# Date 2008-01-16 Time 05:53:33 PST -0800 (1200491613.25 s)
#phil __OFF__

Command line arguments: "../924.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17246
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 924

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.3993, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95145
Completeness in resolution range: 0.921575
Completeness with d_max=infinity: 0.918852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95145
Completeness in resolution range: 0.921575
Completeness with d_max=infinity: 0.918852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1768 [2234/2263]  2012   222   9.9%
  bin  2:  4.1768 -  3.3272 [2138/2161]  1924   214  10.0%
  bin  3:  3.3272 -  2.9101 [2107/2132]  1892   215  10.2%
  bin  4:  2.9101 -  2.6456 [2093/2109]  1890   203   9.7%
  bin  5:  2.6456 -  2.4569 [2078/2122]  1870   208  10.0%
  bin  6:  2.4569 -  2.3126 [2079/2107]  1871   208  10.0%
  bin  7:  2.3126 -  2.1971 [2057/2093]  1848   209  10.2%
  bin  8:  2.1971 -  2.1017 [2045/2087]  1840   205  10.0%
  bin  9:  2.1017 -  2.0210 [2048/2094]  1847   201   9.8%
  bin 10:  2.0210 -  1.9514 [ 710/2088]   636    74  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_924/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.46 -     2.15: 19
        2.15 -     2.84: 1008
        2.84 -     3.52: 4443
        3.52 -     4.21: 9319
        4.21 -     4.90: 13638
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.461 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.528 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.792 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 396 "  1.829 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28422 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_924/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_924/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.3993 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4208   r_free= 0.4201   ksol= 0.00   Bsol= 0.00   scale= 0.925    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.222047                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6592 0.99   1451  164 0.3293 0.3308      6.4711      6.4568|
|  2:  4.6592 -  3.7167 0.99   1386  149 0.3429 0.3301      6.6778      6.6863|
|  3:  3.7167 -  3.2523 0.99   1370  155 0.3767 0.3837      6.5596      6.6245|
|  4:  3.2523 -  2.9575 0.99   1355  148 0.4056 0.3953       6.425      6.4205|
|  5:  2.9575 -  2.7469 0.98   1344  147 0.4296 0.4086      6.2765      6.2691|
|  6:  2.7469 -  2.5858 0.99   1344  158 0.4518 0.4519      6.2143      6.1415|
|  7:  2.5858 -  2.4569 0.98   1338  141 0.4488 0.4145      6.1847      6.1427|
|  8:  2.4569 -  2.3503 0.99   1331  150 0.4728 0.4849      6.1146      6.1737|
|  9:  2.3503 -  2.2602 0.99   1335  151 0.4848 0.4650      6.1095      6.0642|
| 10:  2.2602 -  2.1824 0.98   1327  147 0.4875 0.5060       6.042      6.1206|
| 11:  2.1824 -  2.1144 0.97   1303  136 0.4819 0.5819      5.9993      6.0063|
| 12:  2.1144 -  2.0541 0.99   1336  154 0.4958 0.5256      5.9241      5.9783|
| 13:  2.0541 -  2.0001 0.83   1109  130 0.5025 0.4434      5.8597      5.8108|
| 14:  2.0001 -  1.9514 0.22    301   29 0.5799 0.4997      5.8206      5.8142|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6592  1451   164  0.75  29.80   0.85     0.77      54102.71|
|  2:  4.6592 -  3.7167  1386   149  0.76  29.86   0.95     0.85      76265.37|
|  3:  3.7167 -  3.2523  1370   155  0.68  36.83   0.94     0.85      83143.26|
|  4:  3.2523 -  2.9575  1355   148  0.60  43.61   0.95     0.81      76199.02|
|  5:  2.9575 -  2.7469  1344   147  0.54  48.45   0.91     0.75      61860.95|
|  6:  2.7469 -  2.5858  1344   158  0.53  49.78   0.94     0.72      52828.85|
|  7:  2.5858 -  2.4569  1338   141  0.53  49.94   0.95     0.70      48352.66|
|  8:  2.4569 -  2.3503  1331   150  0.48  53.82   0.92     0.68      47473.96|
|  9:  2.3503 -  2.2602  1335   151  0.46  55.63   0.96     0.66      45396.12|
| 10:  2.2602 -  2.1824  1327   147  0.40  60.28   0.97     0.58      46867.07|
| 11:  2.1824 -  2.1144  1303   136  0.34  64.32   0.96     0.52      45356.97|
| 12:  2.1144 -  2.0541  1336   154  0.29  68.50   0.96     0.48      44763.62|
| 13:  2.0541 -  2.0001  1109   130  0.30  67.56   0.94     0.48      37272.46|
| 14:  2.0001 -  1.9514   301    29  0.32  65.79   0.89     0.50      29850.19|
|alpha:            min =        0.48 max =            0.85 mean =         0.68|
|beta:             min =    29850.19 max =        83143.26 mean =     55326.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.42|
|phase err.(test): min =        0.00 max =           89.93 mean =        50.37|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.848652              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.836   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.882389              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.428   (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 |  1.461 -  1.805:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.805 -  2.149:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.149 -  2.493:       27 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.493 -  2.837:      981 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.837 -  3.180:     2015 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.180 -  3.524:     2428 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.524 -  3.868:     4615 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.868 -  4.212:     4704 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.212 -  4.556:     6193 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.556 -  4.900:     7445 |
|-----------------------------------------------------------------------------|
|-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 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.461 |       0.484 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4208   r_free= 0.4201   ksol= 0.00   Bsol= 0.00   scale= 0.925    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.222047                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4109   r_free= 0.4107   ksol= 0.30   Bsol= 50.00   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,0.00,2.75,0.00,0.00,0.00); trace/3= 0.32                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.214467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.186463              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.907   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.847370              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.216   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4109      final r-factor (work) = 0.2902          |
| start r-factor (free) = 0.4107      final r-factor (free) = 0.3232          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3955 = 6.19 * 0.50 * 6.2112 + 1.00 * 0.1827                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8101 = 6.19 * 0.50 * 6.0463 + 1.00 * 0.1075                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2902      final r-factor (work) = 0.2648          |
| start r-factor (free) = 0.3232      final r-factor (free) = 0.3305          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1298 = 0.85 * 1.00 * 6.0463 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0047 = 0.85 * 1.00 * 5.8888 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.95   18.34    None  None   None       |
|    all(noH): 2823   0      0.00    92.95   18.34    None  None   None       |
|    Sol.    : 438    0      4.18    92.95   41.36    None  None   None       |
|    Mac.    : 2385   0      0.00    92.46   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 -   9.295:  856   |   5:    46.476 -  55.771:   85        |
|      1:     9.295 -  18.590: 1023   |   6:    55.771 -  65.066:   66        |
|      2:    18.590 -  27.886:  410   |   7:    65.066 -  74.361:   38        |
|      3:    27.886 -  37.181:  189   |   8:    74.361 -  83.656:    8        |
|      4:    37.181 -  46.476:  143   |   9:    83.656 -  92.952:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2648 r_free = 0.3305             target_work(ml) = 5.896         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2644 r_free = 0.3306             target_work(ml) = 5.894         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2644   r_free= 0.3306   ksol= 0.30   Bsol= 50.00   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,0.00,2.75,0.00,0.00,0.00); trace/3= 0.32                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.894391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2629   r_free= 0.3271   ksol= 0.33   Bsol= 60.56   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-1.11,0.14,-0.00,0.00,0.00); trace/3= -1.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.891372                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.246900              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.349   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.478287              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.764  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2629      final r-factor (work) = 0.2005          |
| start r-factor (free) = 0.3271      final r-factor (free) = 0.2572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6711 = 3.25 * 0.50 * 5.8909 + 1.00 * 0.1075                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4575 = 3.25 * 0.50 * 5.7872 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| 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) = 0.1883          |
| start r-factor (free) = 0.2572      final r-factor (free) = 0.2439          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7826 = 0.48 * 1.00 * 5.7872 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7050 = 0.48 * 1.00 * 5.6332 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.28   18.11    None  None   None       |
|    all(noH): 2823   0      0.00    88.28   18.11    None  None   None       |
|    Sol.    : 438    0      5.46    88.28   42.06    None  None   None       |
|    Mac.    : 2385   0      0.00    86.47   13.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.828:  772   |   5:    44.141 -  52.969:  114        |
|      1:     8.828 -  17.656: 1175   |   6:    52.969 -  61.797:   68        |
|      2:    17.656 -  26.484:  343   |   7:    61.797 -  70.625:   40        |
|      3:    26.484 -  35.312:  152   |   8:    70.625 -  79.453:   21        |
|      4:    35.312 -  44.141:  129   |   9:    79.453 -  88.281:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1883 r_free = 0.2439             target_work(ml) = 5.608         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1881 r_free = 0.2439             target_work(ml) = 5.607         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1881   r_free= 0.2439   ksol= 0.33   Bsol= 60.56   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-1.11,0.14,-0.00,0.00,0.00); trace/3= -1.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.607445                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1881   r_free= 0.2436   ksol= 0.33   Bsol= 60.56   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-1.59,-1.13,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.606041                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.414407              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.868  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.299997              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.773  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1881      final r-factor (work) = 0.1421          |
| start r-factor (free) = 0.2436      final r-factor (free) = 0.1892          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4974 = 4.41 * 0.50 * 5.6339 + 1.00 * 0.0622                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1889 = 4.41 * 0.50 * 5.4938 + 1.00 * 0.0629                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1421      final r-factor (work) = 0.1308          |
| start r-factor (free) = 0.1892      final r-factor (free) = 0.1776          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6588 = 0.30 * 1.00 * 5.4938 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6181 = 0.30 * 1.00 * 5.3109 + 1.00 * 0.0248                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.34   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    87.34   17.74    None  None   None       |
|    Sol.    : 438    0      5.17    87.34   41.95    None  None   None       |
|    Mac.    : 2385   0      0.00    85.67   13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.734:  683   |   5:    43.671 -  52.405:  123        |
|      1:     8.734 -  17.468: 1338   |   6:    52.405 -  61.139:   67        |
|      2:    17.468 -  26.203:  296   |   7:    61.139 -  69.874:   38        |
|      3:    26.203 -  34.937:  129   |   8:    69.874 -  78.608:   22        |
|      4:    34.937 -  43.671:  119   |   9:    78.608 -  87.342:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1308 r_free = 0.1776             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1307 r_free = 0.1773             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1307   r_free= 0.1773   ksol= 0.33   Bsol= 60.56   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-1.59,-1.13,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.274191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1767   ksol= 0.32   Bsol= 50.76   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.10,-1.94,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.275342                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.539469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.584  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.654537              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.060   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8109 = 2.54 * 0.50 * 5.3145 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7132 = 2.54 * 0.50 * 5.2394 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1194      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1645      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4413 = 0.65 * 1.00 * 5.2394 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4045 = 0.65 * 1.00 * 5.1870 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.62    96.63   17.63    None  None   None       |
|    all(noH): 2823   0      1.62    96.63   17.63    None  None   None       |
|    Sol.    : 438    0      5.10    82.45   41.95    None  None   None       |
|    Mac.    : 2385   0      1.62    96.63   13.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.621 -  11.122: 1247   |   5:    49.127 -  58.628:  104        |
|      1:    11.122 -  20.624:  952   |   6:    58.628 -  68.129:   47        |
|      2:    20.624 -  30.125:  197   |   7:    68.129 -  77.630:   26        |
|      3:    30.125 -  39.626:  122   |   8:    77.630 -  87.131:   12        |
|      4:    39.626 -  49.127:  112   |   9:    87.131 -  96.633:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1628             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1628             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1628   ksol= 0.32   Bsol= 50.76   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.10,-1.94,-0.00,-0.00,-0.00); trace/3= -2.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180896                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1627   ksol= 0.32   Bsol= 50.76   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.11,-2.08,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180754                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.896980              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.367  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.321517              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.476  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1627      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5734 = 2.90 * 0.50 * 5.1867 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5441 = 2.90 * 0.50 * 5.1612 + 1.00 * 0.0682                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6689 = 0.32 * 1.00 * 5.1612 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6641 = 0.32 * 1.00 * 5.1491 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.93    97.36   17.20    None  None   None       |
|    all(noH): 2823   0      1.93    97.36   17.20    None  None   None       |
|    Sol.    : 438    0      5.91    79.59   40.19    None  None   None       |
|    Mac.    : 2385   0      1.93    97.36   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.932 -  11.474: 1358   |   5:    49.644 -  59.187:   82        |
|      1:    11.474 -  21.017:  864   |   6:    59.187 -  68.729:   43        |
|      2:    21.017 -  30.559:  196   |   7:    68.729 -  78.272:   17        |
|      3:    30.559 -  40.102:  123   |   8:    78.272 -  87.814:    6        |
|      4:    40.102 -  49.644:  130   |   9:    87.814 -  97.357:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1098 r_free = 0.1588             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1098 r_free = 0.1587             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1587   ksol= 0.32   Bsol= 50.76   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.11,-2.08,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146443                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6592 0.99   1451  164 0.0954 0.1283      5.3544      5.5385|
|  2:  4.6592 -  3.7167 0.99   1386  149 0.0809 0.1019      5.3853      5.6019|
|  3:  3.7167 -  3.2523 0.99   1370  155 0.1031 0.1661      5.4417      5.8813|
|  4:  3.2523 -  2.9575 0.99   1355  148 0.1247 0.1529      5.4586      5.5888|
|  5:  2.9575 -  2.7469 0.98   1344  147 0.1296 0.1826      5.3165      5.5123|
|  6:  2.7469 -  2.5858 0.99   1344  158 0.1224 0.1848       5.205      5.4339|
|  7:  2.5858 -  2.4569 0.98   1338  141 0.1204 0.1693      5.1487      5.3755|
|  8:  2.4569 -  2.3503 0.99   1331  150 0.1158 0.1714      5.0531       5.285|
|  9:  2.3503 -  2.2602 0.99   1335  151 0.1145 0.1920      5.0161      5.3119|
| 10:  2.2602 -  2.1824 0.98   1327  147 0.1110 0.1678       4.961      5.2453|
| 11:  2.1824 -  2.1144 0.97   1303  136 0.1132 0.1940      4.9234      5.2557|
| 12:  2.1144 -  2.0541 0.99   1336  154 0.1097 0.1656      4.8568      5.0737|
| 13:  2.0541 -  2.0001 0.83   1109  130 0.1159 0.1796      4.7816      5.0188|
| 14:  2.0001 -  1.9514 0.22    301   29 0.1149 0.1494      4.6688      4.8993|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6592  1451   164  0.94   8.71   0.98     0.95       6744.64|
|  2:  4.6592 -  3.7167  1386   149  0.95   7.65   1.01     1.00       8303.14|
|  3:  3.7167 -  3.2523  1370   155  0.94  11.05   1.02     1.02       9882.76|
|  4:  3.2523 -  2.9575  1355   148  0.91  14.70   1.01     0.98      10781.97|
|  5:  2.9575 -  2.7469  1344   147  0.89  16.62   0.99     0.97       8482.13|
|  6:  2.7469 -  2.5858  1344   158  0.90  16.24   0.99     0.96       7096.71|
|  7:  2.5858 -  2.4569  1338   141  0.91  15.18   0.99     0.96       6148.48|
|  8:  2.4569 -  2.3503  1331   150  0.90  16.15   0.99     0.96       5446.64|
|  9:  2.3503 -  2.2602  1335   151  0.90  16.31   1.00     0.96       4989.96|
| 10:  2.2602 -  2.1824  1327   147  0.91  15.20   0.99     0.96       4519.08|
| 11:  2.1824 -  2.1144  1303   136  0.90  16.72   0.99     0.96       4385.48|
| 12:  2.1144 -  2.0541  1336   154  0.91  16.07   1.00     0.99       3977.64|
| 13:  2.0541 -  2.0001  1109   130  0.90  16.38   0.99     0.97       3304.33|
| 14:  2.0001 -  1.9514   301    29  0.90  16.18   0.98     0.95       2598.68|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2598.68 max =        10781.97 mean =      6465.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.32|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1587   ksol= 0.32   Bsol= 50.69   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-1.94,-1.92,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146505                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1587   ksol= 0.32   Bsol= 50.69   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-1.94,-1.92,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146505                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6592 0.99   1451  164 0.0954 0.1284      5.3551      5.5393|
|  2:  4.6592 -  3.7167 0.99   1386  149 0.0809 0.1019      5.3856      5.6019|
|  3:  3.7167 -  3.2523 0.99   1370  155 0.1031 0.1661      5.4416      5.8814|
|  4:  3.2523 -  2.9575 0.99   1355  148 0.1247 0.1529      5.4585      5.5887|
|  5:  2.9575 -  2.7469 0.98   1344  147 0.1295 0.1826      5.3164      5.5122|
|  6:  2.7469 -  2.5858 0.99   1344  158 0.1224 0.1849       5.205       5.434|
|  7:  2.5858 -  2.4569 0.98   1338  141 0.1204 0.1692      5.1489      5.3757|
|  8:  2.4569 -  2.3503 0.99   1331  150 0.1158 0.1714      5.0532      5.2851|
|  9:  2.3503 -  2.2602 0.99   1335  151 0.1145 0.1920      5.0163      5.3118|
| 10:  2.2602 -  2.1824 0.98   1327  147 0.1109 0.1677       4.961      5.2451|
| 11:  2.1824 -  2.1144 0.97   1303  136 0.1132 0.1939      4.9233      5.2556|
| 12:  2.1144 -  2.0541 0.99   1336  154 0.1097 0.1656      4.8565      5.0734|
| 13:  2.0541 -  2.0001 0.83   1109  130 0.1159 0.1795      4.7815      5.0184|
| 14:  2.0001 -  1.9514 0.22    301   29 0.1149 0.1494      4.6688      4.8997|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6592  1451   164  0.94   8.71   0.98     0.95       6753.32|
|  2:  4.6592 -  3.7167  1386   149  0.95   7.65   1.01     1.00       8307.90|
|  3:  3.7167 -  3.2523  1370   155  0.94  11.05   1.03     1.02       9883.37|
|  4:  3.2523 -  2.9575  1355   148  0.91  14.70   1.01     0.99      10780.53|
|  5:  2.9575 -  2.7469  1344   147  0.89  16.62   0.99     0.97       8481.73|
|  6:  2.7469 -  2.5858  1344   158  0.90  16.24   0.99     0.96       7096.79|
|  7:  2.5858 -  2.4569  1338   141  0.91  15.19   0.99     0.97       6149.70|
|  8:  2.4569 -  2.3503  1331   150  0.90  16.15   1.00     0.96       5447.28|
|  9:  2.3503 -  2.2602  1335   151  0.90  16.31   1.00     0.97       4989.80|
| 10:  2.2602 -  2.1824  1327   147  0.91  15.20   0.99     0.96       4518.40|
| 11:  2.1824 -  2.1144  1303   136  0.90  16.72   1.00     0.96       4384.21|
| 12:  2.1144 -  2.0541  1336   154  0.91  16.06   1.00     0.99       3975.03|
| 13:  2.0541 -  2.0001  1109   130  0.90  16.38   0.99     0.98       3303.24|
| 14:  2.0001 -  1.9514   301    29  0.90  16.18   0.99     0.96       2599.00|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2599.00 max =        10780.53 mean =      6466.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.32|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.86    97.29   17.13    None  None   None       |
|    all(noH): 2823   0      1.86    97.29   17.13    None  None   None       |
|    Sol.    : 438    0      5.84    79.52   40.12    None  None   None       |
|    Mac.    : 2385   0      1.86    97.29   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.862 -  11.405: 1358   |   5:    49.575 -  59.117:   82        |
|      1:    11.405 -  20.947:  864   |   6:    59.117 -  68.660:   43        |
|      2:    20.947 -  30.490:  196   |   7:    68.660 -  78.202:   17        |
|      3:    30.490 -  40.032:  123   |   8:    78.202 -  87.745:    6        |
|      4:    40.032 -  49.575:  130   |   9:    87.745 -  97.287:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.518 - 5.868
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 309
   mapped sites are within: 0.710 - 5.868

peak=    5.789 closest distance to " NH2 ARG A  56 " =    2.209
peak=    5.663 closest distance to " CB  SER A  63 " =    1.227
peak=    5.565 closest distance to " CB  GLN A 223 " =    1.480
peak=    5.466 closest distance to " CG  PRO A  54 " =    1.169
peak=    4.888 closest distance to " CB  ARG A 275 " =    0.919
peak=    4.841 closest distance to " O   HOH Z 193 " =    1.902
peak=    4.832 closest distance to " CB  GLN A 183 " =    1.290
peak=    4.740 closest distance to " O   HOH Z  15 " =    2.067
peak=    4.658 closest distance to " CB  SER A   3 " =    1.366
peak=    4.593 closest distance to " OD2 ASP A 286 " =    2.837
peak=    4.576 closest distance to " O   HOH Z 232 " =    2.272
peak=    4.525 closest distance to " CG  PRO A 213 " =    1.172
peak=    4.503 closest distance to " O   HOH Z 134 " =    1.557
peak=    4.478 closest distance to " CB  TYR A 169 " =    0.819
peak=    4.476 closest distance to " CB  PRO A  54 " =    0.824
peak=    4.476 closest distance to " OD1 ASN A  69 " =    2.540
peak=    4.464 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.459 closest distance to " O   HOH Z 368 " =    2.075
peak=    4.422 closest distance to " O   SER A  87 " =    2.210
peak=    4.410 closest distance to " O   HOH Z 234 " =    3.731
peak=    4.400 closest distance to " O   HOH Z 180 " =    2.231
peak=    4.400 closest distance to " CB  LEU A 228 " =    1.116
peak=    4.388 closest distance to " O   HOH Z 298 " =    1.931
peak=    4.387 closest distance to " CB  GLU A 277 " =    3.577
peak=    4.382 closest distance to " CG  PRO A 198 " =    1.310
peak=    4.353 closest distance to " O   PRO A 198 " =    1.539
peak=    4.325 closest distance to " O   HOH Z 126 " =    1.763
peak=    4.319 closest distance to " CA  ALA A  21 " =    1.233
peak=    4.316 closest distance to " CA  TYR A  30 " =    0.950
peak=    4.281 closest distance to " O   HOH Z 236 " =    1.857
peak=    4.272 closest distance to " NE2 GLN A  11 " =    1.042
peak=    4.267 closest distance to " CG  PRO A  90 " =    1.081
peak=    4.247 closest distance to " CA  THR A 221 " =    0.931
peak=    4.239 closest distance to " O   HOH Z 369 " =    2.035
peak=    4.236 closest distance to " CB  GLU A 128 " =    1.164
peak=    4.223 closest distance to " CB  ARG A  79 " =    1.380
peak=    4.219 closest distance to " O   HOH Z 207 " =    1.966
peak=    4.213 closest distance to " CB  VAL A 202 " =    1.620
peak=    4.208 closest distance to " NH2BARG A 145 " =    2.107
peak=    4.190 closest distance to " CB  ASN A 148 " =    1.459
peak=    4.188 closest distance to " O   HOH Z 426 " =    1.504
peak=    4.179 closest distance to " O   HOH Z 108 " =    1.527
peak=    4.170 closest distance to " O   HOH Z 193 " =    2.183
peak=    4.166 closest distance to " O   HOH Z 371 " =    3.386
peak=    4.148 closest distance to " O   HOH Z 403 " =    1.710
peak=    4.122 closest distance to " O   HOH Z  78 " =    1.858
peak=    4.116 closest distance to " O   HOH Z  80 " =    1.625
peak=    4.109 closest distance to " O   HOH Z 389 " =    1.899
peak=    4.092 closest distance to " O   HOH Z  68 " =    1.823
peak=    4.086 closest distance to " O   HOH Z 135 " =    1.809
peak=    4.031 closest distance to " NZ  LYS A 117 " =    3.310
peak=    4.031 closest distance to " O   HOH Z 214 " =    0.960
peak=    3.996 closest distance to " O   HOH Z 313 " =    1.835
peak=    3.994 closest distance to " NH2 ARG A 156 " =    1.178
peak=    3.984 closest distance to " O   HOH Z 411 " =    3.614
peak=    3.979 closest distance to " O   HOH Z 374 " =    2.576
peak=    3.977 closest distance to " O   HOH Z 132 " =    1.047
peak=    3.966 closest distance to " O   HOH Z 126 " =    1.636
peak=    3.963 closest distance to " O   HOH Z 316 " =    2.896
peak=    3.947 closest distance to " CG1 ILE A  33 " =    1.217
peak=    3.944 closest distance to " O   HOH Z 326 " =    1.539
peak=    3.938 closest distance to " O   HOH Z 344 " =    2.971
peak=    3.933 closest distance to " CG2 THR A 221 " =    1.028
peak=    3.932 closest distance to " O   HOH Z  49 " =    2.256
peak=    3.926 closest distance to " O   HOH Z  54 " =    1.721
peak=    3.925 closest distance to " NH1AARG A 145 " =    1.085
peak=    3.924 closest distance to " O   HOH Z  88 " =    3.416
peak=    3.910 closest distance to " O   HOH Z 279 " =    2.246
peak=    3.909 closest distance to " O   HOH Z 427 " =    2.825
peak=    3.907 closest distance to " CD1 LEU A 300 " =    1.222
peak=    3.904 closest distance to " CB  TRP A 179 " =    1.347
peak=    3.904 closest distance to " O   HOH Z 260 " =    1.186
peak=    3.902 closest distance to " O   HOH Z  97 " =    1.897
peak=    3.900 closest distance to " O   HOH Z  20 " =    1.808
peak=    3.891 closest distance to " O   HOH Z 284 " =    2.941
peak=    3.890 closest distance to " O   HOH Z 209 " =    2.362
peak=    3.889 closest distance to " O   MET A 105 " =    1.759
peak=    3.870 closest distance to " ND2 ASN A 187 " =    1.616
peak=    3.859 closest distance to " O   HOH Z 142 " =    1.613
peak=    3.857 closest distance to " O   HOH Z 133 " =    1.620
peak=    3.855 closest distance to " O   HOH Z 261 " =    2.122
peak=    3.842 closest distance to " O   HOH Z  40 " =    1.637
peak=    3.825 closest distance to " CB  ARG A 139 " =    0.975
peak=    3.824 closest distance to " O   HOH Z 124 " =    1.381
peak=    3.822 closest distance to " O   HOH Z 108 " =    1.954
peak=    3.819 closest distance to " CB  SER A 141 " =    1.016
peak=    3.815 closest distance to " O   HOH Z 272 " =    1.863
peak=    3.812 closest distance to " O   HOH Z  93 " =    2.518
peak=    3.798 closest distance to " CA  ALA A  51 " =    0.903
peak=    3.795 closest distance to " O   HOH Z 132 " =    2.111
peak=    3.786 closest distance to " NZ  LYS A  76 " =    1.184
peak=    3.777 closest distance to " O   HOH Z 247 " =    1.321
peak=    3.768 closest distance to " O   HOH Z  59 " =    2.391
peak=    3.758 closest distance to " CA  ASN A 215 " =    1.251
peak=    3.756 closest distance to " O   HOH Z  61 " =    1.614
peak=    3.747 closest distance to " O   HOH Z 203 " =    1.894
peak=    3.746 closest distance to " O   ALA A 165 " =    1.341
peak=    3.715 closest distance to " O   HOH Z   6 " =    2.173
peak=    3.711 closest distance to " O   HOH Z  21 " =    1.709
peak=    3.704 closest distance to " CG  ARG A  66 " =    2.524
peak=    3.703 closest distance to " CG1BVAL A  72 " =    1.594
peak=    3.699 closest distance to " O   HOH Z 132 " =    2.657
peak=    3.698 closest distance to " CA  ASP A 124 " =    0.710
peak=    3.694 closest distance to " NH2AARG A 190 " =    1.398
peak=    3.691 closest distance to " O   HOH Z 183 " =    1.576
peak=    3.690 closest distance to " OG BSER A 164 " =    2.548
peak=    3.689 closest distance to " CB  VAL A 265 " =    1.219
peak=    3.676 closest distance to " CD BLYS A 290 " =    1.072
peak=    3.675 closest distance to " O   HOH Z 214 " =    2.022
peak=    3.662 closest distance to " CG  PRO A 243 " =    1.150
peak=    3.662 closest distance to " OD2 ASP A 298 " =    4.093
peak=    3.661 closest distance to " O   HOH Z 281 " =    4.205
peak=    3.661 closest distance to " O   HOH Z 116 " =    1.852
peak=    3.658 closest distance to " O   HOH Z 128 " =    2.196
peak=    3.655 closest distance to " O   HOH Z 197 " =    2.561
peak=    3.652 closest distance to " CD  LYS A 119 " =    1.332
peak=    3.641 closest distance to " OE1 GLN A  11 " =    1.905
peak=    3.629 closest distance to " O   ALA A   1 " =    1.485
peak=    3.628 closest distance to " O   HOH Z 215 " =    1.743
peak=    3.624 closest distance to " O   HOH Z 406 " =    1.672
peak=    3.622 closest distance to " O   HOH Z 346 " =    1.595
peak=    3.618 closest distance to " O   HOH Z  19 " =    2.208
peak=    3.609 closest distance to " CA  MET A  40 " =    1.048
peak=    3.609 closest distance to " O   HOH Z  43 " =    2.092
peak=    3.608 closest distance to " N   ASN A  39 " =    1.330
peak=    3.601 closest distance to " O   HOH Z 227 " =    1.696
peak=    3.600 closest distance to " O   HOH Z 303 " =    2.103
peak=    3.597 closest distance to " O   HOH Z 295 " =    1.469
peak=    3.592 closest distance to " O   HOH Z 423 " =    1.950
peak=    3.592 closest distance to " CB  MET A  47 " =    0.990
peak=    3.590 closest distance to " O   HOH Z 261 " =    2.009
peak=    3.574 closest distance to " CA  ASP A 191 " =    0.804
peak=    3.572 closest distance to " O   HOH Z  10 " =    1.822
peak=    3.571 closest distance to " OD1 ASN A 217 " =    1.841
peak=    3.569 closest distance to " O   HOH Z  63 " =    2.009
peak=    3.569 closest distance to " CD  LYS A 166 " =    1.349
peak=    3.568 closest distance to " O   HOH Z 345 " =    3.241
peak=    3.535 closest distance to " O   HOH Z 163 " =    1.516
peak=    3.533 closest distance to " O   HOH Z 174 " =    2.591
peak=    3.529 closest distance to " O   HOH Z 276 " =    1.279
peak=    3.520 closest distance to " CB  ARG A 190 " =    1.696
peak=    3.513 closest distance to " O   HOH Z 147 " =    1.718
peak=    3.511 closest distance to " O   HOH Z 425 " =    1.308
peak=    3.507 closest distance to " O   HOH Z 278 " =    1.074
peak=    3.505 closest distance to " O   HOH Z  44 " =    1.832
peak=    3.502 closest distance to " O   HOH Z 250 " =    1.435
peak=    3.498 closest distance to " O   HOH Z  98 " =    2.050
peak=    3.493 closest distance to " CA  ASP A 140 " =    1.154
peak=    3.485 closest distance to " CA  LYS A 117 " =    1.216
peak=    3.482 closest distance to " CD2 LEU A 255 " =    1.308
peak=    3.479 closest distance to " OG ASER A  99 " =    2.054
peak=    3.473 closest distance to " O   HOH Z 166 " =    1.504
peak=    3.470 closest distance to " O   HOH Z 102 " =    1.205
peak=    3.470 closest distance to " CD  ARG A 269 " =    0.916
peak=    3.465 closest distance to " O   HOH Z 128 " =    2.322
peak=    3.464 closest distance to " CG  GLN A  58 " =    2.529
peak=    3.461 closest distance to " CG BARG A 102 " =    1.934
peak=    3.459 closest distance to " O   HOH Z 189 " =    2.052
peak=    3.455 closest distance to " O   HOH Z 345 " =    1.748
peak=    3.449 closest distance to " O   HOH Z 368 " =    2.597
peak=    3.447 closest distance to " O   HOH Z 245 " =    1.349
peak=    3.435 closest distance to " O   HOH Z  50 " =    2.025
peak=    3.427 closest distance to " CG1 VAL A 202 " =    2.111
peak=    3.424 closest distance to " O   HOH Z  54 " =    2.317
peak=    3.402 closest distance to " CA  ALA A 160 " =    0.828
peak=    3.400 closest distance to " CG2 VAL A 197 " =    1.133
peak=    3.399 closest distance to " CB  ASN A 285 " =    0.924
peak=    3.399 closest distance to " O   HOH Z 118 " =    1.520
peak=    3.388 closest distance to " O   HOH Z 173 " =    1.960
peak=    3.385 closest distance to " O   SER A  26 " =    1.738
peak=    3.382 closest distance to " O   HOH Z 214 " =    2.167
peak=    3.379 closest distance to " CB  ARG A 259 " =    1.868
peak=    3.377 closest distance to " O   HOH Z  48 " =    1.380
peak=    3.372 closest distance to " O   HOH Z 411 " =    1.689
peak=    3.371 closest distance to " CB  ASP A 140 " =    0.719
peak=    3.366 closest distance to " O   TRP A 274 " =    1.857
peak=    3.366 closest distance to " O   HOH Z 215 " =    1.529
peak=    3.365 closest distance to " CD2 LEU A 297 " =    0.888
peak=    3.362 closest distance to " CB  GLU A 152 " =    1.528
peak=    3.362 closest distance to " CB  LEU A 143 " =    1.095
peak=    3.354 closest distance to " CG2 THR A 220 " =    1.006
peak=    3.353 closest distance to " O   HOH Z 248 " =    1.550
peak=    3.352 closest distance to " ND1 HIS A  81 " =    1.534
peak=    3.351 closest distance to " O   HOH Z 427 " =    3.116
peak=    3.348 closest distance to " O   HOH Z 334 " =    1.467
peak=    3.345 closest distance to " O   HOH Z 234 " =    1.793
peak=    3.343 closest distance to " O   HOH Z 341 " =    1.672
peak=    3.340 closest distance to " OG  SER A  22 " =    2.842
peak=    3.336 closest distance to " O   HOH Z 263 " =    2.279
peak=    3.333 closest distance to " O   HOH Z 368 " =    3.657
peak=    3.333 closest distance to " CB  SER A 216 " =    0.777
peak=    3.333 closest distance to " O   HOH Z 368 " =    2.446
peak=    3.327 closest distance to " O   HOH Z 357 " =    1.934
peak=    3.324 closest distance to " CB  TRP A 266 " =    0.939
peak=    3.324 closest distance to " O   HOH Z 387 " =    2.626
peak=    3.321 closest distance to " CA  ARG A 195 " =    1.283
peak=    3.321 closest distance to " NH2 ARG A 219 " =    1.877
peak=    3.317 closest distance to " O   HOH Z 358 " =    2.182
peak=    3.317 closest distance to " CE1 TYR A 186 " =    1.161
peak=    3.314 closest distance to " O   HOH Z 106 " =    2.270
peak=    3.309 closest distance to " O   GLY A  57 " =    2.559
peak=    3.303 closest distance to " O   HOH Z 114 " =    1.436
peak=    3.302 closest distance to " CB  ALA A 291 " =    1.352
peak=    3.302 closest distance to " O   HOH Z  61 " =    1.525
peak=    3.302 closest distance to " O   HOH Z 188 " =    2.065
peak=    3.301 closest distance to " OG  SER A  62 " =    3.092
peak=    3.300 closest distance to " CA  ARG A  36 " =    1.178
peak=    3.298 closest distance to " O   HOH Z 410 " =    1.873
peak=    3.297 closest distance to " CG  MET A 185 " =    1.187
peak=    3.296 closest distance to " O   ALA A 158 " =    1.237
peak=    3.296 closest distance to " CB  TYR A  30 " =    1.442
peak=    3.296 closest distance to " CG2 ILE A 120 " =    1.192
peak=    3.295 closest distance to " CG  GLN A  77 " =    1.901
peak=    3.291 closest distance to " CD  ARG A 159 " =    0.799
peak=    3.285 closest distance to " CA  GLN A 223 " =    0.914
peak=    3.280 closest distance to " O   HOH Z 185 " =    1.749
peak=    3.280 closest distance to " O   HOH Z   4 " =    1.904
peak=    3.280 closest distance to " CB  MET A  40 " =    0.908
peak=    3.276 closest distance to " O   HOH Z 266 " =    1.582
peak=    3.269 closest distance to " CA  ASN A  74 " =    1.187
peak=    3.269 closest distance to " O   GLY A 229 " =    1.994
peak=    3.267 closest distance to " CG AARG A 275 " =    1.026
peak=    3.264 closest distance to " CB  SER A 212 " =    1.085
peak=    3.262 closest distance to " O   HOH Z 329 " =    3.423
peak=    3.259 closest distance to " NH1BARG A 145 " =    1.038
peak=    3.257 closest distance to " O   HOH Z 193 " =    1.501
peak=    3.257 closest distance to " CZ  PHE A 218 " =    1.038
peak=    3.256 closest distance to " N   ASN A 127 " =    1.266
peak=    3.252 closest distance to " CA  THR A 264 " =    0.876
peak=    3.250 closest distance to " O   HOH Z 286 " =    2.154
peak=    3.247 closest distance to " O   HOH Z 273 " =    2.761
peak=    3.240 closest distance to " O   HOH Z 211 " =    2.371
peak=    3.240 closest distance to " O   HOH Z 388 " =    1.820
peak=    3.238 closest distance to " CB  SER A  62 " =    1.244
peak=    3.237 closest distance to " O   HOH Z 394 " =    1.670
peak=    3.236 closest distance to " CB  TYR A 116 " =    1.004
peak=    3.235 closest distance to " C   SER A  32 " =    1.018
peak=    3.235 closest distance to " CA  LEU A 282 " =    1.181
peak=    3.234 closest distance to " CB  ALA A 295 " =    1.292
peak=    3.233 closest distance to " CB  ALA A 248 " =    0.940
peak=    3.230 closest distance to " O   HOH Z 158 " =    2.913
peak=    3.228 closest distance to " C   PRO A 163 " =    1.750
peak=    3.225 closest distance to " O   HOH Z 163 " =    1.858
peak=    3.223 closest distance to " O   GLY A 211 " =    1.215
peak=    3.222 closest distance to " CZ2 TRP A 179 " =    1.726
peak=    3.222 closest distance to " O   HOH Z 171 " =    3.866
peak=    3.216 closest distance to " O   HOH Z   1 " =    2.235
peak=    3.215 closest distance to " CA  LEU A  83 " =    1.477
peak=    3.211 closest distance to " CB  ASN A  39 " =    0.820
peak=    3.209 closest distance to " O   HOH Z 157 " =    1.619
peak=    3.208 closest distance to " OE1 GLN A  58 " =    5.868
peak=    3.206 closest distance to " CA  ALA A 158 " =    1.086
peak=    3.204 closest distance to " O   HOH Z 353 " =    2.719
peak=    3.204 closest distance to " CA  GLY A 267 " =    1.087
peak=    3.203 closest distance to " O   HOH Z 366 " =    3.041
peak=    3.203 closest distance to " O   HOH Z 337 " =    3.716
peak=    3.197 closest distance to " CB  TRP A 150 " =    1.609
peak=    3.197 closest distance to " CB  PRO A 198 " =    0.956
peak=    3.195 closest distance to " O   HOH Z 227 " =    1.681
peak=    3.188 closest distance to " O   HOH Z  30 " =    1.331
peak=    3.185 closest distance to " O   HOH Z 261 " =    1.495
peak=    3.182 closest distance to " CA  ILE A  33 " =    1.610
peak=    3.182 closest distance to " CG2 VAL A 174 " =    1.337
peak=    3.182 closest distance to " CG1 ILE A 151 " =    0.893
peak=    3.175 closest distance to " O   HOH Z 271 " =    2.141
peak=    3.174 closest distance to " O   HOH Z 189 " =    1.432
peak=    3.173 closest distance to " O   HOH Z 343 " =    2.433
peak=    3.171 closest distance to " CA  GLY A  80 " =    1.149
peak=    3.171 closest distance to " O   HOH Z 194 " =    2.036
peak=    3.167 closest distance to " O   HOH Z 409 " =    3.147
peak=    3.158 closest distance to " O   HOH Z 438 " =    2.047
peak=    3.158 closest distance to " O   THR A 251 " =    1.251
peak=    3.157 closest distance to " CD2 TRP A 179 " =    1.377
peak=    3.155 closest distance to " CB  PHE A  16 " =    0.994
peak=    3.154 closest distance to " O   HOH Z 171 " =    2.567
peak=    3.154 closest distance to " CD  PRO A  54 " =    1.190
peak=    3.148 closest distance to " O   HOH Z 207 " =    1.854
peak=    3.142 closest distance to " CA  VAL A 126 " =    1.098
peak=    3.140 closest distance to " NZ  LYS A 166 " =    2.973
peak=    3.139 closest distance to " OH  TYR A  30 " =    1.219
peak=    3.137 closest distance to " CA  ASP A 162 " =    1.169
peak=    3.136 closest distance to " CD1AILE A 234 " =    0.988
peak=    3.133 closest distance to " O   HOH Z 416 " =    2.811
peak=    3.133 closest distance to " CB  SER A  62 " =    0.760
peak=    3.128 closest distance to " CA  ALA A 291 " =    0.955
peak=    3.127 closest distance to " CG  ARG A 219 " =    1.255
peak=    3.127 closest distance to " CA  ALA A 248 " =    1.189
peak=    3.124 closest distance to " O   HOH Z 109 " =    2.762
peak=    3.121 closest distance to " O   HOH Z 130 " =    2.206
peak=    3.118 closest distance to " CG  MET A 113 " =    1.504
peak=    3.118 closest distance to " O   HOH Z 112 " =    1.578
peak=    3.117 closest distance to " O   HOH Z 166 " =    3.249
peak=    3.107 closest distance to " O   HOH Z 227 " =    2.152
peak=    3.103 closest distance to " O   HOH Z 128 " =    1.675
peak=    3.100 closest distance to " CB  MET A 105 " =    1.258
peak=    3.097 closest distance to " CD  PRO A 280 " =    1.057
peak=    3.093 closest distance to " CD  ARG A  66 " =    3.026
peak=    3.091 closest distance to " NE2 GLN A  58 " =    4.364
peak=    3.078 closest distance to " CD  LYS A 166 " =    1.480
peak=    3.078 closest distance to " N   SER A 135 " =    1.362
peak=    3.071 closest distance to " O   HOH Z 285 " =    1.960
peak=    3.067 closest distance to " O   HOH Z 299 " =    2.312
peak=    3.044 closest distance to " CA  ALA A 233 " =    1.446
peak=    3.017 closest distance to " O   HOH Z 197 " =    2.050

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.784 - 5.149
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.784 - 5.149

peak=   -4.657 closest distance to " O   HOH Z 266 " =    4.175
peak=   -4.321 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.237 closest distance to " O   ILE A 109 " =    2.644
peak=   -4.216 closest distance to " O   HOH Z 377 " =    2.009
peak=   -4.192 closest distance to " O   HOH Z  52 " =    1.467
peak=   -4.148 closest distance to " OG  SER A  97 " =    2.169
peak=   -4.146 closest distance to " O   VAL A  67 " =    2.785
peak=   -4.144 closest distance to " OXT GLY A 302 " =    2.898
peak=   -4.144 closest distance to " O   HOH Z 290 " =    1.061
peak=   -4.101 closest distance to " O   HOH Z  13 " =    1.451
peak=   -4.045 closest distance to " O   HOH Z 407 " =    3.341
peak=   -4.040 closest distance to " N   ALA A  43 " =    2.507
peak=   -4.034 closest distance to " O   HOH Z  19 " =    2.161
peak=   -4.030 closest distance to " CD2 LEU A 300 " =    2.951
peak=   -3.981 closest distance to " O   HOH Z 292 " =    4.485
peak=   -3.969 closest distance to " CD1 LEU A 228 " =    2.312
peak=   -3.946 closest distance to " O   HOH Z  92 " =    1.548
peak=   -3.926 closest distance to " O   HOH Z 353 " =    2.237
peak=   -3.918 closest distance to " O   HOH Z  17 " =    1.420
peak=   -3.909 closest distance to " CB  PRO A 243 " =    2.609
peak=   -3.908 closest distance to " CD2 LEU A 143 " =    2.546
peak=   -3.891 closest distance to " CB  ALA A 291 " =    2.403
peak=   -3.888 closest distance to " OG  SER A  62 " =    1.487
peak=   -3.875 closest distance to " O   HOH Z 388 " =    2.019
peak=   -3.867 closest distance to " O   HOH Z  11 " =    1.834
peak=   -3.867 closest distance to " NH2 ARG A  66 " =    1.799
peak=   -3.864 closest distance to " N   GLN A  58 " =    1.698
peak=   -3.852 closest distance to " O   SER A 210 " =    1.922
peak=   -3.850 closest distance to " CD  ARG A 139 " =    1.627
peak=   -3.836 closest distance to " O   HOH Z 372 " =    2.537
peak=   -3.834 closest distance to " CB  TYR A  15 " =    2.218
peak=   -3.833 closest distance to " O   HOH Z  10 " =    1.624
peak=   -3.825 closest distance to " N   MET A 188 " =    1.848
peak=   -3.812 closest distance to " O   PRO A 163 " =    2.102
peak=   -3.795 closest distance to " O   HOH Z 231 " =    2.170
peak=   -3.792 closest distance to " C   ALA A 158 " =    1.196
peak=   -3.783 closest distance to " O   HOH Z  43 " =    1.552
peak=   -3.775 closest distance to " CD2 LEU A 237 " =    2.589
peak=   -3.766 closest distance to " CG  ASP A 231 " =    0.897
peak=   -3.764 closest distance to " C   HIS A 108 " =    1.111
peak=   -3.749 closest distance to " OG ASER A 134 " =    1.319
peak=   -3.743 closest distance to " CH2 TRP A 179 " =    1.235
peak=   -3.743 closest distance to " N   SER A 276 " =    1.356
peak=   -3.742 closest distance to " O   HOH Z  97 " =    1.629
peak=   -3.738 closest distance to " O   HOH Z 385 " =    2.046
peak=   -3.737 closest distance to " CD1 LEU A 101 " =    2.538
peak=   -3.727 closest distance to " O   HOH Z  93 " =    1.445
peak=   -3.702 closest distance to " OG BSER A 134 " =    1.707
peak=   -3.698 closest distance to " O   HOH Z 377 " =    1.100
peak=   -3.697 closest distance to " ND2 ASN A  45 " =    0.960
peak=   -3.687 closest distance to " ND2 ASN A 187 " =    1.544
peak=   -3.687 closest distance to " O   HOH Z  38 " =    1.386
peak=   -3.687 closest distance to " CD  ARG A  14 " =    3.402
peak=   -3.682 closest distance to " CE  MET A  93 " =    1.209
peak=   -3.675 closest distance to " OD1 ASN A 148 " =    1.683
peak=   -3.675 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.668 closest distance to " CD  ARG A 195 " =    5.149
peak=   -3.660 closest distance to " O   HOH Z 166 " =    1.817
peak=   -3.650 closest distance to " O   GLY A 196 " =    1.156
peak=   -3.623 closest distance to " CG  GLU A  53 " =    1.505
peak=   -3.611 closest distance to " SG ACYS A 201 " =    2.179
peak=   -3.586 closest distance to " O   HOH Z 166 " =    1.453
peak=   -3.585 closest distance to " CB  ASN A  39 " =    2.268
peak=   -3.585 closest distance to " CD  LYS A 289 " =    2.534
peak=   -3.566 closest distance to " NE2 GLN A  58 " =    0.958
peak=   -3.558 closest distance to " O   HOH Z 234 " =    4.193
peak=   -3.552 closest distance to " CG  ARG A  66 " =    2.365
peak=   -3.551 closest distance to " CE2 TYR A  30 " =    2.784
peak=   -3.549 closest distance to " C   ASN A 285 " =    2.515
peak=   -3.546 closest distance to " CB  ASP A 132 " =    2.318
peak=   -3.544 closest distance to " CA  VAL A  67 " =    2.797
peak=   -3.544 closest distance to " NH2 ARG A  79 " =    1.847
peak=   -3.543 closest distance to " CZ  PHE A  59 " =    1.732
peak=   -3.537 closest distance to " O   HOH Z 283 " =    1.718
peak=   -3.536 closest distance to " CD1 LEU A 101 " =    2.742
peak=   -3.533 closest distance to " O   HOH Z  98 " =    1.910
peak=   -3.521 closest distance to " O   HOH Z 118 " =    2.876
peak=   -3.520 closest distance to " CB  SER A 245 " =    2.425
peak=   -3.518 closest distance to " O   HOH Z 151 " =    1.424
peak=   -3.507 closest distance to " O   GLY A 211 " =    1.467
peak=   -3.505 closest distance to " O   HOH Z  11 " =    1.955
peak=   -3.500 closest distance to " CG  GLN A  58 " =    1.285
peak=   -3.493 closest distance to " O   HOH Z 185 " =    2.241
peak=   -3.484 closest distance to " O   HOH Z 435 " =    2.503
peak=   -3.483 closest distance to " N   THR A 157 " =    1.627
peak=   -3.481 closest distance to " CD2 PHE A  59 " =    2.454
peak=   -3.481 closest distance to " CB  CYS A 254 " =    2.453
peak=   -3.480 closest distance to " OE1 GLN A 223 " =    1.988
peak=   -3.471 closest distance to " CA  VAL A 232 " =    2.458
peak=   -3.465 closest distance to " N   GLN A 122 " =    1.595
peak=   -3.463 closest distance to " O   VAL A 153 " =    2.352
peak=   -3.462 closest distance to " OG BSER A 134 " =    1.266
peak=   -3.458 closest distance to " OE2 GLU A   2 " =    1.612
peak=   -3.455 closest distance to " O   HOH Z  71 " =    1.214
peak=   -3.449 closest distance to " NH1 ARG A 195 " =    2.572
peak=   -3.445 closest distance to " CE  MET A 105 " =    2.042
peak=   -3.426 closest distance to " O   HOH Z 361 " =    3.407
peak=   -3.423 closest distance to " O   HOH Z  76 " =    2.024
peak=   -3.422 closest distance to " ND2 ASN A  45 " =    1.195
peak=   -3.415 closest distance to " CD1 PHE A  59 " =    1.846
peak=   -3.411 closest distance to " O   VAL A 174 " =    2.087
peak=   -3.411 closest distance to " CB  LEU A 167 " =    2.160
peak=   -3.408 closest distance to " CD  GLN A 223 " =    1.357
peak=   -3.408 closest distance to " CD  GLN A  88 " =    2.026
peak=   -3.401 closest distance to " OD1 ASP A 191 " =    1.702
peak=   -3.393 closest distance to " CB  ALA A 248 " =    1.941
peak=   -3.392 closest distance to " O   HOH Z 311 " =    3.640
peak=   -3.392 closest distance to " N   ALA A 226 " =    2.083
peak=   -3.389 closest distance to " O   HOH Z 266 " =    4.608
peak=   -3.386 closest distance to " O   ALA A 160 " =    1.531
peak=   -3.384 closest distance to " CA  ASP A 298 " =    1.092
peak=   -3.384 closest distance to " O   GLY A 118 " =    2.153
peak=   -3.373 closest distance to " CG  PHE A 283 " =    2.649
peak=   -3.365 closest distance to " C   GLN A 240 " =    2.328
peak=   -3.360 closest distance to " O   HOH Z  15 " =    1.647
peak=   -3.352 closest distance to " CG  ASP A  50 " =    2.452
peak=   -3.350 closest distance to " O   ASN A 301 " =    1.461
peak=   -3.344 closest distance to " O   HOH Z 108 " =    2.393
peak=   -3.339 closest distance to " O   HOH Z 409 " =    4.691
peak=   -3.338 closest distance to " CB  SER A 258 " =    2.080
peak=   -3.335 closest distance to " O   HOH Z 313 " =    0.974
peak=   -3.334 closest distance to " O   HOH Z 165 " =    2.057
peak=   -3.330 closest distance to " NH2 ARG A  66 " =    5.066
peak=   -3.321 closest distance to " O   HOH Z 350 " =    1.588
peak=   -3.314 closest distance to " O   HOH Z 275 " =    1.458
peak=   -3.310 closest distance to " CG  LEU A  83 " =    1.933
peak=   -3.310 closest distance to " O   HOH Z 385 " =    3.724
peak=   -3.300 closest distance to " O   HOH Z  60 " =    1.967
peak=   -3.299 closest distance to " O   HOH Z  98 " =    2.304
peak=   -3.298 closest distance to " OD2 ASP A 171 " =    1.672
peak=   -3.295 closest distance to " O   HOH Z 128 " =    2.459
peak=   -3.289 closest distance to " O   HOH Z 396 " =    1.623
peak=   -3.287 closest distance to " CZ  TYR A 169 " =    1.921
peak=   -3.286 closest distance to " O   HOH Z  15 " =    2.059
peak=   -3.281 closest distance to " C   LEU A 143 " =    1.318
peak=   -3.280 closest distance to " O   HOH Z 393 " =    1.537
peak=   -3.279 closest distance to " OE1 GLN A  77 " =    1.785
peak=   -3.276 closest distance to " O   ALA A  34 " =    2.645
peak=   -3.275 closest distance to " OG  SER A  26 " =    1.284
peak=   -3.275 closest distance to " CB  PRO A 163 " =    2.709
peak=   -3.274 closest distance to " CB  ALA A  51 " =    1.853
peak=   -3.270 closest distance to " CA  GLY A 203 " =    2.111
peak=   -3.268 closest distance to " O   VAL A 125 " =    2.114
peak=   -3.268 closest distance to " O   SER A 135 " =    1.581
peak=   -3.263 closest distance to " CG  PRO A 163 " =    2.494
peak=   -3.262 closest distance to " O   LEU A 167 " =    1.520
peak=   -3.253 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.252 closest distance to " O   HOH Z  88 " =    2.116
peak=   -3.250 closest distance to " OG  SER A  87 " =    1.413
peak=   -3.248 closest distance to " O   HOH Z 196 " =    2.150
peak=   -3.230 closest distance to " O   PHE A 218 " =    1.469
peak=   -3.230 closest distance to " ND2 ASN A 249 " =    1.989
peak=   -3.229 closest distance to " CE  LYS A  76 " =    2.950
peak=   -3.228 closest distance to " CD2 TYR A 293 " =    2.126
peak=   -3.228 closest distance to " O   HOH Z  98 " =    1.395
peak=   -3.225 closest distance to " O   HOH Z   6 " =    1.836
peak=   -3.222 closest distance to " N   GLY A 133 " =    1.881
peak=   -3.222 closest distance to " CB  ALA A  43 " =    2.346
peak=   -3.218 closest distance to " CD  GLN A  88 " =    0.784
peak=   -3.217 closest distance to " CG  TRP A 266 " =    1.608
peak=   -3.214 closest distance to " O   HOH Z 148 " =    3.498
peak=   -3.209 closest distance to " OD1 ASP A 171 " =    1.589
peak=   -3.207 closest distance to " O   HOH Z 176 " =    0.896
peak=   -3.205 closest distance to " O   HOH Z 265 " =    1.965
peak=   -3.202 closest distance to " OD2 ASP A  65 " =    1.704
peak=   -3.199 closest distance to " CG2 ILE A  49 " =    2.766
peak=   -3.197 closest distance to " OD2 ASP A 171 " =    2.320
peak=   -3.196 closest distance to " CB  CYS A 201 " =    2.501
peak=   -3.185 closest distance to " NH2 ARG A 159 " =    2.420
peak=   -3.175 closest distance to " CG  GLU A 152 " =    2.239
peak=   -3.175 closest distance to " CB  ASP A 286 " =    2.120
peak=   -3.171 closest distance to " ND2 ASN A 215 " =    2.157
peak=   -3.168 closest distance to " CE3 TRP A  70 " =    1.683
peak=   -3.167 closest distance to " CB  PHE A 192 " =    1.915
peak=   -3.166 closest distance to " O   HOH Z 264 " =    1.841
peak=   -3.161 closest distance to " O   HOH Z 417 " =    2.624
peak=   -3.157 closest distance to " ND2 ASN A  60 " =    1.510
peak=   -3.156 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.149 closest distance to " OG ASER A 216 " =    1.044
peak=   -3.138 closest distance to " N   ALA A 248 " =    1.692
peak=   -3.136 closest distance to " CB  TRP A  85 " =    2.493
peak=   -3.133 closest distance to " O   HOH Z  90 " =    1.860
peak=   -3.130 closest distance to " CZ  ARG A 259 " =    0.873
peak=   -3.129 closest distance to " NE  ARG A 259 " =    1.151
peak=   -3.127 closest distance to " OH  TYR A 169 " =    0.995
peak=   -3.114 closest distance to " CG2 VAL A 189 " =    2.160
peak=   -3.111 closest distance to " CB  ILE A 239 " =    2.016
peak=   -3.109 closest distance to " CG2AVAL A  41 " =    2.819
peak=   -3.107 closest distance to " CD1 PHE A  16 " =    2.684
peak=   -3.107 closest distance to " CG  ARG A 259 " =    2.847
peak=   -3.107 closest distance to " OE1 GLN A 223 " =    2.104
peak=   -3.102 closest distance to " O   HOH Z 310 " =    3.491
peak=   -3.097 closest distance to " CG1 VAL A 197 " =    2.249
peak=   -3.088 closest distance to " CB  PHE A 208 " =    2.227
peak=   -3.085 closest distance to " O   HOH Z 323 " =    1.356
peak=   -3.070 closest distance to " OD1 ASP A 200 " =    1.361
peak=   -3.063 closest distance to " CZ  ARG A  66 " =    0.968
peak=   -3.054 closest distance to " O   HOH Z 222 " =    1.239
peak=   -3.050 closest distance to " CD2 LEU A 237 " =    2.437
peak=   -3.047 closest distance to " O   PRO A 198 " =    1.729
peak=   -3.046 closest distance to " O   HOH Z 423 " =    2.339
peak=   -3.042 closest distance to " CA  ARG A 139 " =    0.988

================= 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    :  0.4208 0.4201   6.222047e+00   6.224215e+00
   1_bss:  0.4109 0.4107   6.214467e+00   6.209623e+00
   1_xyz:  0.2902 0.3232   5.947389e+00   6.030518e+00
   1_adp:  0.2648 0.3305   5.895500e+00   6.046092e+00
   1_occ:  0.2644 0.3306   5.894391e+00   6.045391e+00
   2_bss:  0.2629 0.3271   5.891372e+00   6.041181e+00
   2_xyz:  0.2005 0.2572   5.658587e+00   5.853105e+00
   2_adp:  0.1883 0.2439   5.607841e+00   5.805831e+00
   2_occ:  0.1881 0.2439   5.607445e+00   5.805355e+00
   3_bss:  0.1881 0.2436   5.606041e+00   5.803426e+00
   3_xyz:  0.1421 0.1892   5.346812e+00   5.567578e+00
   3_adp:  0.1308 0.1776   5.274953e+00   5.498800e+00
   3_occ:  0.1307 0.1773   5.274191e+00   5.497908e+00
   4_bss:  0.1309 0.1767   5.275342e+00   5.497740e+00
   4_xyz:  0.1194 0.1645   5.199874e+00   5.428052e+00
   4_adp:  0.1158 0.1628   5.181213e+00   5.416657e+00
   4_occ:  0.1157 0.1628   5.180896e+00   5.416562e+00
   5_bss:  0.1157 0.1627   5.180754e+00   5.416430e+00
   5_xyz:  0.1103 0.1596   5.150531e+00   5.397145e+00
   5_adp:  0.1098 0.1588   5.146805e+00   5.393231e+00
   5_occ:  0.1098 0.1587   5.146443e+00   5.393096e+00
   5_bss:  0.1098 0.1587   5.146505e+00   5.393110e+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:  0.300  50.000  -1.801   0.002   2.748   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -1.801   0.002   2.748   0.000   0.000   0.000
   1_adp:  0.300  50.000  -1.801   0.002   2.748   0.000   0.000   0.000
   1_occ:  0.300  50.000  -1.801   0.002   2.748   0.000   0.000   0.000
   2_bss:  0.327  60.564  -2.146  -1.114   0.139  -0.000   0.000   0.000
   2_xyz:  0.327  60.564  -2.146  -1.114   0.139  -0.000   0.000   0.000
   2_adp:  0.327  60.564  -2.146  -1.114   0.139  -0.000   0.000   0.000
   2_occ:  0.327  60.564  -2.146  -1.114   0.139  -0.000   0.000   0.000
   3_bss:  0.327  60.564  -2.268  -1.591  -1.130  -0.000  -0.000  -0.000
   3_xyz:  0.327  60.564  -2.268  -1.591  -1.130  -0.000  -0.000  -0.000
   3_adp:  0.327  60.564  -2.268  -1.591  -1.130  -0.000  -0.000  -0.000
   3_occ:  0.327  60.564  -2.268  -1.591  -1.130  -0.000  -0.000  -0.000
   4_bss:  0.322  50.764  -2.511  -2.095  -1.941  -0.000  -0.000  -0.000
   4_xyz:  0.322  50.764  -2.511  -2.095  -1.941  -0.000  -0.000  -0.000
   4_adp:  0.322  50.764  -2.511  -2.095  -1.941  -0.000  -0.000  -0.000
   4_occ:  0.322  50.764  -2.511  -2.095  -1.941  -0.000  -0.000  -0.000
   5_bss:  0.322  50.764  -2.437  -2.115  -2.083  -0.000  -0.000  -0.000
   5_xyz:  0.322  50.764  -2.437  -2.115  -2.083  -0.000  -0.000  -0.000
   5_adp:  0.322  50.764  -2.437  -2.115  -2.083  -0.000  -0.000  -0.000
   5_occ:  0.322  50.764  -2.437  -2.115  -2.083  -0.000  -0.000  -0.000
   5_bss:  0.322  50.695  -2.245  -1.936  -1.920  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.417 0.5148  0.6829    55322.287
   1_bss:  48.677 0.5346  0.7201    51290.512
   1_xyz:  34.067 0.7124  0.9265    28687.918
   1_adp:  35.273 0.6973  0.9161    30150.004
   1_occ:  35.228 0.6978  0.9166    30085.576
   2_bss:  34.877 0.7018  0.8799    29612.893
   2_xyz:  26.483 0.7945  0.9624    17724.800
   2_adp:  24.501 0.8164  0.9704    15797.873
   2_occ:  24.504 0.8163  0.9702    15792.053
   3_bss:  24.394 0.8174  0.9492    15688.181
   3_xyz:  18.259 0.8772  0.9890     9281.515
   3_adp:  16.608 0.8927  0.9940     8166.488
   3_occ:  16.584 0.8929  0.9939     8150.872
   4_bss:  16.570 0.8931  0.9752     8140.031
   4_xyz:  15.038 0.9061  0.9800     6944.930
   4_adp:  14.752 0.9088  0.9764     6770.920
   4_occ:  14.745 0.9088  0.9763     6769.231
   5_bss:  14.742 0.9089  0.9753     6770.366
   5_xyz:  14.395 0.9116  0.9762     6514.365
   5_adp:  14.275 0.9128  0.9725     6469.595
   5_occ:  14.267 0.9128  0.9723     6465.150
   5_bss:  14.268 0.9128  0.9760     6465.874
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8269e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8269e-01
   1_xyz:   1.391  0.011  0.085 15.686  0.005  4.113   1.0750e-01
   1_adp:   1.391  0.011  0.085 15.686  0.005  4.113   1.0750e-01
   1_occ:   1.391  0.011  0.085 15.686  0.005  4.113   1.0750e-01
   2_bss:   1.391  0.011  0.085 15.686  0.005  4.113   1.0750e-01
   2_xyz:   1.085  0.007  0.072 14.019  0.005  4.127   6.2238e-02
   2_adp:   1.085  0.007  0.072 14.019  0.005  4.127   6.2238e-02
   2_occ:   1.085  0.007  0.072 14.019  0.005  4.127   6.2238e-02
   3_bss:   1.085  0.007  0.072 14.019  0.005  4.127   6.2238e-02
   3_xyz:   1.056  0.007  0.073 14.361  0.004  4.113   6.2906e-02
   3_adp:   1.056  0.007  0.073 14.361  0.004  4.113   6.2906e-02
   3_occ:   1.056  0.007  0.073 14.361  0.004  4.113   6.2906e-02
   4_bss:   1.056  0.007  0.073 14.361  0.004  4.113   6.2906e-02
   4_xyz:   1.029  0.007  0.074 14.499  0.004  4.116   6.0599e-02
   4_adp:   1.029  0.007  0.074 14.499  0.004  4.116   6.0599e-02
   4_occ:   1.029  0.007  0.074 14.499  0.004  4.116   6.0599e-02
   5_bss:   1.029  0.007  0.074 14.499  0.004  4.116   6.0599e-02
   5_xyz:   1.094  0.009  0.078 14.632  0.004  4.111   6.8198e-02
   5_adp:   1.094  0.009  0.078 14.632  0.004  4.111   6.8198e-02
   5_occ:   1.094  0.009  0.078 14.632  0.004  4.111   6.8198e-02
   5_bss:   1.094  0.009  0.078 14.632  0.004  4.111   6.8198e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.461   2.4114e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.461   2.4114e-01
   1_xyz:   8.639  0.067  0.316 88.221  0.032  2.086   1.0630e-01
   1_adp:   8.639  0.067  0.316 88.221  0.032  2.086   1.0630e-01
   1_occ:   8.639  0.067  0.316 88.221  0.032  2.086   1.0630e-01
   2_bss:   8.639  0.067  0.316 88.221  0.032  2.086   1.0630e-01
   2_xyz:   7.200  0.045  0.272 86.466  0.051  2.348   4.9757e-02
   2_adp:   7.200  0.045  0.272 86.466  0.051  2.348   4.9757e-02
   2_occ:   7.200  0.045  0.272 86.466  0.051  2.348   4.9757e-02
   3_bss:   7.200  0.045  0.272 86.466  0.051  2.348   4.9757e-02
   3_xyz:   7.173  0.054  0.328 79.920  0.035  2.320   4.5953e-02
   3_adp:   7.173  0.054  0.328 79.920  0.035  2.320   4.5953e-02
   3_occ:   7.173  0.054  0.328 79.920  0.035  2.320   4.5953e-02
   4_bss:   7.173  0.054  0.328 79.920  0.035  2.320   4.5953e-02
   4_xyz:   7.298  0.037  0.235 84.051  0.032  2.328   4.4169e-02
   4_adp:   7.298  0.037  0.235 84.051  0.032  2.328   4.4169e-02
   4_occ:   7.298  0.037  0.235 84.051  0.032  2.328   4.4169e-02
   5_bss:   7.298  0.037  0.235 84.051  0.032  2.328   4.4169e-02
   5_xyz:   7.131  0.045  0.246 82.426  0.034  2.269   5.6563e-02
   5_adp:   7.131  0.045  0.246 82.426  0.034  2.269   5.6563e-02
   5_occ:   7.131  0.045  0.246 82.426  0.034  2.269   5.6563e-02
   5_bss:   7.131  0.045  0.246 82.426  0.034  2.269   5.6563e-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:  92.95   0.00  18.34  92.46   0.00  14.11  92.95   4.18  41.36
   1_occ:  92.95   0.00  18.34  92.46   0.00  14.11  92.95   4.18  41.36
   2_bss:  92.95   0.00  18.34  92.46   0.00  14.11  92.95   4.18  41.36
   2_xyz:  92.95   0.00  18.34  92.46   0.00  14.11  92.95   4.18  41.36
   2_adp:  88.28   0.00  18.11  86.47   0.00  13.71  88.28   5.46  42.06
   2_occ:  88.28   0.00  18.11  86.47   0.00  13.71  88.28   5.46  42.06
   3_bss:  88.28   0.00  18.11  86.47   0.00  13.71  88.28   5.46  42.06
   3_xyz:  88.28   0.00  18.11  86.47   0.00  13.71  88.28   5.46  42.06
   3_adp:  87.34   0.00  17.74  85.67   0.00  13.29  87.34   5.17  41.95
   3_occ:  87.34   0.00  17.74  85.67   0.00  13.29  87.34   5.17  41.95
   4_bss:  87.34   0.00  17.74  85.67   0.00  13.29  87.34   5.17  41.95
   4_xyz:  87.34   0.00  17.74  85.67   0.00  13.29  87.34   5.17  41.95
   4_adp:  96.63   1.62  17.63  96.63   1.62  13.17  82.45   5.10  41.95
   4_occ:  96.63   1.62  17.63  96.63   1.62  13.17  82.45   5.10  41.95
   5_bss:  96.63   1.62  17.63  96.63   1.62  13.17  82.45   5.10  41.95
   5_xyz:  96.63   1.62  17.63  96.63   1.62  13.17  82.45   5.10  41.95
   5_adp:  97.36   1.93  17.20  97.36   1.93  12.98  79.59   5.91  40.19
   5_occ:  97.36   1.93  17.20  97.36   1.93  12.98  79.59   5.91  40.19
   5_bss:  97.29   1.86  17.13  97.29   1.86  12.91  79.52   5.84  40.12
------------------------------------------------------------------------
 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:    1.974    0.019    0.351
   1_adp:    1.974    0.019    0.351
   1_occ:    1.974    0.019    0.351
   2_bss:    1.974    0.019    0.351
   2_xyz:    1.575    0.044    0.458
   2_adp:    1.575    0.044    0.458
   2_occ:    1.575    0.044    0.458
   3_bss:    1.575    0.044    0.458
   3_xyz:    1.638    0.057    0.588
   3_adp:    1.638    0.057    0.588
   3_occ:    1.638    0.057    0.588
   4_bss:    1.638    0.057    0.588
   4_xyz:    1.708    0.060    0.610
   4_adp:    1.708    0.060    0.610
   4_occ:    1.708    0.060    0.610
   5_bss:    1.708    0.060    0.610
   5_xyz:    1.859    0.063    0.632
   5_adp:    1.859    0.063    0.632
   5_occ:    1.859    0.063    0.632
   5_bss:    1.859    0.063    0.632
------------------------------------------------------------------------

CPU time actual refinement: 353.55


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_924/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_924/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_924/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_924/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_924/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.40 
  Macro-tasks:
    bulk solvent and scale       = 40.14  
    individual site refinement   = 145.41 
    weights calculation          = 30.60  
    collect and process          = 6.64   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 222.91 
  Micro-tasks:
    mask                            = 1.92   
    f_calc                          = 116.21 
    alpha_beta                      = 8.26   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 123.67 
    fmodel                         = 6.56   
    r_factors                      = 0.17   
    phase_errors                   = 10.91  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 269.17 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.055 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    634 calls, 115.92 s
gradients_fft:          579 calls, 110.45 s

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

# Date 2008-01-16 Time 05:59:40 PST -0800 (1200491980.57 s)
Start R-work = 0.4208, R-free = 0.4201 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1795 (no bulk solvent and anisotropic scale)

Start R-work = 0.4109, R-free = 0.4107
Final R-work = 0.1098, R-free = 0.1587