 245.24 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.831 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    615 calls, 105.58 s
gradients_fft:          560 calls,  96.95 s

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

# Date 2008-01-16 Time 04:53:33 PST -0800 (1200488013.34 s)
Start R-work = 0.4533, R-free = 0.4494 (no bulk solvent and anisotropic scale)
Final R-work = 0.1376, R-free = 0.1849 (no bulk solvent and anisotropic scale)

Start R-work = 0.4435, R-free = 0.4366
Final R-work = 0.1170, R-free = 0.1688