# Date 2008-01-16 Time 03:56:17 PST -0800 (1200484577.74 s)
#phil __OFF__

Command line arguments: "../107.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14972
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 107

-------------------------------------------------------------------------------
  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: (68.4938, 47.8686, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9941 1.95097
Completeness in resolution range: 0.907781
Completeness with d_max=infinity: 0.905096

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9941
                             d_min =   1.9510

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: (68.4938, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9941 1.95097
Completeness in resolution range: 0.907781
Completeness with d_max=infinity: 0.905096

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9945 -  4.1758 [2261/2289]  2030   231  10.2%
  bin  2:  4.1758 -  3.3264 [2181/2204]  1962   219  10.0%
  bin  3:  3.3264 -  2.9094 [2153/2178]  1947   206   9.6%
  bin  4:  2.9094 -  2.6450 [2114/2141]  1897   217  10.3%
  bin  5:  2.6450 -  2.4563 [2097/2130]  1884   213  10.2%
  bin  6:  2.4563 -  2.3120 [2116/2144]  1908   208   9.8%
  bin  7:  2.3120 -  2.1966 [2079/2115]  1877   202   9.7%
  bin  8:  2.1966 -  2.1012 [2102/2144]  1889   213  10.1%
  bin  9:  2.1012 -  2.0205 [1947/2113]  1757   190   9.8%
  bin 10:  2.0205 -  1.9510 [ 539/2121]   479    60  11.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_107/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: 0.15 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:
        0.92 -     1.72: 9
        1.72 -     2.51: 55
        2.51 -     3.31: 3767
        3.31 -     4.10: 9398
        4.10 -     4.90: 15108
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  0.919 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.174 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.325 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.326 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.442 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28332 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_107/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_107/model_refine_001.geo

CPU time processing inputs: 9.31


============================ 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 = 68.49375 47.8686 87.68585 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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4823   r_free= 0.4797   ksol= 0.00   Bsol= 0.00   scale= 0.879    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.287984                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.6581 0.99   1472  161 0.3783 0.4031      6.5758      6.6219|
|  2:  4.6581 -  3.7158 0.99   1416  156 0.4217 0.4250      6.8224      6.8292|
|  3:  3.7158 -  3.2515 0.99   1376  158 0.4648 0.4594      6.6742      6.6858|
|  4:  3.2515 -  2.9567 0.98   1384  145 0.4816 0.4529      6.5039      6.4924|
|  5:  2.9567 -  2.7462 0.99   1372  157 0.5090 0.5006      6.3587      6.3798|
|  6:  2.7462 -  2.5851 0.99   1370  151 0.5103 0.5302      6.2673      6.1805|
|  7:  2.5851 -  2.4563 0.98   1330  158 0.5150 0.4429      6.2223      6.1409|
|  8:  2.4563 -  2.3498 0.98   1376  145 0.5388 0.5374      6.1639      6.1945|
|  9:  2.3498 -  2.2596 0.99   1339  145 0.5462 0.5187      6.1184      6.1822|
| 10:  2.2596 -  2.1819 0.99   1354  146 0.5270 0.5104      6.0807      6.0942|
| 11:  2.1819 -  2.1139 0.97   1334  157 0.5401 0.5568      6.0054      6.0294|
| 12:  2.1139 -  2.0536 0.98   1333  149 0.5342 0.5221      5.9536      5.9347|
| 13:  2.0536 -  1.9997 0.71    954  104 0.5099 0.5794      5.8602      5.8194|
| 14:  1.9997 -  1.9510 0.16    220   27 0.4932 0.4832      5.9128       5.715|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9945 -  4.6581  1472   161  0.67  36.69   0.82     0.69      79208.40|
|  2:  4.6581 -  3.7158  1416   156  0.68  37.24   0.91     0.77     115995.27|
|  3:  3.7158 -  3.2515  1376   158  0.56  47.15   0.89     0.75     121989.57|
|  4:  3.2515 -  2.9567  1384   145  0.47  54.05   0.89     0.66     103957.21|
|  5:  2.9567 -  2.7462  1372   157  0.40  59.82   0.87     0.58      83636.57|
|  6:  2.7462 -  2.5851  1370   151  0.38  61.76   0.88     0.54      71370.01|
|  7:  2.5851 -  2.4563  1330   158  0.36  63.12   0.89     0.50      66023.63|
|  8:  2.4563 -  2.3498  1376   145  0.33  65.52   0.89     0.49      59666.83|
|  9:  2.3498 -  2.2596  1339   145  0.32  66.43   0.89     0.49      57595.26|
| 10:  2.2596 -  2.1819  1354   146  0.32  66.39   0.90     0.47      51256.89|
| 11:  2.1819 -  2.1139  1334   157  0.25  71.20   0.89     0.41      51283.88|
| 12:  2.1139 -  2.0536  1333   149  0.20  74.89   0.92     0.34      48903.37|
| 13:  2.0536 -  1.9997   954   104  0.18  76.35   0.94     0.32      43205.68|
| 14:  1.9997 -  1.9510   220    27  0.30  67.37   0.97     0.37      30188.07|
|alpha:            min =        0.32 max =            0.77 mean =         0.54|
|beta:             min =    30188.07 max =       121989.57 mean =     73908.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.47|
|phase err.(test): min =        0.00 max =           89.96 mean =        59.57|
|-----------------------------------------------------------------------------|

============================== 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 = 13.506046             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.537   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.080041              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.776   (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 |  0.919 -  1.318:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.318 -  1.716:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.716 -  2.114:       12 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.114 -  2.512:       43 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.512 -  2.910:     1428 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.910 -  3.308:     2339 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.308 -  3.706:     3709 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.706 -  4.104:     5689 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.104 -  4.502:     6616 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.502 -  4.900:     8492 |
|-----------------------------------------------------------------------------|
|-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 |        0.227 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  0.919 |       1.120 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    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 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4823   r_free= 0.4797   ksol= 0.00   Bsol= 0.00   scale= 0.879    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.287984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4761   r_free= 0.4701   ksol= 0.30   Bsol= 30.54   scale= 0.923   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,2.78,0.78,0.00,0.00,0.00); trace/3= 0.89                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.284063                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.208596             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.038   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.594268              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.337   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4761      final r-factor (work) = 0.3652          |
| start r-factor (free) = 0.4701      final r-factor (free) = 0.3954          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.4399 = 11.21 * 0.50 * 6.2833 + 1.00 * 0.2266                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.7705 = 11.21 * 0.50 * 6.1774 + 1.00 * 0.1504                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3652      final r-factor (work) = 0.3253          |
| start r-factor (free) = 0.3954      final r-factor (free) = 0.3999          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8544 = 1.59 * 1.00 * 6.1774 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6813 = 1.59 * 1.00 * 6.0580 + 1.00 * 0.0233                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.41  20.31    None  None   None       |
|    all(noH): 2823   0      0.00    102.41  20.31    None  None   None       |
|    Sol.    : 438    0      0.00    102.41  40.49    None  None   None       |
|    Mac.    : 2385   0      0.00    94.23   16.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.241:  915   |   5:    51.207 -  61.448:   81        |
|      1:    10.241 -  20.483:  828   |   6:    61.448 -  71.689:   55        |
|      2:    20.483 -  30.724:  485   |   7:    71.689 -  81.931:   28        |
|      3:    30.724 -  40.965:  250   |   8:    81.931 -  92.172:    3        |
|      4:    40.965 -  51.207:  173   |   9:    92.172 - 102.413:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3253 r_free = 0.3999             target_work(ml) = 6.063         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3251 r_free = 0.3999             target_work(ml) = 6.062         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3251   r_free= 0.3999   ksol= 0.30   Bsol= 30.54   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,2.78,0.78,0.00,0.00,0.00); trace/3= 0.89                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.062423                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3239   r_free= 0.3964   ksol= 0.31   Bsol= 49.64   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,1.15,0.34,0.00,0.00,0.00); trace/3= -0.02                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.058850                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.850164              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.305   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.507765              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.515  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3239      final r-factor (work) = 0.2583          |
| start r-factor (free) = 0.3964      final r-factor (free) = 0.3160          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9262 = 7.85 * 0.50 * 6.0573 + 1.00 * 0.1506                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5579 = 7.85 * 0.50 * 5.9794 + 1.00 * 0.0881                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2583      final r-factor (work) = 0.2411          |
| start r-factor (free) = 0.3160      final r-factor (free) = 0.3021          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0596 = 0.51 * 1.00 * 5.9794 + 1.00 * 0.0235                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9767 = 0.51 * 1.00 * 5.8378 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.86   19.14    None  None   None       |
|    all(noH): 2823   0      0.00    97.86   19.14    None  None   None       |
|    Sol.    : 438    0      2.50    97.86   40.46    None  None   None       |
|    Mac.    : 2385   0      0.00    89.58   15.22    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 -   9.786:  890   |   5:    48.928 -  58.714:   99        |
|      1:     9.786 -  19.571:  999   |   6:    58.714 -  68.499:   44        |
|      2:    19.571 -  29.357:  370   |   7:    68.499 -  78.285:   27        |
|      3:    29.357 -  39.142:  244   |   8:    78.285 -  88.070:   10        |
|      4:    39.142 -  48.928:  136   |   9:    88.070 -  97.856:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2411 r_free = 0.3021             target_work(ml) = 5.815         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2411 r_free = 0.3019             target_work(ml) = 5.814         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2411   r_free= 0.3019   ksol= 0.31   Bsol= 49.64   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,1.15,0.34,0.00,0.00,0.00); trace/3= -0.02                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.814103                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2406   r_free= 0.3020   ksol= 0.31   Bsol= 49.64   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-0.13,-0.27,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.813659                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.177150              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.783   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.179434              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.932  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2406      final r-factor (work) = 0.1911          |
| start r-factor (free) = 0.3020      final r-factor (free) = 0.2389          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3636 = 3.18 * 0.50 * 5.8388 + 1.00 * 0.0881                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1622 = 3.18 * 0.50 * 5.7241 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1911      final r-factor (work) = 0.1758          |
| start r-factor (free) = 0.2389      final r-factor (free) = 0.2330          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7637 = 1.18 * 1.00 * 5.7241 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5734 = 1.18 * 1.00 * 5.5610 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.72   19.56    None  None   None       |
|    all(noH): 2823   0      0.00    93.72   19.56    None  None   None       |
|    Sol.    : 438    0      5.36    93.70   46.28    None  None   None       |
|    Mac.    : 2385   0      0.00    93.72   14.65    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 -   9.372:  833   |   5:    46.859 -  56.231:  107        |
|      1:     9.372 -  18.744: 1110   |   6:    56.231 -  65.603:   71        |
|      2:    18.744 -  28.116:  327   |   7:    65.603 -  74.975:   59        |
|      3:    28.116 -  37.487:  147   |   8:    74.975 -  84.347:   23        |
|      4:    37.487 -  46.859:  121   |   9:    84.347 -  93.719:   25        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1758 r_free = 0.2330             target_work(ml) = 5.546         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1757 r_free = 0.2331             target_work(ml) = 5.546         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1757   r_free= 0.2331   ksol= 0.31   Bsol= 49.64   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-0.13,-0.27,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.546015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1754   r_free= 0.2325   ksol= 0.32   Bsol= 59.01   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.34,-1.25,-0.95,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.545825                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.353824              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.610   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.807764              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.752  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1754      final r-factor (work) = 0.1485          |
| start r-factor (free) = 0.2325      final r-factor (free) = 0.2031          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6201 = 2.35 * 0.50 * 5.5663 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5016 = 2.35 * 0.50 * 5.4745 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1485      final r-factor (work) = 0.1420          |
| start r-factor (free) = 0.2031      final r-factor (free) = 0.1945          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4367 = 0.81 * 1.00 * 5.4745 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3600 = 0.81 * 1.00 * 5.3816 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.82    101.19  19.04    None  None   None       |
|    all(noH): 2823   0      0.82    101.19  19.04    None  None   None       |
|    Sol.    : 438    0      6.34    93.79   46.34    None  None   None       |
|    Mac.    : 2385   0      0.82    101.19  14.03    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:     0.816 -  10.854: 1121   |   5:    51.004 -  61.042:   97        |
|      1:    10.854 -  20.891: 1028   |   6:    61.042 -  71.079:   66        |
|      2:    20.891 -  30.929:  210   |   7:    71.079 -  81.117:   35        |
|      3:    30.929 -  40.967:  122   |   8:    81.117 -  91.155:   22        |
|      4:    40.967 -  51.004:  111   |   9:    91.155 - 101.192:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1420 r_free = 0.1945             target_work(ml) = 5.359         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1419 r_free = 0.1944             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1944   ksol= 0.32   Bsol= 59.01   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.34,-1.25,-0.95,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.358431                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1422   r_free= 0.1947   ksol= 0.33   Bsol= 64.02   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.50,-1.60,-1.02,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.359532                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.950708              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.397  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.774202              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.676  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1422      final r-factor (work) = 0.1318          |
| start r-factor (free) = 0.1947      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3085 = 1.95 * 0.50 * 5.3825 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2507 = 1.95 * 0.50 * 5.3280 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1318      final r-factor (work) = 0.1299          |
| start r-factor (free) = 0.1825      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1378 = 0.77 * 1.00 * 5.3280 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1079 = 0.77 * 1.00 * 5.2902 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    105.50  18.69    None  None   None       |
|    all(noH): 2823   0      0.70    105.50  18.69    None  None   None       |
|    Sol.    : 438    0      5.81    100.29  45.71    None  None   None       |
|    Mac.    : 2385   0      0.70    105.50  13.73    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:     0.699 -  11.179: 1202   |   5:    53.099 -  63.579:   77        |
|      1:    11.179 -  21.659:  999   |   6:    63.579 -  74.059:   60        |
|      2:    21.659 -  32.139:  192   |   7:    74.059 -  84.539:   34        |
|      3:    32.139 -  42.619:  119   |   8:    84.539 -  95.019:   14        |
|      4:    42.619 -  53.099:  118   |   9:    95.019 - 105.499:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1299 r_free = 0.1792             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1298 r_free = 0.1792             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1792   ksol= 0.33   Bsol= 64.02   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.50,-1.60,-1.02,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280142                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.6581 0.99   1472  161 0.1013 0.1406      5.4195      5.6436|
|  2:  4.6581 -  3.7158 0.99   1416  156 0.0889 0.1070      5.4709      5.6457|
|  3:  3.7158 -  3.2515 0.99   1376  158 0.1215 0.1678      5.5697      5.9012|
|  4:  3.2515 -  2.9567 0.98   1384  145 0.1477 0.1975      5.5755       5.773|
|  5:  2.9567 -  2.7462 0.99   1372  157 0.1608 0.1937      5.4905       5.664|
|  6:  2.7462 -  2.5851 0.99   1370  151 0.1478 0.2350      5.3467      5.5685|
|  7:  2.5851 -  2.4563 0.98   1330  158 0.1451 0.1908      5.2997      5.4699|
|  8:  2.4563 -  2.3498 0.98   1376  145 0.1447 0.2200       5.243      5.4974|
|  9:  2.3498 -  2.2596 0.99   1339  145 0.1362 0.1954      5.1599      5.3881|
| 10:  2.2596 -  2.1819 0.99   1354  146 0.1383 0.2017      5.0929      5.2862|
| 11:  2.1819 -  2.1139 0.97   1334  157 0.1347 0.2030      5.0224      5.3704|
| 12:  2.1139 -  2.0536 0.98   1333  149 0.1334 0.1691      4.9609      5.1548|
| 13:  2.0536 -  1.9997 0.71    954  104 0.1306 0.2123      4.8938      5.1749|
| 14:  1.9997 -  1.9510 0.16    220   27 0.1278 0.2011      4.8946      5.0152|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9945 -  4.6581  1472   161  0.93   9.94   0.96     0.94       7953.52|
|  2:  4.6581 -  3.7158  1416   156  0.95   8.61   1.02     1.01       9926.84|
|  3:  3.7158 -  3.2515  1376   158  0.92  12.98   1.03     1.02      12136.77|
|  4:  3.2515 -  2.9567  1384   145  0.89  16.97   1.02     1.01      13162.44|
|  5:  2.9567 -  2.7462  1372   157  0.88  19.00   1.01     1.00      11722.73|
|  6:  2.7462 -  2.5851  1370   151  0.87  19.47   0.98     0.94       9255.36|
|  7:  2.5851 -  2.4563  1330   158  0.87  19.14   1.00     0.97       8641.61|
|  8:  2.4563 -  2.3498  1376   145  0.87  19.70   1.00     0.95       7761.16|
|  9:  2.3498 -  2.2596  1339   145  0.88  19.09   0.99     0.94       6742.71|
| 10:  2.2596 -  2.1819  1354   146  0.87  18.92   1.00     0.96       5860.01|
| 11:  2.1819 -  2.1139  1334   157  0.88  18.85   0.99     0.94       5236.75|
| 12:  2.1139 -  2.0536  1333   149  0.89  18.01   0.99     0.99       4589.70|
| 13:  2.0536 -  1.9997   954   104  0.87  19.25   0.99     0.97       4248.65|
| 14:  1.9997 -  1.9510   220    27  0.89  16.93   0.96     0.91       3719.22|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3719.22 max =        13162.44 mean =      8312.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.92 mean =        16.78|
|phase err.(test): min =        0.00 max =           89.24 mean =        16.28|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1792   ksol= 0.33   Bsol= 64.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.48,-1.58,-0.99,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280162                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1792   ksol= 0.33   Bsol= 64.00   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.48,-1.58,-0.99,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280162                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9945 -  4.6581 0.99   1472  161 0.1014 0.1406      5.4198      5.6435|
|  2:  4.6581 -  3.7158 0.99   1416  156 0.0889 0.1070      5.4708      5.6456|
|  3:  3.7158 -  3.2515 0.99   1376  158 0.1215 0.1678      5.5697      5.9013|
|  4:  3.2515 -  2.9567 0.98   1384  145 0.1477 0.1975      5.5755       5.773|
|  5:  2.9567 -  2.7462 0.99   1372  157 0.1608 0.1937      5.4906       5.664|
|  6:  2.7462 -  2.5851 0.99   1370  151 0.1478 0.2350      5.3467      5.5685|
|  7:  2.5851 -  2.4563 0.98   1330  158 0.1451 0.1908      5.2998      5.4699|
|  8:  2.4563 -  2.3498 0.98   1376  145 0.1447 0.2200       5.243      5.4974|
|  9:  2.3498 -  2.2596 0.99   1339  145 0.1362 0.1954      5.1599      5.3881|
| 10:  2.2596 -  2.1819 0.99   1354  146 0.1383 0.2017      5.0929      5.2862|
| 11:  2.1819 -  2.1139 0.97   1334  157 0.1347 0.2030      5.0224      5.3704|
| 12:  2.1139 -  2.0536 0.98   1333  149 0.1334 0.1691      4.9609      5.1548|
| 13:  2.0536 -  1.9997 0.71    954  104 0.1306 0.2123      4.8938      5.1749|
| 14:  1.9997 -  1.9510 0.16    220   27 0.1278 0.2011      4.8946      5.0152|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9945 -  4.6581  1472   161  0.93   9.94   0.97     0.94       7957.34|
|  2:  4.6581 -  3.7158  1416   156  0.95   8.61   1.02     1.01       9926.14|
|  3:  3.7158 -  3.2515  1376   158  0.92  12.98   1.03     1.02      12133.71|
|  4:  3.2515 -  2.9567  1384   145  0.89  16.97   1.02     1.01      13162.53|
|  5:  2.9567 -  2.7462  1372   157  0.88  19.00   1.01     1.00      11723.32|
|  6:  2.7462 -  2.5851  1370   151  0.87  19.48   0.98     0.94       9255.65|
|  7:  2.5851 -  2.4563  1330   158  0.87  19.14   1.00     0.97       8641.83|
|  8:  2.4563 -  2.3498  1376   145  0.87  19.70   1.00     0.95       7761.21|
|  9:  2.3498 -  2.2596  1339   145  0.88  19.09   0.99     0.94       6742.78|
| 10:  2.2596 -  2.1819  1354   146  0.87  18.92   1.00     0.96       5860.04|
| 11:  2.1819 -  2.1139  1334   157  0.88  18.85   0.99     0.94       5236.79|
| 12:  2.1139 -  2.0536  1333   149  0.89  18.01   0.99     0.99       4589.73|
| 13:  2.0536 -  1.9997   954   104  0.87  19.25   0.99     0.97       4248.68|
| 14:  1.9997 -  1.9510   220    27  0.89  16.93   0.96     0.91       3719.25|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3719.25 max =        13162.53 mean =      8312.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.92 mean =        16.78|
|phase err.(test): min =        0.00 max =           89.05 mean =        16.28|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.821)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    105.48  18.67    None  None   None       |
|    all(noH): 2823   0      0.68    105.48  18.67    None  None   None       |
|    Sol.    : 438    0      5.79    100.27  45.69    None  None   None       |
|    Mac.    : 2385   0      0.68    105.48  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:     0.676 -  11.156: 1202   |   5:    53.076 -  63.556:   77        |
|      1:    11.156 -  21.636:  999   |   6:    63.556 -  74.036:   60        |
|      2:    21.636 -  32.116:  192   |   7:    74.036 -  84.516:   34        |
|      3:    32.116 -  42.596:  119   |   8:    84.516 -  94.996:   14        |
|      4:    42.596 -  53.076:  118   |   9:    94.996 - 105.476:    8        |
|                               =>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: 0.571 - 4.511
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 309
   mapped sites are within: 0.717 - 4.511

peak=   11.198 closest distance to " O  BHOH Z  74 " =    1.439
peak=    7.865 closest distance to " O   HOH Z 203 " =    0.978
peak=    6.865 closest distance to " O   HOH Z 117 " =    1.585
peak=    6.859 closest distance to " O   HOH Z 255 " =    1.228
peak=    6.684 closest distance to " O   HOH Z  81 " =    1.169
peak=    5.548 closest distance to " O   HOH Z 248 " =    1.544
peak=    5.481 closest distance to " O   HOH Z 124 " =    1.286
peak=    5.340 closest distance to " O   HOH Z 102 " =    1.568
peak=    5.170 closest distance to " O   HOH Z 210 " =    1.265
peak=    5.065 closest distance to " O   HOH Z 403 " =    2.163
peak=    5.003 closest distance to " O   HOH Z  49 " =    1.502
peak=    4.993 closest distance to " CG  PRO A  54 " =    1.360
peak=    4.992 closest distance to " CZ3 TRP A 266 " =    1.060
peak=    4.876 closest distance to " O   GLN A  11 " =    0.953
peak=    4.862 closest distance to " CD2 TRP A 179 " =    1.353
peak=    4.851 closest distance to " O   HOH Z 394 " =    1.689
peak=    4.824 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.800 closest distance to " O   HOH Z  65 " =    1.159
peak=    4.789 closest distance to " O   HOH Z 113 " =    2.100
peak=    4.781 closest distance to " O   HOH Z 401 " =    1.401
peak=    4.739 closest distance to " CA  TYR A  30 " =    0.967
peak=    4.731 closest distance to " NH1AARG A 275 " =    1.151
peak=    4.719 closest distance to " O   HOH Z  54 " =    1.280
peak=    4.607 closest distance to " CB  GLN A 223 " =    1.408
peak=    4.559 closest distance to " O   HOH Z  43 " =    2.190
peak=    4.541 closest distance to " CB  ASN A 285 " =    1.003
peak=    4.478 closest distance to " CG AARG A 275 " =    1.252
peak=    4.401 closest distance to " O   HOH Z 412 " =    3.715
peak=    4.396 closest distance to " O   HOH Z 188 " =    2.768
peak=    4.359 closest distance to " O   HOH Z 417 " =    2.813
peak=    4.358 closest distance to " CG2BVAL A  41 " =    0.831
peak=    4.358 closest distance to " O   HOH Z 404 " =    1.295
peak=    4.333 closest distance to " CB  SER A  62 " =    1.071
peak=    4.314 closest distance to " O   HOH Z  97 " =    1.396
peak=    4.292 closest distance to " CZ  PHE A 218 " =    1.225
peak=    4.274 closest distance to " CA  ARG A  36 " =    1.103
peak=    4.268 closest distance to " O   HOH Z 178 " =    1.059
peak=    4.212 closest distance to " O   HOH Z 232 " =    2.418
peak=    4.199 closest distance to " O   HOH Z 433 " =    1.623
peak=    4.197 closest distance to " O   HOH Z 188 " =    1.455
peak=    4.191 closest distance to " O   HOH Z 134 " =    1.737
peak=    4.189 closest distance to " O   HOH Z 402 " =    1.621
peak=    4.185 closest distance to " O   HOH Z 132 " =    2.680
peak=    4.181 closest distance to " CB  PRO A  54 " =    1.082
peak=    4.175 closest distance to " NZ  LYS A 117 " =    2.979
peak=    4.134 closest distance to " O   HOH Z 186 " =    2.970
peak=    4.123 closest distance to " O   HOH Z  63 " =    1.975
peak=    4.113 closest distance to " O   HOH Z 128 " =    1.499
peak=    4.081 closest distance to " O   GLY A  23 " =    2.450
peak=    4.074 closest distance to " CG  PRO A 243 " =    1.132
peak=    4.072 closest distance to " CG  GLN A  58 " =    1.046
peak=    4.062 closest distance to " CB  SER A  63 " =    1.202
peak=    4.032 closest distance to " O   THR A 251 " =    1.310
peak=    4.029 closest distance to " CG  PRO A  90 " =    1.256
peak=    4.025 closest distance to " CB  GLN A 183 " =    1.238
peak=    4.024 closest distance to " O   HOH Z 414 " =    1.674
peak=    4.021 closest distance to " O   HOH Z 346 " =    1.769
peak=    4.015 closest distance to " O   HOH Z 116 " =    1.324
peak=    4.011 closest distance to " O   HOH Z 369 " =    1.943
peak=    4.011 closest distance to " O   HOH Z 298 " =    1.805
peak=    4.003 closest distance to " O   HOH Z 287 " =    1.484
peak=    3.983 closest distance to " O   HOH Z 250 " =    1.455
peak=    3.976 closest distance to " CB  ASN A 148 " =    1.355
peak=    3.973 closest distance to " O   HOH Z 193 " =    1.612
peak=    3.948 closest distance to " O   HOH Z 130 " =    2.518
peak=    3.921 closest distance to " CG  PRO A 198 " =    1.361
peak=    3.921 closest distance to " CB  ASN A 187 " =    1.353
peak=    3.890 closest distance to " O   HOH Z  80 " =    2.013
peak=    3.888 closest distance to " CA  ALA A 100 " =    1.170
peak=    3.876 closest distance to " CA  ARG A 195 " =    1.140
peak=    3.866 closest distance to " O   HOH Z 261 " =    2.347
peak=    3.859 closest distance to " O   HOH Z  39 " =    1.517
peak=    3.852 closest distance to " NH2BARG A 145 " =    2.305
peak=    3.846 closest distance to " CA  THR A 246 " =    1.092
peak=    3.840 closest distance to " CG  GLN A  11 " =    1.361
peak=    3.828 closest distance to " CD  ARG A 269 " =    1.039
peak=    3.822 closest distance to " O   HOH Z  69 " =    1.093
peak=    3.810 closest distance to " O   PRO A 198 " =    1.555
peak=    3.809 closest distance to " O   HOH Z 126 " =    1.498
peak=    3.808 closest distance to " CG1 ILE A  33 " =    1.227
peak=    3.799 closest distance to " O   THR A 220 " =    1.160
peak=    3.799 closest distance to " CB  TRP A 179 " =    1.253
peak=    3.796 closest distance to " O   HOH Z 214 " =    1.205
peak=    3.776 closest distance to " O   HOH Z 209 " =    2.205
peak=    3.771 closest distance to " CG  ARG A  66 " =    1.081
peak=    3.768 closest distance to " CD  PRO A  54 " =    1.077
peak=    3.759 closest distance to " O   HOH Z 406 " =    1.562
peak=    3.756 closest distance to " CA  ALA A 160 " =    0.961
peak=    3.755 closest distance to " O   HOH Z 298 " =    4.187
peak=    3.755 closest distance to " CA  ALA A  51 " =    1.000
peak=    3.753 closest distance to " CE  LYS A  76 " =    0.865
peak=    3.753 closest distance to " CD  LYS A  76 " =    1.709
peak=    3.753 closest distance to " O   HOH Z 236 " =    1.652
peak=    3.749 closest distance to " O   HOH Z 423 " =    1.802
peak=    3.746 closest distance to " CB  SER A  26 " =    1.784
peak=    3.743 closest distance to " CA  ARG A 156 " =    1.017
peak=    3.737 closest distance to " O   HOH Z 426 " =    1.296
peak=    3.735 closest distance to " O   VAL A  72 " =    1.371
peak=    3.719 closest distance to " O   HOH Z 272 " =    1.997
peak=    3.714 closest distance to " O   HOH Z 361 " =    3.097
peak=    3.713 closest distance to " O   HOH Z 234 " =    3.496
peak=    3.711 closest distance to " OE1 GLN A  55 " =    1.510
peak=    3.711 closest distance to " CB  GLU A 128 " =    1.172
peak=    3.710 closest distance to " CB  PRO A  90 " =    0.905
peak=    3.702 closest distance to " CZ  PHE A  38 " =    1.092
peak=    3.694 closest distance to " CG2AVAL A 121 " =    2.111
peak=    3.694 closest distance to " CD  ARG A 195 " =    1.040
peak=    3.692 closest distance to " OG BSER A 258 " =    2.868
peak=    3.689 closest distance to " O   HOH Z  35 " =    2.191
peak=    3.686 closest distance to " O   HOH Z  88 " =    3.501
peak=    3.678 closest distance to " O   ALA A 165 " =    1.461
peak=    3.665 closest distance to " CB  VAL A 265 " =    1.217
peak=    3.655 closest distance to " O   HOH Z 422 " =    0.717
peak=    3.648 closest distance to " O   HOH Z 340 " =    1.264
peak=    3.647 closest distance to " CB  GLU A 277 " =    3.706
peak=    3.643 closest distance to " O   HOH Z 421 " =    2.199
peak=    3.639 closest distance to " NH2 ARG A  56 " =    1.123
peak=    3.639 closest distance to " CB  ALA A 114 " =    0.831
peak=    3.637 closest distance to " O   HOH Z 357 " =    2.053
peak=    3.635 closest distance to " CB  GLN A 194 " =    0.921
peak=    3.634 closest distance to " O   SER A  87 " =    2.220
peak=    3.628 closest distance to " CB  PHE A  16 " =    1.151
peak=    3.627 closest distance to " O   HOH Z 299 " =    4.181
peak=    3.626 closest distance to " CB  ARG A 190 " =    1.820
peak=    3.611 closest distance to " O   HOH Z  48 " =    1.773
peak=    3.609 closest distance to " O   HOH Z 425 " =    1.400
peak=    3.609 closest distance to " O   THR A 182 " =    1.540
peak=    3.605 closest distance to " NE2 GLN A  11 " =    1.198
peak=    3.603 closest distance to " O   HOH Z 427 " =    3.266
peak=    3.603 closest distance to " CD  ARG A 139 " =    1.187
peak=    3.601 closest distance to " CD  LYS A 119 " =    1.727
peak=    3.587 closest distance to " O   HOH Z 282 " =    2.129
peak=    3.585 closest distance to " O   HOH Z 389 " =    1.839
peak=    3.580 closest distance to " O   HOH Z 279 " =    2.219
peak=    3.579 closest distance to " OD1 ASN A 217 " =    1.595
peak=    3.578 closest distance to " O   HOH Z 251 " =    1.563
peak=    3.576 closest distance to " CB  THR A  52 " =    0.801
peak=    3.559 closest distance to " O   HOH Z 298 " =    2.217
peak=    3.554 closest distance to " O   HOH Z  21 " =    1.835
peak=    3.553 closest distance to " CD  ARG A 159 " =    0.813
peak=    3.544 closest distance to " CD  LYS A 166 " =    1.586
peak=    3.543 closest distance to " O   HOH Z 365 " =    2.425
peak=    3.542 closest distance to " O   HOH Z 431 " =    1.141
peak=    3.541 closest distance to " O   HOH Z 291 " =    1.290
peak=    3.540 closest distance to " CB  SER A  62 " =    3.772
peak=    3.540 closest distance to " O   HOH Z 131 " =    2.475
peak=    3.532 closest distance to " N   SER A 164 " =    0.996
peak=    3.530 closest distance to " O   HOH Z  44 " =    2.523
peak=    3.529 closest distance to " CA  GLU A 152 " =    0.834
peak=    3.525 closest distance to " O   HOH Z 132 " =    2.153
peak=    3.523 closest distance to " CE1 TYR A 186 " =    1.284
peak=    3.512 closest distance to " O   HOH Z 417 " =    1.799
peak=    3.510 closest distance to " CB  SER A 141 " =    1.131
peak=    3.509 closest distance to " CB  GLU A 175 " =    1.343
peak=    3.506 closest distance to " O   HOH Z  22 " =    2.611
peak=    3.499 closest distance to " O   HOH Z 345 " =    1.838
peak=    3.491 closest distance to " O   HOH Z  89 " =    2.276
peak=    3.486 closest distance to " N   HIS A 108 " =    1.797
peak=    3.485 closest distance to " CB  GLN A  88 " =    1.174
peak=    3.485 closest distance to " O   HOH Z  68 " =    1.799
peak=    3.478 closest distance to " CA  ASP A 162 " =    1.163
peak=    3.475 closest distance to " O   HOH Z  85 " =    1.501
peak=    3.472 closest distance to " CB  ALA A 248 " =    1.417
peak=    3.470 closest distance to " N   ASN A  39 " =    1.258
peak=    3.466 closest distance to " CB  ASP A 191 " =    1.199
peak=    3.463 closest distance to " CB  LEU A 300 " =    0.877
peak=    3.461 closest distance to " O   HOH Z  40 " =    1.947
peak=    3.456 closest distance to " O   HOH Z 247 " =    1.344
peak=    3.454 closest distance to " CG  ASP A  65 " =    1.062
peak=    3.450 closest distance to " NH2 ARG A 156 " =    1.090
peak=    3.445 closest distance to " CG2 VAL A 197 " =    1.170
peak=    3.441 closest distance to " N   CYS A 260 " =    0.924
peak=    3.430 closest distance to " O   HOH Z  78 " =    1.699
peak=    3.427 closest distance to " OG  SER A 245 " =    1.364
peak=    3.425 closest distance to " O   HOH Z 371 " =    2.896
peak=    3.421 closest distance to " O   HOH Z  76 " =    0.902
peak=    3.420 closest distance to " O   HOH Z 316 " =    3.056
peak=    3.417 closest distance to " O   HOH Z 284 " =    2.922
peak=    3.416 closest distance to " O   HOH Z  15 " =    2.459
peak=    3.413 closest distance to " O   HOH Z 343 " =    2.691
peak=    3.409 closest distance to " CA  VAL A 112 " =    1.145
peak=    3.407 closest distance to " CD  ARG A  24 " =    1.138
peak=    3.402 closest distance to " O   HOH Z  63 " =    2.052
peak=    3.392 closest distance to " OE1 GLN A  11 " =    2.079
peak=    3.387 closest distance to " CG  ARG A  56 " =    1.169
peak=    3.384 closest distance to " CD2 LEU A 297 " =    1.139
peak=    3.384 closest distance to " O   HOH Z 380 " =    1.946
peak=    3.383 closest distance to " O   HOH Z 418 " =    1.463
peak=    3.382 closest distance to " CB  ARG A 219 " =    1.137
peak=    3.381 closest distance to " CG2 ILE A  20 " =    1.370
peak=    3.363 closest distance to " NE2 GLN A  77 " =    3.088
peak=    3.354 closest distance to " O   HOH Z 141 " =    1.789
peak=    3.353 closest distance to " OG BSER A 212 " =    2.555
peak=    3.352 closest distance to " CB  PRO A 198 " =    1.228
peak=    3.351 closest distance to " CB  ARG A  79 " =    0.799
peak=    3.347 closest distance to " CB  PRO A 213 " =    1.188
peak=    3.346 closest distance to " O   HOH Z 368 " =    2.186
peak=    3.345 closest distance to " CB  ASN A 110 " =    0.965
peak=    3.345 closest distance to " O   HOH Z 163 " =    1.529
peak=    3.343 closest distance to " CD  GLN A 194 " =    1.673
peak=    3.338 closest distance to " CB  TYR A 116 " =    1.082
peak=    3.336 closest distance to " O   HOH Z 393 " =    3.283
peak=    3.336 closest distance to " CB  MET A  40 " =    0.975
peak=    3.329 closest distance to " O   ASP A 200 " =    1.425
peak=    3.328 closest distance to " CB  GLU A 152 " =    1.027
peak=    3.328 closest distance to " O   HOH Z  56 " =    1.502
peak=    3.327 closest distance to " N   THR A  52 " =    1.185
peak=    3.327 closest distance to " CE  LYS A 119 " =    1.221
peak=    3.326 closest distance to " O   HOH Z 344 " =    3.093
peak=    3.326 closest distance to " O   HOH Z 375 " =    1.778
peak=    3.321 closest distance to " O   HOH Z  44 " =    3.480
peak=    3.319 closest distance to " O   HOH Z 213 " =    1.583
peak=    3.316 closest distance to " CB  ASN A  45 " =    1.151
peak=    3.316 closest distance to " O   HOH Z  78 " =    2.072
peak=    3.315 closest distance to " CA  ASN A 176 " =    1.301
peak=    3.314 closest distance to " O   GLY A  91 " =    1.205
peak=    3.314 closest distance to " O   HOH Z 412 " =    3.594
peak=    3.311 closest distance to " N   GLU A  44 " =    1.381
peak=    3.297 closest distance to " O   HOH Z 350 " =    2.098
peak=    3.295 closest distance to " O   HOH Z  28 " =    1.990
peak=    3.284 closest distance to " O   HOH Z 111 " =    1.407
peak=    3.280 closest distance to " CB  ASN A 187 " =    2.364
peak=    3.277 closest distance to " O   HOH Z 221 " =    1.036
peak=    3.276 closest distance to " CB  VAL A 202 " =    1.390
peak=    3.274 closest distance to " O   HOH Z   4 " =    1.643
peak=    3.273 closest distance to " CB  PRO A 243 " =    1.194
peak=    3.269 closest distance to " CG2 THR A 220 " =    0.759
peak=    3.268 closest distance to " CB  LYS A 289 " =    1.089
peak=    3.268 closest distance to " O   HOH Z 344 " =    1.959
peak=    3.265 closest distance to " O   HOH Z 244 " =    1.680
peak=    3.263 closest distance to " CG2 THR A 221 " =    1.221
peak=    3.262 closest distance to " CG1 ILE A  20 " =    1.327
peak=    3.262 closest distance to " CA  ARG A 139 " =    1.299
peak=    3.262 closest distance to " CB  GLU A   2 " =    1.062
peak=    3.261 closest distance to " O   HOH Z 139 " =    4.511
peak=    3.261 closest distance to " O   HOH Z 285 " =    2.728
peak=    3.259 closest distance to " CG  MET A 185 " =    1.215
peak=    3.257 closest distance to " O   HOH Z 418 " =    3.150
peak=    3.254 closest distance to " ND2 ASN A 249 " =    0.925
peak=    3.253 closest distance to " CB  TYR A 169 " =    0.751
peak=    3.251 closest distance to " CA  ALA A 129 " =    1.117
peak=    3.251 closest distance to " CB  ASN A  39 " =    0.833
peak=    3.248 closest distance to " CB  TRP A 179 " =    1.817
peak=    3.246 closest distance to " CG2 ILE A 120 " =    1.290
peak=    3.239 closest distance to " OE1 GLU A   2 " =    1.366
peak=    3.230 closest distance to " CG2 VAL A 257 " =    0.817
peak=    3.230 closest distance to " CA  PRO A  90 " =    0.927
peak=    3.228 closest distance to " OD2 ASP A 298 " =    3.383
peak=    3.227 closest distance to " O   HOH Z  85 " =    1.519
peak=    3.227 closest distance to " CA  THR A  82 " =    1.701
peak=    3.225 closest distance to " O   HOH Z 306 " =    1.341
peak=    3.223 closest distance to " CA  LEU A  83 " =    1.268
peak=    3.221 closest distance to " CA  ILE A 106 " =    0.848
peak=    3.215 closest distance to " O   HOH Z 142 " =    1.916
peak=    3.210 closest distance to " CA  GLY A 241 " =    0.973
peak=    3.200 closest distance to " CG  LEU A 167 " =    1.170
peak=    3.199 closest distance to " NE2 GLN A 183 " =    1.219
peak=    3.199 closest distance to " CB  ARG A 269 " =    1.796
peak=    3.195 closest distance to " N   ASN A 252 " =    1.205
peak=    3.194 closest distance to " CA  ASP A 149 " =    1.313
peak=    3.193 closest distance to " OD1 ASN A 301 " =    1.064
peak=    3.192 closest distance to " CB  ARG A  79 " =    1.602
peak=    3.192 closest distance to " O   HOH Z 419 " =    2.500
peak=    3.181 closest distance to " O   TYR A 116 " =    1.430
peak=    3.181 closest distance to " CG  ARG A 138 " =    1.366
peak=    3.178 closest distance to " O   HOH Z 394 " =    3.593
peak=    3.174 closest distance to " CG AARG A 190 " =    1.228
peak=    3.173 closest distance to " CE1 TYR A  30 " =    1.084
peak=    3.173 closest distance to " CB  SER A 273 " =    0.910
peak=    3.173 closest distance to " NH1AARG A 145 " =    1.537
peak=    3.172 closest distance to " ND2 ASN A 187 " =    1.542
peak=    3.171 closest distance to " CD2 LEU A 297 " =    0.841
peak=    3.168 closest distance to " N   PHE A 130 " =    1.371
peak=    3.166 closest distance to " CB  THR A  31 " =    1.680
peak=    3.164 closest distance to " CA  ASN A 217 " =    1.256
peak=    3.162 closest distance to " NH2AARG A 145 " =    1.179
peak=    3.155 closest distance to " C   ALA A 299 " =    1.090
peak=    3.146 closest distance to " CB  ASP A 140 " =    1.105
peak=    3.142 closest distance to " O   HOH Z 359 " =    1.579
peak=    3.141 closest distance to " O   GLU A   2 " =    1.653
peak=    3.141 closest distance to " OE1 GLN A 223 " =    2.286
peak=    3.138 closest distance to " CE  MET A  40 " =    0.950
peak=    3.137 closest distance to " CE3 TRP A 150 " =    1.111
peak=    3.132 closest distance to " O   HOH Z 437 " =    1.325
peak=    3.129 closest distance to " O   HOH Z 358 " =    1.347
peak=    3.129 closest distance to " CB  GLN A  58 " =    1.103
peak=    3.124 closest distance to " CD2 LEU A 143 " =    1.393
peak=    3.121 closest distance to " O   HOH Z 435 " =    1.866
peak=    3.118 closest distance to " CE2 TYR A  30 " =    0.788
peak=    3.117 closest distance to " CB  ASN A 142 " =    1.182
peak=    3.117 closest distance to " O   HOH Z 163 " =    1.952
peak=    3.115 closest distance to " ND2BASN A 224 " =    0.808
peak=    3.109 closest distance to " N   TRP A 150 " =    1.249
peak=    3.107 closest distance to " O   PHE A  61 " =    1.467
peak=    3.105 closest distance to " SG BCYS A 201 " =    1.244
peak=    3.100 closest distance to " CB  ALA A 291 " =    1.030
peak=    3.095 closest distance to " CB  ASP A 253 " =    1.032
peak=    3.091 closest distance to " O   HOH Z 132 " =    1.277
peak=    3.091 closest distance to " O   PRO A 213 " =    1.328
peak=    3.091 closest distance to " CA  GLN A  58 " =    1.129
peak=    3.079 closest distance to " O   HOH Z   1 " =    2.732
peak=    3.078 closest distance to " CB  GLU A  46 " =    1.388
peak=    3.077 closest distance to " CA  ASP A 191 " =    0.888
peak=    3.044 closest distance to " OG  SER A  62 " =    2.696
peak=    3.039 closest distance to " CB  LEU A  83 " =    0.742

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.698 - 5.993
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 215
   mapped sites are within: 0.746 - 5.993

peak=   -4.565 closest distance to " O   PRO A 198 " =    1.350
peak=   -4.458 closest distance to " CG2BVAL A  41 " =    2.835
peak=   -4.334 closest distance to " CG2 ILE A  49 " =    2.863
peak=   -4.272 closest distance to " O   HOH Z 266 " =    5.513
peak=   -4.239 closest distance to " O   HOH Z 203 " =    0.746
peak=   -4.193 closest distance to " CD2 TYR A  30 " =    2.706
peak=   -4.164 closest distance to " CG  GLN A  58 " =    0.983
peak=   -4.155 closest distance to " O   GLN A  11 " =    1.175
peak=   -4.152 closest distance to " C   HIS A 108 " =    1.048
peak=   -4.130 closest distance to " CD  GLN A 223 " =    1.597
peak=   -4.072 closest distance to " OG BSER A 134 " =    1.434
peak=   -4.060 closest distance to " CG  PRO A 243 " =    1.651
peak=   -4.059 closest distance to " O   HOH Z 150 " =    1.732
peak=   -4.057 closest distance to " CD2 LEU A 237 " =    2.470
peak=   -4.038 closest distance to " O   HOH Z 422 " =    0.886
peak=   -4.033 closest distance to " CG2 ILE A  20 " =    2.854
peak=   -4.007 closest distance to " NE  ARG A 156 " =    2.000
peak=   -3.984 closest distance to " CD2 TYR A 293 " =    1.764
peak=   -3.951 closest distance to " CD  ARG A  14 " =    3.288
peak=   -3.926 closest distance to " O   HOH Z 102 " =    1.158
peak=   -3.924 closest distance to " O   HOH Z  13 " =    1.926
peak=   -3.909 closest distance to " O   HOH Z 166 " =    1.770
peak=   -3.883 closest distance to " O   PHE A 218 " =    1.468
peak=   -3.874 closest distance to " CB  ALA A  43 " =    2.605
peak=   -3.862 closest distance to " O   TRP A  92 " =    2.084
peak=   -3.859 closest distance to " CG  GLN A  11 " =    1.405
peak=   -3.844 closest distance to " O   HOH Z 377 " =    2.194
peak=   -3.843 closest distance to " O   HOH Z 214 " =    2.733
peak=   -3.839 closest distance to " O   HOH Z  41 " =    1.856
peak=   -3.836 closest distance to " CG2 VAL A 189 " =    2.097
peak=   -3.832 closest distance to " C   THR A 279 " =    1.234
peak=   -3.827 closest distance to " CG  GLU A  53 " =    1.313
peak=   -3.805 closest distance to " OXT GLY A 302 " =    2.990
peak=   -3.801 closest distance to " CA  GLY A 133 " =    1.980
peak=   -3.765 closest distance to " CH2 TRP A 150 " =    1.049
peak=   -3.760 closest distance to " O   HOH Z 183 " =    1.670
peak=   -3.759 closest distance to " O   HOH Z 203 " =    1.650
peak=   -3.758 closest distance to " CD1 ILE A 106 " =    2.207
peak=   -3.756 closest distance to " O   HOH Z 221 " =    0.916
peak=   -3.722 closest distance to " O   HOH Z 423 " =    4.037
peak=   -3.712 closest distance to " O   HOH Z 165 " =    1.720
peak=   -3.701 closest distance to " O   HOH Z 203 " =    0.934
peak=   -3.701 closest distance to " O   VAL A 174 " =    2.113
peak=   -3.694 closest distance to " NE2 GLN A 223 " =    1.317
peak=   -3.692 closest distance to " OD2 ASP A 298 " =    1.033
peak=   -3.665 closest distance to " SD  MET A 105 " =    1.014
peak=   -3.650 closest distance to " CD1 PHE A  59 " =    1.942
peak=   -3.647 closest distance to " O   SER A 273 " =    0.996
peak=   -3.639 closest distance to " O   HOH Z  67 " =    1.468
peak=   -3.636 closest distance to " O   HOH Z 366 " =    1.549
peak=   -3.635 closest distance to " CD1 TRP A 179 " =    1.164
peak=   -3.623 closest distance to " CD  GLN A  73 " =    0.746
peak=   -3.621 closest distance to " CD2 PHE A  61 " =    2.113
peak=   -3.620 closest distance to " O   HOH Z  81 " =    0.748
peak=   -3.611 closest distance to " O   HOH Z 351 " =    1.664
peak=   -3.606 closest distance to " O   SER A 146 " =    1.089
peak=   -3.599 closest distance to " OG  SER A  97 " =    2.189
peak=   -3.593 closest distance to " CG2BVAL A  41 " =    1.974
peak=   -3.587 closest distance to " O   HOH Z   7 " =    1.453
peak=   -3.565 closest distance to " NE2 GLN A 194 " =    2.072
peak=   -3.565 closest distance to " O   VAL A 257 " =    1.449
peak=   -3.552 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.550 closest distance to " O   GLY A 241 " =    2.235
peak=   -3.548 closest distance to " CE3 TRP A 150 " =    2.304
peak=   -3.548 closest distance to " CZ  PHE A  38 " =    2.182
peak=   -3.536 closest distance to " O   HOH Z 278 " =    1.054
peak=   -3.535 closest distance to " O   HOH Z 418 " =    1.136
peak=   -3.523 closest distance to " O   HOH Z 423 " =    2.475
peak=   -3.521 closest distance to " ND2BASN A 224 " =    1.969
peak=   -3.510 closest distance to " O   HOH Z 191 " =    5.993
peak=   -3.508 closest distance to " O   HOH Z 145 " =    2.976
peak=   -3.498 closest distance to " CD1 LEU A 101 " =    2.468
peak=   -3.491 closest distance to " O   HOH Z 166 " =    1.538
peak=   -3.485 closest distance to " CG1 VAL A  78 " =    2.749
peak=   -3.481 closest distance to " NE  ARG A  79 " =    1.347
peak=   -3.468 closest distance to " CB  ALA A 248 " =    2.195
peak=   -3.466 closest distance to " CD2 LEU A 237 " =    2.581
peak=   -3.451 closest distance to " O   HOH Z 174 " =    2.222
peak=   -3.440 closest distance to " CZ  ARG A  66 " =    0.996
peak=   -3.439 closest distance to " O   HOH Z 424 " =    1.196
peak=   -3.439 closest distance to " O   HOH Z 196 " =    1.709
peak=   -3.424 closest distance to " O   ASN A 110 " =    2.344
peak=   -3.419 closest distance to " O   HOH Z  46 " =    1.244
peak=   -3.417 closest distance to " C   GLY A 133 " =    1.124
peak=   -3.416 closest distance to " O   HOH Z 193 " =    1.169
peak=   -3.415 closest distance to " O   PRO A  54 " =    1.828
peak=   -3.410 closest distance to " OE2 GLU A 152 " =    1.486
peak=   -3.409 closest distance to " CG  ASP A 286 " =    1.156
peak=   -3.406 closest distance to " C   ASN A 285 " =    2.202
peak=   -3.398 closest distance to " CE1 TYR A 247 " =    2.663
peak=   -3.396 closest distance to " CZ  TYR A 172 " =    1.829
peak=   -3.393 closest distance to " O   HOH Z  52 " =    1.945
peak=   -3.393 closest distance to " O   HOH Z 234 " =    3.893
peak=   -3.392 closest distance to " NE2 GLN A 223 " =    1.146
peak=   -3.392 closest distance to " CZ  TYR A 169 " =    2.004
peak=   -3.392 closest distance to " CB  ALA A 161 " =    2.531
peak=   -3.389 closest distance to " O   HOH Z 434 " =    2.551
peak=   -3.388 closest distance to " O   HOH Z 113 " =    1.980
peak=   -3.388 closest distance to " O   HOH Z 250 " =    1.737
peak=   -3.381 closest distance to " SD  MET A  93 " =    1.695
peak=   -3.379 closest distance to " O   SER A  95 " =    1.733
peak=   -3.377 closest distance to " ND2 ASN A  45 " =    1.812
peak=   -3.375 closest distance to " O   HOH Z 424 " =    3.567
peak=   -3.369 closest distance to " O   HOH Z 297 " =    2.643
peak=   -3.366 closest distance to " OE2 GLU A   2 " =    1.508
peak=   -3.365 closest distance to " CA  VAL A 197 " =    1.046
peak=   -3.363 closest distance to " O   HOH Z 171 " =    2.489
peak=   -3.362 closest distance to " O   HOH Z  81 " =    0.960
peak=   -3.362 closest distance to " CG  GLN A 103 " =    2.373
peak=   -3.351 closest distance to " O   HOH Z 156 " =    3.581
peak=   -3.349 closest distance to " O   HOH Z 345 " =    2.812
peak=   -3.347 closest distance to " O   HOH Z 120 " =    1.203
peak=   -3.345 closest distance to " O   GLY A  80 " =    2.725
peak=   -3.332 closest distance to " O   HOH Z 215 " =    2.199
peak=   -3.332 closest distance to " O   GLU A 128 " =    1.156
peak=   -3.330 closest distance to " CG2 THR A 182 " =    2.391
peak=   -3.325 closest distance to " CB  ALA A 129 " =    2.515
peak=   -3.319 closest distance to " CD2 PHE A 225 " =    1.398
peak=   -3.315 closest distance to " CG1 VAL A 112 " =    2.524
peak=   -3.314 closest distance to " O   HOH Z 244 " =    1.337
peak=   -3.309 closest distance to " N   ASP A 272 " =    1.097
peak=   -3.309 closest distance to " O   HOH Z  56 " =    1.020
peak=   -3.307 closest distance to " CG  GLN A  58 " =    1.307
peak=   -3.304 closest distance to " O   HOH Z 281 " =    2.385
peak=   -3.302 closest distance to " O   HOH Z 124 " =    1.471
peak=   -3.302 closest distance to " O   SER A   3 " =    0.959
peak=   -3.300 closest distance to " O   HOH Z 388 " =    2.065
peak=   -3.299 closest distance to " CB  SER A 141 " =    2.141
peak=   -3.294 closest distance to " O   HOH Z  54 " =    1.813
peak=   -3.284 closest distance to " O   HOH Z 401 " =    1.446
peak=   -3.283 closest distance to " N   ALA A 226 " =    1.841
peak=   -3.282 closest distance to " CE1 HIS A 207 " =    1.950
peak=   -3.281 closest distance to " NE2 GLN A  88 " =    1.610
peak=   -3.279 closest distance to " CD1 PHE A 130 " =    2.377
peak=   -3.277 closest distance to " CD  LYS A 289 " =    2.374
peak=   -3.276 closest distance to " N   GLN A 223 " =    1.022
peak=   -3.275 closest distance to " O   SER A 210 " =    1.729
peak=   -3.270 closest distance to " OD2 ASP A 191 " =    1.536
peak=   -3.267 closest distance to " O   HOH Z 274 " =    1.178
peak=   -3.267 closest distance to " CZ2 TRP A  85 " =    2.159
peak=   -3.262 closest distance to " CB  PRO A 213 " =    2.110
peak=   -3.260 closest distance to " N   ASP A 191 " =    1.386
peak=   -3.259 closest distance to " O   HOH Z 205 " =    0.824
peak=   -3.258 closest distance to " O   HOH Z 251 " =    4.581
peak=   -3.256 closest distance to " OG  SER A  87 " =    1.721
peak=   -3.255 closest distance to " CA  SER A 288 " =    1.284
peak=   -3.254 closest distance to " CE1 PHE A 218 " =    1.234
peak=   -3.237 closest distance to " O   HOH Z 280 " =    1.526
peak=   -3.233 closest distance to " O  BHOH Z 338 " =    1.282
peak=   -3.230 closest distance to " O   HOH Z 150 " =    1.383
peak=   -3.228 closest distance to " OD2 ASP A 171 " =    1.742
peak=   -3.227 closest distance to " O   HOH Z 126 " =    2.006
peak=   -3.227 closest distance to " O   HOH Z 174 " =    3.718
peak=   -3.226 closest distance to " O   HOH Z  59 " =    3.932
peak=   -3.226 closest distance to " N   GLY A  17 " =    1.544
peak=   -3.224 closest distance to " NE2 GLN A 278 " =    1.907
peak=   -3.223 closest distance to " O   HOH Z 109 " =    3.713
peak=   -3.218 closest distance to " O   SER A 135 " =    1.724
peak=   -3.217 closest distance to " O   HOH Z 397 " =    1.082
peak=   -3.217 closest distance to " O   HOH Z 433 " =    0.999
peak=   -3.213 closest distance to " OE1 GLN A  55 " =    1.565
peak=   -3.212 closest distance to " O   HOH Z 331 " =    1.107
peak=   -3.207 closest distance to " O   HOH Z  63 " =    1.254
peak=   -3.207 closest distance to " SD  MET A  40 " =    1.855
peak=   -3.206 closest distance to " O   ALA A  34 " =    2.428
peak=   -3.204 closest distance to " CA  ALA A 114 " =    0.968
peak=   -3.202 closest distance to " CG  ASP A 124 " =    0.936
peak=   -3.199 closest distance to " O   HOH Z 285 " =    1.160
peak=   -3.198 closest distance to " CE BMET A  47 " =    1.473
peak=   -3.195 closest distance to " OH  TYR A 169 " =    0.911
peak=   -3.192 closest distance to " O   HOH Z 246 " =    1.306
peak=   -3.186 closest distance to " CB  ASN A  45 " =    2.009
peak=   -3.174 closest distance to " CB  ALA A 291 " =    2.486
peak=   -3.170 closest distance to " ND2 ASN A  60 " =    2.179
peak=   -3.169 closest distance to " CB  SER A 210 " =    1.098
peak=   -3.169 closest distance to " OXT GLY A 302 " =    3.206
peak=   -3.167 closest distance to " O   ASP A 171 " =    0.900
peak=   -3.161 closest distance to " O   HOH Z   1 " =    4.418
peak=   -3.158 closest distance to " O   HOH Z 152 " =    1.186
peak=   -3.152 closest distance to " O   HOH Z   9 " =    2.559
peak=   -3.151 closest distance to " CG  ASN A 252 " =    1.454
peak=   -3.148 closest distance to " OG BSER A  99 " =    1.045
peak=   -3.147 closest distance to " O   HOH Z 219 " =    4.582
peak=   -3.145 closest distance to " OE1 GLN A 223 " =    2.265
peak=   -3.145 closest distance to " CA  GLY A  57 " =    2.270
peak=   -3.143 closest distance to " O   HOH Z 313 " =    1.829
peak=   -3.143 closest distance to " O   HOH Z 110 " =    1.401
peak=   -3.140 closest distance to " O   HOH Z 148 " =    3.779
peak=   -3.139 closest distance to " OH  TYR A  30 " =    1.012
peak=   -3.138 closest distance to " CA  ALA A 137 " =    2.556
peak=   -3.134 closest distance to " O   ARG A  79 " =    0.990
peak=   -3.131 closest distance to " O   HOH Z  10 " =    1.640
peak=   -3.130 closest distance to " O   HOH Z 340 " =    1.216
peak=   -3.130 closest distance to " CB  GLN A  55 " =    1.478
peak=   -3.128 closest distance to " CB  PRO A 243 " =    2.799
peak=   -3.124 closest distance to " CD1 ILE A 109 " =    2.819
peak=   -3.121 closest distance to " O   HOH Z 120 " =    1.987
peak=   -3.120 closest distance to " O   HOH Z   1 " =    2.233
peak=   -3.115 closest distance to " SD  MET A 105 " =    2.390
peak=   -3.109 closest distance to " O   HOH Z 154 " =    1.623
peak=   -3.107 closest distance to " O   HOH Z 252 " =    3.474
peak=   -3.099 closest distance to " O   HOH Z 287 " =    1.868
peak=   -3.091 closest distance to " N   LEU A 282 " =    2.282
peak=   -3.087 closest distance to " OG  SER A 273 " =    2.249
peak=   -3.081 closest distance to " CB  ASN A 110 " =    1.012
peak=   -3.079 closest distance to " CB  PRO A 213 " =    1.721
peak=   -3.074 closest distance to " O   HOH Z 203 " =    1.491
peak=   -3.072 closest distance to " OG BSER A 258 " =    5.183
peak=   -3.071 closest distance to " OD2 ASP A 171 " =    2.331
peak=   -3.050 closest distance to " CG  GLN A  88 " =    0.900
peak=   -3.042 closest distance to " O   HOH Z  54 " =    1.973
peak=   -3.033 closest distance to " O   HOH Z 428 " =    1.626

================= 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    :  0.4823 0.4797   6.287984e+00   6.283401e+00
   1_bss:  0.4761 0.4701   6.284063e+00   6.278421e+00
   1_xyz:  0.3652 0.3954   6.116134e+00   6.170472e+00
   1_adp:  0.3253 0.3999   6.063116e+00   6.183027e+00
   1_occ:  0.3251 0.3999   6.062423e+00   6.183187e+00
   2_bss:  0.3239 0.3964   6.058850e+00   6.180421e+00
   2_xyz:  0.2583 0.3160   5.862176e+00   6.022228e+00
   2_adp:  0.2411 0.3021   5.814741e+00   5.982849e+00
   2_occ:  0.2411 0.3019   5.814103e+00   5.982398e+00
   3_bss:  0.2406 0.3020   5.813659e+00   5.981801e+00
   3_xyz:  0.1911 0.2389   5.602570e+00   5.787420e+00
   3_adp:  0.1758 0.2330   5.546096e+00   5.753954e+00
   3_occ:  0.1757 0.2331   5.546015e+00   5.754039e+00
   4_bss:  0.1754 0.2325   5.545825e+00   5.751404e+00
   4_xyz:  0.1485 0.2031   5.399519e+00   5.627922e+00
   4_adp:  0.1420 0.1945   5.358558e+00   5.582658e+00
   4_occ:  0.1419 0.1944   5.358431e+00   5.582492e+00
   5_bss:  0.1422 0.1947   5.359532e+00   5.582020e+00
   5_xyz:  0.1318 0.1825   5.296130e+00   5.525682e+00
   5_adp:  0.1299 0.1792   5.280198e+00   5.506995e+00
   5_occ:  0.1298 0.1792   5.280142e+00   5.506971e+00
   5_bss:  0.1298 0.1792   5.280162e+00   5.506962e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.297  30.538  -0.895   2.781   0.779   0.000   0.000   0.000
   1_xyz:  0.297  30.538  -0.895   2.781   0.779   0.000   0.000   0.000
   1_adp:  0.297  30.538  -0.895   2.781   0.779   0.000   0.000   0.000
   1_occ:  0.297  30.538  -0.895   2.781   0.779   0.000   0.000   0.000
   2_bss:  0.311  49.637  -1.560   1.153   0.345   0.000   0.000   0.000
   2_xyz:  0.311  49.637  -1.560   1.153   0.345   0.000   0.000   0.000
   2_adp:  0.311  49.637  -1.560   1.153   0.345   0.000   0.000   0.000
   2_occ:  0.311  49.637  -1.560   1.153   0.345   0.000   0.000   0.000
   3_bss:  0.314  49.637  -2.580  -0.133  -0.270  -0.000  -0.000  -0.000
   3_xyz:  0.314  49.637  -2.580  -0.133  -0.270  -0.000  -0.000  -0.000
   3_adp:  0.314  49.637  -2.580  -0.133  -0.270  -0.000  -0.000  -0.000
   3_occ:  0.314  49.637  -2.580  -0.133  -0.270  -0.000  -0.000  -0.000
   4_bss:  0.321  59.013  -3.345  -1.245  -0.950  -0.000  -0.000  -0.000
   4_xyz:  0.321  59.013  -3.345  -1.245  -0.950  -0.000  -0.000  -0.000
   4_adp:  0.321  59.013  -3.345  -1.245  -0.950  -0.000  -0.000  -0.000
   4_occ:  0.321  59.013  -3.345  -1.245  -0.950  -0.000  -0.000  -0.000
   5_bss:  0.329  64.023  -3.502  -1.603  -1.018  -0.000  -0.000  -0.000
   5_xyz:  0.329  64.023  -3.502  -1.603  -1.018  -0.000  -0.000  -0.000
   5_adp:  0.329  64.023  -3.502  -1.603  -1.018  -0.000  -0.000  -0.000
   5_occ:  0.329  64.023  -3.502  -1.603  -1.018  -0.000  -0.000  -0.000
   5_bss:  0.330  64.000  -3.478  -1.580  -0.995  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.483 0.4002  0.5447    73902.128
   1_bss:  58.570 0.4107  0.5808    71459.451
   1_xyz:  43.830 0.5969  0.8192    45518.355
   1_adp:  44.938 0.5826  0.8158    47563.386
   1_occ:  44.912 0.5829  0.8153    47454.298
   2_bss:  44.596 0.5865  0.7969    46634.298
   2_xyz:  34.556 0.7049  0.9281    28261.410
   2_adp:  32.025 0.7347  0.9460    25326.796
   2_occ:  31.987 0.7352  0.9461    25271.726
   3_bss:  31.901 0.7361  0.9149    25174.936
   3_xyz:  24.092 0.8199  0.9860    14915.628
   3_adp:  22.918 0.8326  0.9889    14023.411
   3_occ:  22.920 0.8326  0.9890    14033.447
   4_bss:  22.821 0.8335  0.9609    13924.164
   4_xyz:  19.582 0.8650  0.9760    10502.143
   4_adp:  18.439 0.8763  0.9732     9667.924
   4_occ:  18.441 0.8763  0.9732     9672.678
   5_bss:  18.437 0.8764  0.9671     9682.632
   5_xyz:  17.176 0.8878  0.9743     8578.776
   5_adp:  16.734 0.8919  0.9715     8312.424
   5_occ:  16.733 0.8920  0.9713     8311.859
   5_bss:  16.733 0.8920  0.9713     8311.992
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.2657e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.2657e-01
   1_xyz:   1.685  0.013  0.097 15.648  0.006  4.102   1.5043e-01
   1_adp:   1.685  0.013  0.097 15.648  0.006  4.102   1.5043e-01
   1_occ:   1.685  0.013  0.097 15.648  0.006  4.102   1.5043e-01
   2_bss:   1.685  0.013  0.097 15.648  0.006  4.102   1.5043e-01
   2_xyz:   1.251  0.009  0.089 15.129  0.004  4.124   8.8120e-02
   2_adp:   1.251  0.009  0.089 15.129  0.004  4.124   8.8120e-02
   2_occ:   1.251  0.009  0.089 15.129  0.004  4.124   8.8120e-02
   3_bss:   1.251  0.009  0.089 15.129  0.004  4.124   8.8120e-02
   3_xyz:   1.055  0.008  0.067 14.324  0.005  4.113   6.9031e-02
   3_adp:   1.055  0.008  0.067 14.324  0.005  4.113   6.9031e-02
   3_occ:   1.055  0.008  0.067 14.324  0.005  4.113   6.9031e-02
   4_bss:   1.055  0.008  0.067 14.324  0.005  4.113   6.9031e-02
   4_xyz:   1.033  0.007  0.072 14.306  0.004  4.122   5.8624e-02
   4_adp:   1.033  0.007  0.072 14.306  0.004  4.122   5.8624e-02
   4_occ:   1.033  0.007  0.072 14.306  0.004  4.122   5.8624e-02
   5_bss:   1.033  0.007  0.072 14.306  0.004  4.122   5.8624e-02
   5_xyz:   0.969  0.006  0.070 14.330  0.004  4.113   5.4066e-02
   5_adp:   0.969  0.006  0.070 14.330  0.004  4.113   5.4066e-02
   5_occ:   0.969  0.006  0.070 14.330  0.004  4.113   5.4066e-02
   5_bss:   0.969  0.006  0.070 14.330  0.004  4.113   5.4066e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.919   2.4591e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.919   2.4591e-01
   1_xyz:   9.531  0.080  0.340 80.887  0.022  1.793   1.5788e-01
   1_adp:   9.531  0.080  0.340 80.887  0.022  1.793   1.5788e-01
   1_occ:   9.531  0.080  0.340 80.887  0.022  1.793   1.5788e-01
   2_bss:   9.531  0.080  0.340 80.887  0.022  1.793   1.5788e-01
   2_xyz:   7.980  0.042  0.273 82.076  0.023  2.020   1.4002e-01
   2_adp:   7.980  0.042  0.273 82.076  0.023  2.020   1.4002e-01
   2_occ:   7.980  0.042  0.273 82.076  0.023  2.020   1.4002e-01
   3_bss:   7.980  0.042  0.273 82.076  0.023  2.020   1.4002e-01
   3_xyz:   7.527  0.049  0.226 78.837  0.040  2.149   1.4067e-01
   3_adp:   7.527  0.049  0.226 78.837  0.040  2.149   1.4067e-01
   3_occ:   7.527  0.049  0.226 78.837  0.040  2.149   1.4067e-01
   4_bss:   7.527  0.049  0.226 78.837  0.040  2.149   1.4067e-01
   4_xyz:   7.703  0.039  0.219 77.550  0.044  2.239   4.4554e-02
   4_adp:   7.703  0.039  0.219 77.550  0.044  2.239   4.4554e-02
   4_occ:   7.703  0.039  0.219 77.550  0.044  2.239   4.4554e-02
   5_bss:   7.703  0.039  0.219 77.550  0.044  2.239   4.4554e-02
   5_xyz:   6.847  0.046  0.224 80.380  0.039  2.376   3.4586e-02
   5_adp:   6.847  0.046  0.224 80.380  0.039  2.376   3.4586e-02
   5_occ:   6.847  0.046  0.224 80.380  0.039  2.376   3.4586e-02
   5_bss:   6.847  0.046  0.224 80.380  0.039  2.376   3.4586e-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: 102.41   0.00  20.31  94.23   0.00  16.61 102.41   0.00  40.49
   1_occ: 102.41   0.00  20.31  94.23   0.00  16.61 102.41   0.00  40.49
   2_bss: 102.41   0.00  20.31  94.23   0.00  16.61 102.41   0.00  40.49
   2_xyz: 102.41   0.00  20.31  94.23   0.00  16.61 102.41   0.00  40.49
   2_adp:  97.86   0.00  19.14  89.58   0.00  15.22  97.86   2.50  40.46
   2_occ:  97.86   0.00  19.14  89.58   0.00  15.22  97.86   2.50  40.46
   3_bss:  97.86   0.00  19.14  89.58   0.00  15.22  97.86   2.50  40.46
   3_xyz:  97.86   0.00  19.14  89.58   0.00  15.22  97.86   2.50  40.46
   3_adp:  93.72   0.00  19.56  93.72   0.00  14.65  93.70   5.36  46.28
   3_occ:  93.72   0.00  19.56  93.72   0.00  14.65  93.70   5.36  46.28
   4_bss:  93.72   0.00  19.56  93.72   0.00  14.65  93.70   5.36  46.28
   4_xyz:  93.72   0.00  19.56  93.72   0.00  14.65  93.70   5.36  46.28
   4_adp: 101.19   0.82  19.04 101.19   0.82  14.03  93.79   6.34  46.34
   4_occ: 101.19   0.82  19.04 101.19   0.82  14.03  93.79   6.34  46.34
   5_bss: 101.19   0.82  19.04 101.19   0.82  14.03  93.79   6.34  46.34
   5_xyz: 101.19   0.82  19.04 101.19   0.82  14.03  93.79   6.34  46.34
   5_adp: 105.50   0.70  18.69 105.50   0.70  13.73 100.29   5.81  45.71
   5_occ: 105.50   0.70  18.69 105.50   0.70  13.73 100.29   5.81  45.71
   5_bss: 105.48   0.68  18.67 105.48   0.68  13.71 100.27   5.79  45.69
------------------------------------------------------------------------
 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:    3.699    0.031    0.414
   1_adp:    3.699    0.031    0.414
   1_occ:    3.699    0.031    0.414
   2_bss:    3.699    0.031    0.414
   2_xyz:    3.834    0.022    0.573
   2_adp:    3.834    0.022    0.573
   2_occ:    3.834    0.022    0.573
   3_bss:    3.834    0.022    0.573
   3_xyz:    4.018    0.026    0.712
   3_adp:    4.018    0.026    0.712
   3_occ:    4.018    0.026    0.712
   4_bss:    4.018    0.026    0.712
   4_xyz:    4.143    0.052    0.770
   4_adp:    4.143    0.052    0.770
   4_occ:    4.143    0.052    0.770
   5_bss:    4.143    0.052    0.770
   5_xyz:    4.207    0.052    0.801
   5_adp:    4.207    0.052    0.801
   5_occ:    4.207    0.052    0.801
   5_bss:    4.207    0.052    0.801
------------------------------------------------------------------------

CPU time actual refinement: 345.72


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_107/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_107/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_107/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_107/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_107/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.57 
  Macro-tasks:
    bulk solvent and scale       = 38.97  
    individual site refinement   = 144.27 
    weights calculation          = 30.40  
    collect and process          = 6.61   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 220.37 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 111.65 
    alpha_beta                      = 8.43   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 119.93 
    fmodel                         = 6.67   
    r_factors                      = 0.21   
    phase_errors                   = 10.46  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 261.15 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.923 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    644 calls, 111.25 s
gradients_fft:          589 calls, 106.75 s

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

# Date 2008-01-16 Time 04:02:16 PST -0800 (1200484936.80 s)
Start R-work = 0.4823, R-free = 0.4797 (no bulk solvent and anisotropic scale)
Final R-work = 0.1536, R-free = 0.1981 (no bulk solvent and anisotropic scale)

Start R-work = 0.4761, R-free = 0.4701
Final R-work = 0.1298, R-free = 0.1792