# Date 2008-01-16 Time 04:51:57 PST -0800 (1200487917.27 s)
#phil __OFF__

Command line arguments: "../494.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31865
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 494

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.7567, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.95339
Completeness in resolution range: 0.924489
Completeness with d_max=infinity: 0.921835

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0370
                             d_min =   1.9534

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.95339
Completeness in resolution range: 0.924489
Completeness with d_max=infinity: 0.921835

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0375 -  4.1811 [2218/2244]  1994   224  10.1%
  bin  2:  4.1811 -  3.3305 [2150/2170]  1941   209   9.7%
  bin  3:  3.3305 -  2.9130 [2109/2128]  1898   211  10.0%
  bin  4:  2.9130 -  2.6483 [2088/2118]  1869   219  10.5%
  bin  5:  2.6483 -  2.4593 [2090/2109]  1882   208  10.0%
  bin  6:  2.4593 -  2.3149 [2064/2089]  1864   200   9.7%
  bin  7:  2.3149 -  2.1993 [2049/2077]  1842   207  10.1%
  bin  8:  2.1993 -  2.1038 [2067/2103]  1854   213  10.3%
  bin  9:  2.1038 -  2.0230 [1958/2075]  1775   183   9.3%
  bin 10:  2.0230 -  1.9534 [ 796/2076]   711    85  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_494/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.22 -     1.96: 19
        1.96 -     2.69: 155
        2.69 -     3.43: 4549
        3.43 -     4.16: 9401
        4.16 -     4.90: 14326
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.219 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.492 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 104 "  1.587 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.588 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.590 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28445 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_494/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_494/model_refine_001.geo

CPU time processing inputs: 9.26


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.75675 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4859   r_free= 0.4891   ksol= 0.00   Bsol= 0.00   scale= 0.875    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.298902                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.6640 0.99   1443  159 0.4001 0.3994      6.6329      6.6054|
|  2:  4.6640 -  3.7205 0.99   1390  159 0.4358 0.4438      6.8469      6.8508|
|  3:  3.7205 -  3.2556 0.99   1380  149 0.4643 0.4519      6.7043      6.6833|
|  4:  3.2556 -  2.9604 0.99   1339  151 0.4897 0.5046      6.5523      6.5411|
|  5:  2.9604 -  2.7496 0.99   1352  152 0.5186 0.5173      6.3689      6.4216|
|  6:  2.7496 -  2.5884 0.99   1346  143 0.5172 0.5217      6.2847      6.1995|
|  7:  2.5884 -  2.4593 0.99   1334  158 0.5117 0.5305      6.2398       6.194|
|  8:  2.4593 -  2.3527 0.98   1328  145 0.5311 0.5257      6.1671      6.1547|
|  9:  2.3527 -  2.2624 0.98   1308  141 0.5120 0.5442       6.123      6.1915|
| 10:  2.2624 -  2.1846 1.00   1363  152 0.5335 0.5422      6.0752      6.1168|
| 11:  2.1846 -  2.1165 0.98   1302  147 0.5155 0.5103      6.0189      6.0137|
| 12:  2.1165 -  2.0561 0.98   1309  137 0.5172 0.5006      5.9407      5.9491|
| 13:  2.0561 -  2.0021 0.83   1108  129 0.5188 0.4941      5.8914      5.7769|
| 14:  2.0021 -  1.9534 0.25    328   37 0.5280 0.5186      5.8591      5.9003|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0375 -  4.6640  1443   159  0.69  34.95   0.80     0.76      78090.50|
|  2:  4.6640 -  3.7205  1390   159  0.64  40.29   0.88     0.75     133992.09|
|  3:  3.7205 -  3.2556  1380   149  0.49  52.51   0.90     0.67     145560.26|
|  4:  3.2556 -  2.9604  1339   151  0.35  63.21   0.88     0.52     137530.73|
|  5:  2.9604 -  2.7496  1352   152  0.30  67.06   0.85     0.46      96837.24|
|  6:  2.7496 -  2.5884  1346   143  0.28  69.12   0.88     0.41      82943.93|
|  7:  2.5884 -  2.4593  1334   158  0.31  66.58   0.91     0.43      68696.30|
|  8:  2.4593 -  2.3527  1328   145  0.30  67.64   0.89     0.44      63393.10|
|  9:  2.3527 -  2.2624  1308   141  0.30  67.92   0.92     0.44      58232.07|
| 10:  2.2624 -  2.1846  1363   152  0.29  68.71   0.91     0.44      52419.39|
| 11:  2.1846 -  2.1165  1302   147  0.28  68.82   0.94     0.45      51437.28|
| 12:  2.1165 -  2.0561  1309   137  0.29  68.04   0.93     0.48      44300.43|
| 13:  2.0561 -  2.0021  1108   129  0.31  66.95   0.93     0.52      38429.92|
| 14:  2.0021 -  1.9534   328    37  0.39  60.50   1.01     0.58      29364.65|
|alpha:            min =        0.41 max =            0.76 mean =         0.52|
|beta:             min =    29364.65 max =       145560.26 mean =     80949.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.99 mean =        61.32|
|phase err.(test): min =        0.00 max =           89.93 mean =        61.66|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.600298             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.614   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.782964              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.693   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.219 -  1.587:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.587 -  1.955:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.955 -  2.323:       20 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.323 -  2.691:      135 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.691 -  3.059:     2240 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.059 -  3.427:     2309 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.427 -  3.796:     4083 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.796 -  4.164:     5318 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.164 -  4.532:     6410 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.532 -  4.900:     7916 |
|-----------------------------------------------------------------------------|
|-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 |        0.201 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.219 |       0.758 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.692)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4859   r_free= 0.4891   ksol= 0.00   Bsol= 0.00   scale= 0.875    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.298902                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4751   r_free= 0.4804   ksol= 0.33   Bsol= 26.39   scale= 0.912   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.38,1.21,3.55,0.00,0.00,0.00); trace/3= 0.46                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.294259                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.365632             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.542   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.555712              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.425   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4751      final r-factor (work) = 0.3992          |
| start r-factor (free) = 0.4804      final r-factor (free) = 0.4479          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.6612 = 16.37 * 0.50 * 6.2888 + 1.00 * 0.2012                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.0101 = 16.37 * 0.50 * 6.2141 + 1.00 * 0.1612                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3992      final r-factor (work) = 0.3699          |
| start r-factor (free) = 0.4479      final r-factor (free) = 0.4528          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6734 = 1.56 * 1.00 * 6.2141 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5896 = 1.56 * 1.00 * 6.1516 + 1.00 * 0.0195                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.692)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.31   18.42    None  None   None       |
|    all(noH): 2823   0      0.00    97.31   18.42    None  None   None       |
|    Sol.    : 438    0      0.00    97.31   32.88    None  None   None       |
|    Mac.    : 2385   0      0.00    75.37   15.76    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 -   9.731:  821   |   5:    48.657 -  58.389:   70        |
|      1:     9.731 -  19.463:  943   |   6:    58.389 -  68.120:   21        |
|      2:    19.463 -  29.194:  555   |   7:    68.120 -  77.851:   14        |
|      3:    29.194 -  38.926:  282   |   8:    77.851 -  87.583:    5        |
|      4:    38.926 -  48.657:  111   |   9:    87.583 -  97.314:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3699 r_free = 0.4528             target_work(ml) = 6.156         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3694 r_free = 0.4541             target_work(ml) = 6.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3694   r_free= 0.4541   ksol= 0.33   Bsol= 26.39   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.38,1.21,3.55,0.00,0.00,0.00); trace/3= 0.46                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.156259                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3688   r_free= 0.4523   ksol= 0.34   Bsol= 67.61   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,0.54,2.21,0.00,0.00,0.00); trace/3= 0.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.159825                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.401079             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.626  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.808945              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.956  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3688      final r-factor (work) = 0.3232          |
| start r-factor (free) = 0.4523      final r-factor (free) = 0.4118          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.2471 = 11.40 * 0.50 * 6.1549 + 1.00 * 0.1608                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.9894 = 11.40 * 0.50 * 6.1221 + 1.00 * 0.0903                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3232      final r-factor (work) = 0.3117          |
| start r-factor (free) = 0.4118      final r-factor (free) = 0.4020          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9718 = 0.81 * 1.00 * 6.1221 + 1.00 * 0.0194                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9126 = 0.81 * 1.00 * 6.0555 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.692)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.42   18.02    None  None   None       |
|    all(noH): 2823   0      0.00    96.42   18.02    None  None   None       |
|    Sol.    : 438    0      0.00    96.42   33.28    None  None   None       |
|    Mac.    : 2385   0      0.00    71.10   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 -   9.642:  847   |   5:    48.211 -  57.853:   62        |
|      1:     9.642 -  19.284:  992   |   6:    57.853 -  67.495:   31        |
|      2:    19.284 -  28.926:  497   |   7:    67.495 -  77.137:   11        |
|      3:    28.926 -  38.569:  254   |   8:    77.137 -  86.779:    4        |
|      4:    38.569 -  48.211:  124   |   9:    86.779 -  96.421:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3117 r_free = 0.4020             target_work(ml) = 6.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3116 r_free = 0.4021             target_work(ml) = 6.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3116   r_free= 0.4021   ksol= 0.34   Bsol= 67.61   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,0.54,2.21,0.00,0.00,0.00); trace/3= 0.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.046253                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3119   r_free= 0.4023   ksol= 0.34   Bsol= 67.61   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,0.65,2.31,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.046205                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.749984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.953  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.559852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.990  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3119      final r-factor (work) = 0.2571          |
| start r-factor (free) = 0.4023      final r-factor (free) = 0.3394          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.6161 = 9.75 * 0.50 * 6.0566 + 1.00 * 0.0903                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.2475 = 9.75 * 0.50 * 5.9812 + 1.00 * 0.0895                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2571      final r-factor (work) = 0.2328          |
| start r-factor (free) = 0.3394      final r-factor (free) = 0.3226          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3438 = 1.56 * 1.00 * 5.9812 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1366 = 1.56 * 1.00 * 5.8454 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.692)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.92   18.62    None  None   None       |
|    all(noH): 2823   0      0.00    98.92   18.62    None  None   None       |
|    Sol.    : 438    0      0.00    98.92   43.12    None  None   None       |
|    Mac.    : 2385   0      0.00    91.81   14.12    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 -   9.892: 1041   |   5:    49.462 -  59.354:   94        |
|      1:     9.892 -  19.785:  880   |   6:    59.354 -  69.247:   56        |
|      2:    19.785 -  29.677:  361   |   7:    69.247 -  79.139:   31        |
|      3:    29.677 -  39.570:  203   |   8:    79.139 -  89.032:   13        |
|      4:    39.570 -  49.462:  138   |   9:    89.032 -  98.924:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2328 r_free = 0.3226             target_work(ml) = 5.823         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2326 r_free = 0.3223             target_work(ml) = 5.822         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2326   r_free= 0.3223   ksol= 0.34   Bsol= 67.61   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.36,0.65,2.31,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.821890                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2328   r_free= 0.3214   ksol= 0.33   Bsol= 67.61   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.29,1.56,-0.00,0.00,0.00); trace/3= 0.16                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.820197                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.203620              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.434  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.689336              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.439  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2328      final r-factor (work) = 0.1903          |
| start r-factor (free) = 0.3214      final r-factor (free) = 0.2549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2992 = 5.20 * 0.50 * 5.8459 + 1.00 * 0.0894                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0283 = 5.20 * 0.50 * 5.7506 + 1.00 * 0.0664                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1903      final r-factor (work) = 0.1719          |
| start r-factor (free) = 0.2549      final r-factor (free) = 0.2301          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9828 = 0.69 * 1.00 * 5.7506 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8617 = 0.69 * 1.00 * 5.5818 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.692)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.08  17.85    None  None   None       |
|    all(noH): 2823   0      0.00    106.08  17.85    None  None   None       |
|    Sol.    : 438    0      3.13    106.08  45.96    None  None   None       |
|    Mac.    : 2385   0      0.00    95.47   12.68    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 -  10.608: 1320   |   5:    53.042 -  63.650:   97        |
|      1:    10.608 -  21.217:  840   |   6:    63.650 -  74.258:   57        |
|      2:    21.217 -  31.825:  214   |   7:    74.258 -  84.867:   28        |
|      3:    31.825 -  42.433:  133   |   8:    84.867 -  95.475:   10        |
|      4:    42.433 -  53.042:  123   |   9:    95.475 - 106.083:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1719 r_free = 0.2301             target_work(ml) = 5.525         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1717 r_free = 0.2299             target_work(ml) = 5.524         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1717   r_free= 0.2299   ksol= 0.33   Bsol= 67.61   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.29,1.56,-0.00,0.00,0.00); trace/3= 0.16                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.523946                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1716   r_free= 0.2300   ksol= 0.33   Bsol= 67.61   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-1.06,1.18,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.522115                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.851313              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.440  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.269604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.892  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1716      final r-factor (work) = 0.1428          |
| start r-factor (free) = 0.2300      final r-factor (free) = 0.1980          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8157 = 3.85 * 0.50 * 5.5822 + 1.00 * 0.0664                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5666 = 3.85 * 0.50 * 5.4516 + 1.00 * 0.0687                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1428      final r-factor (work) = 0.1364          |
| start r-factor (free) = 0.1980      final r-factor (free) = 0.1862          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4835 = 0.27 * 1.00 * 5.4516 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4518 = 0.27 * 1.00 * 5.3457 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.692)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.81  16.90    None  None   None       |
|    all(noH): 2823   0      0.00    103.81  16.90    None  None   None       |
|    Sol.    : 438    0      4.80    103.81  43.94    None  None   None       |
|    Mac.    : 2385   0      0.00    94.36   11.93    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 -  10.381: 1346   |   5:    51.905 -  62.286:   86        |
|      1:    10.381 -  20.762:  877   |   6:    62.286 -  72.667:   62        |
|      2:    20.762 -  31.143:  198   |   7:    72.667 -  83.048:   20        |
|      3:    31.143 -  41.524:  112   |   8:    83.048 -  93.429:    8        |
|      4:    41.524 -  51.905:  112   |   9:    93.429 - 103.810:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1364 r_free = 0.1862             target_work(ml) = 5.314         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1364 r_free = 0.1861             target_work(ml) = 5.314         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1364   r_free= 0.1861   ksol= 0.33   Bsol= 67.61   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.15,-1.06,1.18,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.313862                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.6640 0.99   1443  159 0.1002 0.1441      5.4396      5.6838|
|  2:  4.6640 -  3.7205 0.99   1390  159 0.0946 0.1277      5.5442      5.7882|
|  3:  3.7205 -  3.2556 0.99   1380  149 0.1296 0.1761      5.6418      5.9155|
|  4:  3.2556 -  2.9604 0.99   1339  151 0.1592 0.2083      5.6509      5.8258|
|  5:  2.9604 -  2.7496 0.99   1352  152 0.1682 0.2108      5.5336      5.7513|
|  6:  2.7496 -  2.5884 0.99   1346  143 0.1579 0.2393      5.4035       5.662|
|  7:  2.5884 -  2.4593 0.99   1334  158 0.1557 0.2039      5.3608      5.5246|
|  8:  2.4593 -  2.3527 0.98   1328  145 0.1592 0.2077      5.3035      5.5166|
|  9:  2.3527 -  2.2624 0.98   1308  141 0.1499 0.2146      5.2149      5.4612|
| 10:  2.2624 -  2.1846 1.00   1363  152 0.1376 0.1797      5.0728      5.2515|
| 11:  2.1846 -  2.1165 0.98   1302  147 0.1363 0.2206       5.062       5.459|
| 12:  2.1165 -  2.0561 0.98   1309  137 0.1418 0.1927      4.9997      5.2122|
| 13:  2.0561 -  2.0021 0.83   1108  129 0.1260 0.1679      4.8699       5.017|
| 14:  2.0021 -  1.9534 0.25    328   37 0.1199 0.1859      4.7559       5.074|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0375 -  4.6640  1443   159  0.93  10.87   0.97     0.95       9232.59|
|  2:  4.6640 -  3.7205  1390   159  0.94   9.66   1.03     1.01      11670.09|
|  3:  3.7205 -  3.2556  1380   149  0.91  14.50   1.05     1.05      14523.06|
|  4:  3.2556 -  2.9604  1339   151  0.88  18.42   1.03     1.00      15463.40|
|  5:  2.9604 -  2.7496  1352   152  0.86  20.30   1.00     0.98      12965.75|
|  6:  2.7496 -  2.5884  1346   143  0.85  21.18   0.99     0.94      10526.75|
|  7:  2.5884 -  2.4593  1334   158  0.86  20.81   1.02     0.97       9730.98|
|  8:  2.4593 -  2.3527  1328   145  0.86  20.69   1.02     0.98       8628.86|
|  9:  2.3527 -  2.2624  1308   141  0.87  19.72   1.01     0.96       7066.24|
| 10:  2.2624 -  2.1846  1363   152  0.88  18.73   1.02     0.98       5569.06|
| 11:  2.1846 -  2.1165  1302   147  0.88  18.49   1.01     0.95       5338.07|
| 12:  2.1165 -  2.0561  1309   137  0.88  18.75   1.03     1.04       4935.80|
| 13:  2.0561 -  2.0021  1108   129  0.88  18.46   1.02     1.00       3931.06|
| 14:  2.0021 -  1.9534   328    37  0.93  12.95   1.00     0.99       2770.26|
|alpha:            min =        0.94 max =            1.05 mean =         0.98|
|beta:             min =     2770.26 max =        15463.40 mean =      9185.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.87 mean =        17.56|
|phase err.(test): min =        0.00 max =           88.42 mean =        16.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1861   ksol= 0.32   Bsol= 57.18   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,-1.48,0.88,-0.00,0.00,0.00); trace/3= -0.69                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.314204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1861   ksol= 0.32   Bsol= 57.18   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.46,-1.48,0.88,-0.00,0.00,0.00); trace/3= -0.69                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.314204                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.6640 0.99   1443  159 0.1032 0.1410       5.443       5.678|
|  2:  4.6640 -  3.7205 0.99   1390  159 0.0952 0.1280      5.5436      5.7854|
|  3:  3.7205 -  3.2556 0.99   1380  149 0.1296 0.1754      5.6415      5.9094|
|  4:  3.2556 -  2.9604 0.99   1339  151 0.1597 0.2092      5.6515      5.8288|
|  5:  2.9604 -  2.7496 0.99   1352  152 0.1679 0.2115      5.5335      5.7526|
|  6:  2.7496 -  2.5884 0.99   1346  143 0.1583 0.2399      5.4046       5.663|
|  7:  2.5884 -  2.4593 0.99   1334  158 0.1558 0.2042      5.3616      5.5256|
|  8:  2.4593 -  2.3527 0.98   1328  145 0.1593 0.2081      5.3038      5.5175|
|  9:  2.3527 -  2.2624 0.98   1308  141 0.1498 0.2139      5.2146      5.4589|
| 10:  2.2624 -  2.1846 1.00   1363  152 0.1374 0.1801      5.0727      5.2537|
| 11:  2.1846 -  2.1165 0.98   1302  147 0.1361 0.2209      5.0611      5.4593|
| 12:  2.1165 -  2.0561 0.98   1309  137 0.1418 0.1922      5.0003      5.2117|
| 13:  2.0561 -  2.0021 0.83   1108  129 0.1260 0.1679      4.8698      5.0166|
| 14:  2.0021 -  1.9534 0.25    328   37 0.1199 0.1860      4.7561      5.0728|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0375 -  4.6640  1443   159  0.93  10.77   0.97     0.94       9040.91|
|  2:  4.6640 -  3.7205  1390   159  0.94   9.61   1.03     1.01      11559.90|
|  3:  3.7205 -  3.2556  1380   149  0.91  14.45   1.04     1.04      14472.25|
|  4:  3.2556 -  2.9604  1339   151  0.88  18.40   1.02     0.99      15423.23|
|  5:  2.9604 -  2.7496  1352   152  0.86  20.30   0.99     0.97      12977.26|
|  6:  2.7496 -  2.5884  1346   143  0.85  21.20   0.97     0.92      10545.90|
|  7:  2.5884 -  2.4593  1334   158  0.86  20.83   1.00     0.96       9755.69|
|  8:  2.4593 -  2.3527  1328   145  0.86  20.70   1.01     0.97       8636.96|
|  9:  2.3527 -  2.2624  1308   141  0.87  19.71   1.00     0.94       7066.97|
| 10:  2.2624 -  2.1846  1363   152  0.88  18.72   1.00     0.97       5571.35|
| 11:  2.1846 -  2.1165  1302   147  0.88  18.49   0.99     0.94       5344.04|
| 12:  2.1165 -  2.0561  1309   137  0.88  18.75   1.01     1.02       4936.59|
| 13:  2.0561 -  2.0021  1108   129  0.88  18.44   1.00     0.98       3926.44|
| 14:  2.0021 -  1.9534   328    37  0.93  12.90   0.98     0.97       2764.32|
|alpha:            min =        0.92 max =            1.04 mean =         0.97|
|beta:             min =     2764.32 max =        15423.23 mean =      9159.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.54|
|phase err.(test): min =        0.00 max =           89.05 mean =        16.79|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.692)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.81  16.90    None  None   None       |
|    all(noH): 2823   0      0.00    103.81  16.90    None  None   None       |
|    Sol.    : 438    0      4.81    103.81  43.95    None  None   None       |
|    Mac.    : 2385   0      0.00    94.37   11.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.384: 1346   |   5:    51.908 -  62.289:   86        |
|      1:    10.384 -  20.765:  877   |   6:    62.289 -  72.670:   62        |
|      2:    20.765 -  31.146:  198   |   7:    72.670 -  83.051:   20        |
|      3:    31.146 -  41.527:  112   |   8:    83.051 -  93.432:    8        |
|      4:    41.527 -  51.908:  112   |   9:    93.432 - 103.813:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.522 - 4.073
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 327
   mapped sites are within: 0.782 - 4.073

peak=    8.557 closest distance to " O   HOH Z 390 " =    1.289
peak=    7.445 closest distance to " O   HOH Z 385 " =    1.929
peak=    6.848 closest distance to " O   HOH Z 381 " =    1.227
peak=    6.737 closest distance to " O   HOH Z 245 " =    1.410
peak=    6.382 closest distance to " O   HOH Z 130 " =    1.282
peak=    6.127 closest distance to " O   HOH Z  77 " =    1.243
peak=    5.989 closest distance to " O   HOH Z 431 " =    1.933
peak=    5.804 closest distance to " O   HOH Z 424 " =    2.004
peak=    5.785 closest distance to " O   HOH Z 103 " =    1.160
peak=    5.672 closest distance to " O   HOH Z 131 " =    1.040
peak=    5.660 closest distance to " O   HOH Z 222 " =    1.696
peak=    5.504 closest distance to " O   HOH Z 105 " =    1.386
peak=    5.485 closest distance to " O   HOH Z 415 " =    1.235
peak=    5.352 closest distance to " O   HOH Z  29 " =    1.856
peak=    5.313 closest distance to " O   HOH Z 422 " =    1.433
peak=    5.218 closest distance to " O   HOH Z  65 " =    1.867
peak=    5.187 closest distance to " O   HOH Z 417 " =    2.869
peak=    5.174 closest distance to " O   HOH Z 287 " =    1.943
peak=    5.168 closest distance to " O   HOH Z  66 " =    1.244
peak=    5.089 closest distance to " O   HOH Z  69 " =    2.152
peak=    5.051 closest distance to " O   ASP A 286 " =    2.572
peak=    4.960 closest distance to " O   HOH Z  63 " =    1.756
peak=    4.929 closest distance to " O   HOH Z 142 " =    1.808
peak=    4.795 closest distance to " O   HOH Z 126 " =    1.998
peak=    4.750 closest distance to " NE2 GLN A  11 " =    1.383
peak=    4.709 closest distance to " CB  PRO A  54 " =    1.166
peak=    4.690 closest distance to " O   HOH Z 403 " =    2.006
peak=    4.688 closest distance to " O   HOH Z 293 " =    1.532
peak=    4.672 closest distance to " O   HOH Z 117 " =    1.404
peak=    4.670 closest distance to " O   HOH Z  46 " =    1.293
peak=    4.636 closest distance to " CG  PRO A  54 " =    1.474
peak=    4.628 closest distance to " O   HOH Z 295 " =    1.289
peak=    4.611 closest distance to " CB  ARG A 275 " =    1.021
peak=    4.604 closest distance to " CG  PRO A  90 " =    1.490
peak=    4.600 closest distance to " O   HOH Z 427 " =    2.055
peak=    4.586 closest distance to " C   VAL A  72 " =    0.991
peak=    4.565 closest distance to " O   HOH Z 418 " =    1.348
peak=    4.557 closest distance to " O   HOH Z 427 " =    1.279
peak=    4.550 closest distance to " O   HOH Z 359 " =    1.822
peak=    4.528 closest distance to " O   HOH Z 139 " =    1.283
peak=    4.520 closest distance to " O  BHOH Z  74 " =    1.116
peak=    4.493 closest distance to " O   HOH Z 380 " =    2.287
peak=    4.448 closest distance to " O   HOH Z 145 " =    1.778
peak=    4.441 closest distance to " O   HOH Z 232 " =    2.167
peak=    4.427 closest distance to " O   PRO A 198 " =    1.447
peak=    4.411 closest distance to " O   HOH Z 120 " =    1.124
peak=    4.395 closest distance to " O   HOH Z  39 " =    1.403
peak=    4.378 closest distance to " CZ3 TRP A 266 " =    1.216
peak=    4.352 closest distance to " O   HOH Z  11 " =    1.259
peak=    4.337 closest distance to " O   HOH Z 298 " =    2.001
peak=    4.332 closest distance to " O   HOH Z  30 " =    1.940
peak=    4.329 closest distance to " O   HOH Z 124 " =    1.506
peak=    4.328 closest distance to " O   HOH Z 181 " =    1.577
peak=    4.277 closest distance to " O   HOH Z 425 " =    1.423
peak=    4.234 closest distance to " CB  SER A 216 " =    1.067
peak=    4.234 closest distance to " O   HOH Z 112 " =    1.330
peak=    4.231 closest distance to " CB  SER A  63 " =    1.373
peak=    4.219 closest distance to " O   HOH Z 358 " =    1.274
peak=    4.212 closest distance to " O   HOH Z  49 " =    1.459
peak=    4.208 closest distance to " O   HOH Z 278 " =    1.459
peak=    4.198 closest distance to " O   HOH Z  97 " =    1.383
peak=    4.198 closest distance to " O   HOH Z 296 " =    1.199
peak=    4.185 closest distance to " O   HOH Z  30 " =    1.487
peak=    4.172 closest distance to " ND2BASN A 224 " =    0.916
peak=    4.165 closest distance to " CB  GLN A 223 " =    1.567
peak=    4.162 closest distance to " NH1AARG A 145 " =    1.122
peak=    4.160 closest distance to " O   HOH Z  91 " =    2.423
peak=    4.146 closest distance to " O   HOH Z  70 " =    1.086
peak=    4.131 closest distance to " O   HOH Z  67 " =    1.408
peak=    4.100 closest distance to " OG ASER A 258 " =    3.025
peak=    4.093 closest distance to " O   HOH Z  41 " =    1.039
peak=    4.082 closest distance to " CG  GLN A  58 " =    1.164
peak=    4.059 closest distance to " O   HOH Z  43 " =    1.356
peak=    4.047 closest distance to " O   HOH Z 258 " =    2.201
peak=    4.043 closest distance to " O   HOH Z 414 " =    2.344
peak=    4.042 closest distance to " O   HOH Z 127 " =    1.074
peak=    4.028 closest distance to " CB  ASN A  39 " =    0.902
peak=    4.025 closest distance to " O   HOH Z  83 " =    1.219
peak=    4.018 closest distance to " O   HOH Z 414 " =    1.466
peak=    4.012 closest distance to " O   HOH Z   9 " =    2.123
peak=    4.010 closest distance to " CB  SER A  99 " =    0.918
peak=    3.997 closest distance to " CB  ALA A 114 " =    0.986
peak=    3.995 closest distance to " CB  PRO A  90 " =    1.126
peak=    3.985 closest distance to " O   HOH Z 119 " =    1.531
peak=    3.976 closest distance to " O   HOH Z  51 " =    1.987
peak=    3.965 closest distance to " CE  LYS A 119 " =    1.359
peak=    3.963 closest distance to " N   GLN A 278 " =    1.078
peak=    3.962 closest distance to " CA  VAL A 125 " =    1.095
peak=    3.961 closest distance to " CG  TRP A 179 " =    2.180
peak=    3.960 closest distance to " O   HOH Z 374 " =    1.317
peak=    3.958 closest distance to " CE3 TRP A 274 " =    1.447
peak=    3.952 closest distance to " CG2 ILE A 120 " =    1.242
peak=    3.931 closest distance to " O   HOH Z 244 " =    1.734
peak=    3.916 closest distance to " CA  SER A  87 " =    0.990
peak=    3.906 closest distance to " CB  ASN A 148 " =    1.405
peak=    3.903 closest distance to " O   HOH Z 424 " =    1.212
peak=    3.900 closest distance to " CG2 VAL A 257 " =    0.901
peak=    3.889 closest distance to " CE  MET A  93 " =    1.390
peak=    3.886 closest distance to " O   HOH Z 289 " =    1.235
peak=    3.881 closest distance to " CB  SER A 276 " =    1.268
peak=    3.875 closest distance to " NE1 TRP A 266 " =    1.871
peak=    3.853 closest distance to " N   ALA A   1 " =    1.620
peak=    3.838 closest distance to " O   HOH Z  71 " =    1.539
peak=    3.821 closest distance to " CA  PHE A 283 " =    1.298
peak=    3.818 closest distance to " CE3 TRP A 150 " =    1.136
peak=    3.817 closest distance to " NH2AARG A 145 " =    1.219
peak=    3.805 closest distance to " OG ASER A 212 " =    1.441
peak=    3.799 closest distance to " O   HOH Z 276 " =    1.441
peak=    3.781 closest distance to " O   HOH Z 363 " =    1.130
peak=    3.778 closest distance to " O   HOH Z 225 " =    1.928
peak=    3.769 closest distance to " CG  GLN A  89 " =    1.590
peak=    3.769 closest distance to " O   HOH Z 259 " =    2.200
peak=    3.764 closest distance to " O   HOH Z 158 " =    1.192
peak=    3.756 closest distance to " CB  GLU A 277 " =    3.656
peak=    3.753 closest distance to " O   HOH Z 405 " =    1.734
peak=    3.745 closest distance to " C   GLN A  73 " =    1.121
peak=    3.742 closest distance to " O   HOH Z  61 " =    1.714
peak=    3.735 closest distance to " CB  ASP A 124 " =    0.955
peak=    3.725 closest distance to " O   HOH Z 368 " =    1.683
peak=    3.718 closest distance to " O   HOH Z 365 " =    2.412
peak=    3.716 closest distance to " CB  GLU A 152 " =    1.175
peak=    3.714 closest distance to " O   HOH Z 411 " =    3.761
peak=    3.710 closest distance to " CA  TYR A  30 " =    1.226
peak=    3.702 closest distance to " O   HOH Z 406 " =    1.644
peak=    3.699 closest distance to " CD  GLN A  77 " =    1.276
peak=    3.698 closest distance to " CE2 PHE A  16 " =    0.782
peak=    3.697 closest distance to " O   HOH Z 100 " =    1.102
peak=    3.696 closest distance to " N   TYR A  15 " =    1.121
peak=    3.689 closest distance to " O   HOH Z 153 " =    3.489
peak=    3.686 closest distance to " CG2 THR A 221 " =    1.111
peak=    3.681 closest distance to " O   HOH Z 130 " =    2.332
peak=    3.678 closest distance to " NZ  LYS A 166 " =    1.115
peak=    3.676 closest distance to " CG  LYS A 119 " =    0.943
peak=    3.675 closest distance to " CA  LEU A 282 " =    1.040
peak=    3.668 closest distance to " NH2 ARG A  56 " =    2.008
peak=    3.667 closest distance to " O   HOH Z 375 " =    1.126
peak=    3.657 closest distance to " O   HOH Z  68 " =    2.091
peak=    3.656 closest distance to " O   HOH Z 180 " =    2.307
peak=    3.648 closest distance to " NH2 ARG A  56 " =    1.051
peak=    3.647 closest distance to " O   HOH Z 104 " =    1.855
peak=    3.644 closest distance to " O   HOH Z  76 " =    1.536
peak=    3.639 closest distance to " O   HOH Z 416 " =    1.333
peak=    3.638 closest distance to " O   HOH Z 434 " =    1.607
peak=    3.631 closest distance to " CG1 VAL A 296 " =    1.037
peak=    3.627 closest distance to " O   HOH Z   7 " =    2.723
peak=    3.627 closest distance to " CD2 TRP A 179 " =    1.347
peak=    3.623 closest distance to " O   HOH Z 368 " =    3.413
peak=    3.622 closest distance to " O   HOH Z 327 " =    1.829
peak=    3.615 closest distance to " CB  ASP A 140 " =    1.029
peak=    3.613 closest distance to " CA  ALA A  51 " =    1.026
peak=    3.605 closest distance to " OE2 GLU A  53 " =    2.087
peak=    3.604 closest distance to " CB  TRP A 179 " =    1.405
peak=    3.600 closest distance to " O   HOH Z 207 " =    1.118
peak=    3.600 closest distance to " CB  ASN A 110 " =    1.065
peak=    3.596 closest distance to " O   ALA A 165 " =    1.450
peak=    3.595 closest distance to " O   HOH Z  40 " =    1.544
peak=    3.593 closest distance to " CB  PHE A 130 " =    0.906
peak=    3.589 closest distance to " CB  ALA A  43 " =    0.865
peak=    3.586 closest distance to " O   HOH Z 201 " =    1.794
peak=    3.586 closest distance to " O   HOH Z 146 " =    1.588
peak=    3.584 closest distance to " CE1 PHE A  61 " =    1.629
peak=    3.580 closest distance to " NZ  LYS A 119 " =    2.218
peak=    3.577 closest distance to " O   HOH Z 282 " =    1.886
peak=    3.574 closest distance to " O   HOH Z 393 " =    1.349
peak=    3.571 closest distance to " NE1 TRP A 274 " =    1.162
peak=    3.563 closest distance to " CG  PRO A 243 " =    1.209
peak=    3.553 closest distance to " O   HOH Z 423 " =    1.984
peak=    3.544 closest distance to " O   HOH Z 220 " =    1.505
peak=    3.541 closest distance to " CB  ASN A 142 " =    0.927
peak=    3.539 closest distance to " O   HOH Z 410 " =    1.529
peak=    3.539 closest distance to " O   HOH Z 193 " =    1.317
peak=    3.535 closest distance to " NZ  LYS A 117 " =    2.913
peak=    3.522 closest distance to " CA  TYR A 116 " =    1.521
peak=    3.517 closest distance to " CG1 ILE A 120 " =    1.413
peak=    3.516 closest distance to " O   HOH Z  26 " =    1.552
peak=    3.514 closest distance to " O   HOH Z 132 " =    0.916
peak=    3.513 closest distance to " O   HOH Z  88 " =    3.564
peak=    3.510 closest distance to " O   HOH Z 213 " =    2.024
peak=    3.507 closest distance to " O   HOH Z   6 " =    1.674
peak=    3.504 closest distance to " CB  MET A  40 " =    0.837
peak=    3.495 closest distance to " O   HOH Z 362 " =    1.927
peak=    3.493 closest distance to " O   ASN A 142 " =    1.049
peak=    3.487 closest distance to " CG AARG A 275 " =    1.313
peak=    3.477 closest distance to " O   HOH Z 215 " =    1.883
peak=    3.477 closest distance to " O   HOH Z 330 " =    1.120
peak=    3.471 closest distance to " O   HOH Z  92 " =    1.239
peak=    3.466 closest distance to " O   HOH Z 425 " =    1.968
peak=    3.464 closest distance to " CA  ARG A 159 " =    1.191
peak=    3.461 closest distance to " O   HOH Z  42 " =    1.471
peak=    3.457 closest distance to " O   HOH Z 378 " =    1.110
peak=    3.452 closest distance to " CG  LYS A  76 " =    1.774
peak=    3.451 closest distance to " O   HOH Z 172 " =    1.746
peak=    3.449 closest distance to " CG  ARG A 159 " =    0.892
peak=    3.449 closest distance to " CB  THR A  31 " =    1.494
peak=    3.447 closest distance to " ND2 ASN A  60 " =    2.941
peak=    3.441 closest distance to " O   HOH Z 392 " =    1.300
peak=    3.438 closest distance to " CZ  PHE A  38 " =    1.328
peak=    3.438 closest distance to " O   HOH Z 426 " =    1.082
peak=    3.437 closest distance to " C   GLU A 277 " =    1.418
peak=    3.434 closest distance to " O   HOH Z 203 " =    1.814
peak=    3.430 closest distance to " O   HOH Z 430 " =    1.958
peak=    3.425 closest distance to " O   HOH Z 424 " =    3.379
peak=    3.424 closest distance to " O   HOH Z 214 " =    2.553
peak=    3.424 closest distance to " O   HOH Z 216 " =    4.073
peak=    3.423 closest distance to " N   CYS A 260 " =    0.935
peak=    3.423 closest distance to " OE2 GLU A  44 " =    1.166
peak=    3.420 closest distance to " O   HOH Z 211 " =    1.313
peak=    3.417 closest distance to " CG2 ILE A 239 " =    0.898
peak=    3.403 closest distance to " NH2AARG A 102 " =    0.920
peak=    3.399 closest distance to " O   HOH Z 394 " =    1.698
peak=    3.395 closest distance to " O   HOH Z 158 " =    2.568
peak=    3.387 closest distance to " O   HOH Z  40 " =    2.142
peak=    3.385 closest distance to " ND2 ASN A 249 " =    0.805
peak=    3.383 closest distance to " CB  LEU A 300 " =    1.063
peak=    3.382 closest distance to " O   HOH Z  21 " =    1.494
peak=    3.381 closest distance to " O   HOH Z 133 " =    0.793
peak=    3.380 closest distance to " CG  PRO A 213 " =    1.259
peak=    3.380 closest distance to " O   HOH Z 143 " =    1.334
peak=    3.378 closest distance to " CA  LEU A  83 " =    1.745
peak=    3.378 closest distance to " NE2 HIS A 207 " =    1.025
peak=    3.377 closest distance to " ND2 ASN A 249 " =    1.915
peak=    3.375 closest distance to " O   HOH Z 272 " =    1.926
peak=    3.372 closest distance to " CB  VAL A 265 " =    1.390
peak=    3.365 closest distance to " O   HOH Z 193 " =    1.419
peak=    3.365 closest distance to " CG  GLU A  37 " =    0.996
peak=    3.364 closest distance to " O   HOH Z 155 " =    1.903
peak=    3.358 closest distance to " O   HOH Z 280 " =    1.635
peak=    3.356 closest distance to " O   HOH Z 371 " =    1.777
peak=    3.350 closest distance to " O   HOH Z 131 " =    2.594
peak=    3.342 closest distance to " CB  ARG A 190 " =    1.720
peak=    3.339 closest distance to " O   HOH Z  47 " =    1.929
peak=    3.338 closest distance to " SD BMET A  47 " =    1.108
peak=    3.337 closest distance to " O   HOH Z 248 " =    1.705
peak=    3.335 closest distance to " CD  ARG A 159 " =    0.848
peak=    3.333 closest distance to " O   HOH Z 357 " =    2.097
peak=    3.332 closest distance to " CB  TYR A 116 " =    1.238
peak=    3.325 closest distance to " O   HOH Z 285 " =    2.375
peak=    3.321 closest distance to " CG  PRO A 198 " =    1.296
peak=    3.316 closest distance to " CB  ALA A 242 " =    1.311
peak=    3.316 closest distance to " CA  ALA A   7 " =    0.895
peak=    3.310 closest distance to " N   PHE A 130 " =    1.276
peak=    3.307 closest distance to " CA  PRO A  54 " =    1.265
peak=    3.307 closest distance to " NZ BLYS A 290 " =    0.994
peak=    3.306 closest distance to " CG  GLN A  73 " =    1.024
peak=    3.301 closest distance to " CD  ARG A 195 " =    3.636
peak=    3.301 closest distance to " CB  ASP A 191 " =    1.227
peak=    3.300 closest distance to " O   HOH Z 157 " =    1.641
peak=    3.300 closest distance to " O   HOH Z 239 " =    1.504
peak=    3.298 closest distance to " O   HOH Z 128 " =    2.011
peak=    3.298 closest distance to " O   HOH Z 217 " =    1.158
peak=    3.294 closest distance to " NH2AARG A 190 " =    1.944
peak=    3.293 closest distance to " CB  TRP A 266 " =    1.040
peak=    3.291 closest distance to " O   HOH Z  53 " =    2.321
peak=    3.291 closest distance to " O   HOH Z  48 " =    1.683
peak=    3.288 closest distance to " O   HOH Z 361 " =    1.419
peak=    3.286 closest distance to " CB  GLU A 128 " =    0.920
peak=    3.285 closest distance to " CB  GLN A  88 " =    1.327
peak=    3.284 closest distance to " CB  LYS A 290 " =    0.895
peak=    3.284 closest distance to " CG2 VAL A 197 " =    1.292
peak=    3.283 closest distance to " CB  VAL A 202 " =    1.613
peak=    3.283 closest distance to " O   HOH Z 106 " =    4.049
peak=    3.280 closest distance to " O   GLN A  55 " =    1.740
peak=    3.280 closest distance to " O   HOH Z 219 " =    3.941
peak=    3.277 closest distance to " CB  ASP A 272 " =    0.999
peak=    3.274 closest distance to " O   HOH Z   1 " =    1.646
peak=    3.257 closest distance to " O   HOH Z 437 " =    2.064
peak=    3.253 closest distance to " CB  TRP A 179 " =    1.550
peak=    3.248 closest distance to " O   HOH Z  27 " =    1.029
peak=    3.246 closest distance to " CB  SER A   3 " =    1.497
peak=    3.244 closest distance to " O   HOH Z 365 " =    1.610
peak=    3.242 closest distance to " O   HOH Z 345 " =    2.029
peak=    3.240 closest distance to " O   HOH Z  32 " =    2.336
peak=    3.238 closest distance to " O   HOH Z 371 " =    3.475
peak=    3.236 closest distance to " CG2 VAL A 202 " =    1.568
peak=    3.232 closest distance to " CB  SER A 210 " =    0.959
peak=    3.230 closest distance to " O   HOH Z  58 " =    1.714
peak=    3.228 closest distance to " CB  SER A  62 " =    1.017
peak=    3.223 closest distance to " C   HIS A 115 " =    0.963
peak=    3.217 closest distance to " OD1 ASN A  45 " =    2.751
peak=    3.215 closest distance to " CG2 THR A 178 " =    0.971
peak=    3.213 closest distance to " O   HOH Z  44 " =    1.921
peak=    3.211 closest distance to " CA  MET A 105 " =    0.919
peak=    3.209 closest distance to " O   HOH Z  88 " =    2.565
peak=    3.205 closest distance to " CB  ALA A 160 " =    1.521
peak=    3.203 closest distance to " CB  ALA A   1 " =    1.250
peak=    3.202 closest distance to " NH2 ARG A 269 " =    1.176
peak=    3.202 closest distance to " OE1 GLU A   2 " =    1.317
peak=    3.201 closest distance to " OD1 ASP A 171 " =    1.162
peak=    3.197 closest distance to " CB  ASN A 285 " =    1.072
peak=    3.194 closest distance to " OG BSER A 164 " =    2.332
peak=    3.194 closest distance to " CA  ALA A 129 " =    1.219
peak=    3.194 closest distance to " NE BARG A 145 " =    1.114
peak=    3.188 closest distance to " CA  ILE A 234 " =    1.138
peak=    3.187 closest distance to " O   HOH Z  44 " =    2.902
peak=    3.186 closest distance to " N   PHE A 208 " =    0.944
peak=    3.182 closest distance to " CG  LEU A 167 " =    1.344
peak=    3.166 closest distance to " CA  ARG A 195 " =    1.281
peak=    3.164 closest distance to " N   SER A  97 " =    0.789
peak=    3.158 closest distance to " N   GLY A 302 " =    0.946
peak=    3.152 closest distance to " O   HOH Z 350 " =    1.428
peak=    3.152 closest distance to " N   GLU A   2 " =    1.362
peak=    3.150 closest distance to " CG  GLN A  11 " =    2.290
peak=    3.149 closest distance to " CA  ALA A 291 " =    0.938
peak=    3.143 closest distance to " CA  ASN A  74 " =    1.324
peak=    3.136 closest distance to " CG2 THR A 294 " =    1.425
peak=    3.130 closest distance to " N   GLY A 241 " =    1.501
peak=    3.129 closest distance to " O   HOH Z  61 " =    1.729
peak=    3.120 closest distance to " O   HOH Z 222 " =    2.337
peak=    3.114 closest distance to " CA  ASN A 127 " =    1.195
peak=    3.106 closest distance to " CB  ASN A 215 " =    1.172
peak=    3.096 closest distance to " O   TYR A 116 " =    1.214
peak=    3.096 closest distance to " O   HOH Z  80 " =    2.457
peak=    3.094 closest distance to " OD1 ASP A  65 " =    1.917
peak=    3.087 closest distance to " CD1 ILE A  33 " =    1.819
peak=    3.087 closest distance to " CB  ASN A 187 " =    0.897
peak=    3.086 closest distance to " O   HOH Z  59 " =    1.879
peak=    3.085 closest distance to " N   GLN A  73 " =    1.564
peak=    3.077 closest distance to " CG2BVAL A  41 " =    0.932
peak=    3.050 closest distance to " O   HOH Z 185 " =    1.570
peak=    3.045 closest distance to " O   HOH Z 422 " =    1.965
peak=    3.037 closest distance to " CA  GLY A  35 " =    0.924
peak=    3.036 closest distance to " C   PHE A 208 " =    1.039
peak=    3.025 closest distance to " CB  ARG A  79 " =    1.183

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.482 - 5.317
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 200
   mapped sites are within: 0.713 - 5.317

peak=   -4.841 closest distance to " O   PRO A 198 " =    1.035
peak=   -4.579 closest distance to " O   HOH Z 313 " =    1.105
peak=   -4.497 closest distance to " O   HOH Z 100 " =    0.817
peak=   -4.496 closest distance to " O   HOH Z  41 " =    0.779
peak=   -4.399 closest distance to " O   HOH Z 385 " =    1.219
peak=   -4.344 closest distance to " O   HOH Z  69 " =    1.338
peak=   -4.254 closest distance to " O   HOH Z  24 " =    0.821
peak=   -4.229 closest distance to " O   HOH Z 415 " =    0.833
peak=   -4.183 closest distance to " CG2 ILE A  49 " =    2.820
peak=   -4.028 closest distance to " CD2 TYR A 293 " =    1.902
peak=   -3.962 closest distance to " O   SER A 135 " =    1.534
peak=   -3.947 closest distance to " O   ALA A  10 " =    1.550
peak=   -3.929 closest distance to " CB  GLN A  55 " =    1.201
peak=   -3.915 closest distance to " O   HOH Z  60 " =    1.790
peak=   -3.902 closest distance to " O   SER A  22 " =    2.669
peak=   -3.900 closest distance to " CB  ALA A 291 " =    2.193
peak=   -3.894 closest distance to " CB  ASP A 171 " =    2.224
peak=   -3.873 closest distance to " CD  ARG A  14 " =    3.081
peak=   -3.841 closest distance to " CG  TRP A 266 " =    1.677
peak=   -3.838 closest distance to " C   VAL A  72 " =    0.891
peak=   -3.827 closest distance to " O   HOH Z 131 " =    1.253
peak=   -3.817 closest distance to " O   HOH Z 216 " =    1.390
peak=   -3.804 closest distance to " CD1 TRP A 179 " =    1.142
peak=   -3.801 closest distance to " CB  ALA A  43 " =    2.411
peak=   -3.794 closest distance to " CB  ASP A 132 " =    2.653
peak=   -3.771 closest distance to " OE1 GLU A  44 " =    2.032
peak=   -3.766 closest distance to " CD1 LEU A 101 " =    2.182
peak=   -3.737 closest distance to " O   HOH Z 198 " =    0.992
peak=   -3.725 closest distance to " OG  SER A  97 " =    2.033
peak=   -3.725 closest distance to " O   HOH Z 244 " =    1.236
peak=   -3.719 closest distance to " O   HOH Z 276 " =    1.007
peak=   -3.716 closest distance to " CG  ARG A 219 " =    2.454
peak=   -3.715 closest distance to " CZ  PHE A  59 " =    1.572
peak=   -3.705 closest distance to " CA  GLY A 241 " =    2.276
peak=   -3.676 closest distance to " O   HOH Z 219 " =    3.811
peak=   -3.656 closest distance to " O   ASN A 170 " =    2.008
peak=   -3.643 closest distance to " CG  MET A 105 " =    0.968
peak=   -3.643 closest distance to " O   HOH Z  28 " =    1.122
peak=   -3.640 closest distance to " O   HOH Z  71 " =    1.121
peak=   -3.616 closest distance to " CZ3 TRP A 179 " =    1.350
peak=   -3.613 closest distance to " O   HOH Z   5 " =    0.932
peak=   -3.612 closest distance to " O   HOH Z 387 " =    2.607
peak=   -3.611 closest distance to " CA  GLY A  98 " =    1.774
peak=   -3.610 closest distance to " CG1BVAL A  41 " =    2.879
peak=   -3.609 closest distance to " CG2 ILE A  20 " =    2.679
peak=   -3.589 closest distance to " O   PRO A 163 " =    1.427
peak=   -3.584 closest distance to " O   HOH Z 266 " =    5.303
peak=   -3.583 closest distance to " O   HOH Z  39 " =    0.934
peak=   -3.580 closest distance to " O   HOH Z  49 " =    1.189
peak=   -3.566 closest distance to " N   GLN A  58 " =    1.293
peak=   -3.563 closest distance to " OD2 ASP A 272 " =    1.516
peak=   -3.563 closest distance to " CG2 ILE A 120 " =    0.852
peak=   -3.559 closest distance to " NZ  LYS A 166 " =    1.652
peak=   -3.558 closest distance to " OG  SER A 245 " =    1.668
peak=   -3.552 closest distance to " CB  ASN A  45 " =    2.047
peak=   -3.551 closest distance to " O   HOH Z 105 " =    1.941
peak=   -3.550 closest distance to " NH2 ARG A 219 " =    1.970
peak=   -3.549 closest distance to " O   HOH Z 414 " =    1.284
peak=   -3.541 closest distance to " CE3 TRP A 274 " =    2.330
peak=   -3.525 closest distance to " O   HOH Z 389 " =    2.321
peak=   -3.516 closest distance to " O   HOH Z  26 " =    0.770
peak=   -3.513 closest distance to " O   ASP A 253 " =    1.850
peak=   -3.508 closest distance to " O   HOH Z 412 " =    3.651
peak=   -3.505 closest distance to " O   HOH Z 111 " =    1.581
peak=   -3.500 closest distance to " O   HOH Z 438 " =    0.906
peak=   -3.495 closest distance to " CD  PRO A 213 " =    2.137
peak=   -3.494 closest distance to " O   HOH Z 100 " =    1.199
peak=   -3.490 closest distance to " O   HOH Z 151 " =    1.172
peak=   -3.489 closest distance to " C   GLU A   2 " =    1.846
peak=   -3.484 closest distance to " O   ASP A 191 " =    1.772
peak=   -3.483 closest distance to " O   HOH Z 275 " =    1.708
peak=   -3.482 closest distance to " OE1 GLU A 277 " =    2.197
peak=   -3.477 closest distance to " CG1 VAL A 125 " =    2.303
peak=   -3.476 closest distance to " CB  ALA A 129 " =    2.620
peak=   -3.467 closest distance to " CD2 HIS A 207 " =    1.472
peak=   -3.458 closest distance to " C   HIS A 207 " =    1.215
peak=   -3.456 closest distance to " N   THR A 157 " =    1.683
peak=   -3.452 closest distance to " C   HIS A 108 " =    1.298
peak=   -3.447 closest distance to " N   PRO A 163 " =    1.551
peak=   -3.445 closest distance to " NE2 GLN A  77 " =    1.437
peak=   -3.441 closest distance to " CA  GLN A  58 " =    1.270
peak=   -3.440 closest distance to " O   HOH Z 100 " =    1.533
peak=   -3.438 closest distance to " CB  ASP A  27 " =    2.436
peak=   -3.433 closest distance to " N   ALA A  43 " =    2.680
peak=   -3.433 closest distance to " CD  GLU A 277 " =    0.943
peak=   -3.430 closest distance to " N   TRP A 274 " =    1.316
peak=   -3.428 closest distance to " ND2 ASN A 285 " =    2.127
peak=   -3.426 closest distance to " O   GLN A 240 " =    3.156
peak=   -3.420 closest distance to " CB  ARG A  79 " =    2.710
peak=   -3.419 closest distance to " O   LYS A  76 " =    2.005
peak=   -3.415 closest distance to " NE2 GLN A 194 " =    1.886
peak=   -3.409 closest distance to " CG1 VAL A 265 " =    2.365
peak=   -3.409 closest distance to " OG BSER A 134 " =    1.591
peak=   -3.405 closest distance to " NE2 GLN A  55 " =    1.087
peak=   -3.399 closest distance to " O   HOH Z 389 " =    0.919
peak=   -3.395 closest distance to " CZ2 TRP A 274 " =    0.926
peak=   -3.383 closest distance to " O   HOH Z 163 " =    1.951
peak=   -3.382 closest distance to " O   HOH Z 381 " =    0.961
peak=   -3.377 closest distance to " SG BCYS A 201 " =    2.378
peak=   -3.376 closest distance to " CD  GLU A 236 " =    1.059
peak=   -3.371 closest distance to " O   HOH Z 181 " =    2.052
peak=   -3.370 closest distance to " O   HOH Z 426 " =    1.576
peak=   -3.370 closest distance to " OE2 GLU A 152 " =    1.436
peak=   -3.368 closest distance to " O   HOH Z 181 " =    1.465
peak=   -3.364 closest distance to " O   HOH Z 126 " =    1.845
peak=   -3.358 closest distance to " O   HOH Z 139 " =    1.017
peak=   -3.356 closest distance to " O   HOH Z 251 " =    0.802
peak=   -3.354 closest distance to " CE BMET A  47 " =    1.336
peak=   -3.349 closest distance to " O   HOH Z 428 " =    2.609
peak=   -3.349 closest distance to " NE2 GLN A 278 " =    1.472
peak=   -3.338 closest distance to " ND2 ASN A  39 " =    1.509
peak=   -3.334 closest distance to " OG  SER A  63 " =    1.243
peak=   -3.326 closest distance to " N   ALA A   1 " =    1.534
peak=   -3.324 closest distance to " CB  PRO A  54 " =    2.285
peak=   -3.319 closest distance to " O   HOH Z 238 " =    0.910
peak=   -3.318 closest distance to " O   HOH Z 129 " =    3.583
peak=   -3.315 closest distance to " CE1 TYR A 293 " =    2.068
peak=   -3.307 closest distance to " ND2 ASN A 209 " =    1.753
peak=   -3.304 closest distance to " O   ILE A  49 " =    1.707
peak=   -3.304 closest distance to " CB  ASN A 285 " =    2.065
peak=   -3.297 closest distance to " O   HOH Z 323 " =    2.010
peak=   -3.297 closest distance to " O   HOH Z 337 " =    1.519
peak=   -3.296 closest distance to " O   HOH Z 324 " =    0.851
peak=   -3.291 closest distance to " OG BSER A 210 " =    2.394
peak=   -3.289 closest distance to " O   HOH Z  67 " =    1.340
peak=   -3.286 closest distance to " C   ALA A   9 " =    1.030
peak=   -3.285 closest distance to " O   GLY A 196 " =    1.321
peak=   -3.282 closest distance to " CD  ARG A 156 " =    2.045
peak=   -3.278 closest distance to " O   HOH Z 140 " =    0.992
peak=   -3.273 closest distance to " O   HOH Z  60 " =    1.259
peak=   -3.264 closest distance to " O   HOH Z 325 " =    1.344
peak=   -3.263 closest distance to " O   HOH Z 359 " =    3.295
peak=   -3.261 closest distance to " O   GLY A 203 " =    2.584
peak=   -3.252 closest distance to " N   ALA A  19 " =    2.358
peak=   -3.251 closest distance to " O   GLU A 152 " =    1.716
peak=   -3.251 closest distance to " O   HOH Z 298 " =    2.500
peak=   -3.247 closest distance to " CG2 THR A 221 " =    2.326
peak=   -3.241 closest distance to " O   HOH Z  70 " =    0.927
peak=   -3.237 closest distance to " CG BMET A  47 " =    3.137
peak=   -3.235 closest distance to " O   HOH Z 250 " =    1.093
peak=   -3.230 closest distance to " N   GLN A 223 " =    2.144
peak=   -3.230 closest distance to " CG2 ILE A 151 " =    2.445
peak=   -3.227 closest distance to " O   HOH Z  89 " =    2.868
peak=   -3.218 closest distance to " O   HOH Z  67 " =    1.476
peak=   -3.218 closest distance to " N   ALA A   1 " =    1.286
peak=   -3.217 closest distance to " CA  TYR A  68 " =    1.190
peak=   -3.217 closest distance to " O   HOH Z  22 " =    2.860
peak=   -3.215 closest distance to " O   ARG A 145 " =    1.228
peak=   -3.214 closest distance to " CB  ASN A 187 " =    1.047
peak=   -3.210 closest distance to " O   HOH Z 141 " =    0.767
peak=   -3.204 closest distance to " CD2 PHE A  61 " =    2.252
peak=   -3.199 closest distance to " O   HOH Z 429 " =    1.368
peak=   -3.193 closest distance to " O   HOH Z  53 " =    1.643
peak=   -3.186 closest distance to " CA  GLY A 133 " =    1.902
peak=   -3.184 closest distance to " OH  TYR A 247 " =    1.426
peak=   -3.183 closest distance to " OG  SER A  87 " =    1.931
peak=   -3.176 closest distance to " CD2 TYR A 116 " =    2.220
peak=   -3.174 closest distance to " N   ASP A 270 " =    1.299
peak=   -3.173 closest distance to " O   HOH Z 143 " =    1.346
peak=   -3.173 closest distance to " CG  GLU A 128 " =    1.747
peak=   -3.171 closest distance to " CA  GLY A 203 " =    2.438
peak=   -3.167 closest distance to " CZ  ARG A 259 " =    0.969
peak=   -3.167 closest distance to " O   HOH Z 340 " =    1.786
peak=   -3.166 closest distance to " O   HOH Z 390 " =    1.148
peak=   -3.162 closest distance to " N   GLU A 277 " =    1.432
peak=   -3.160 closest distance to " CG  GLN A 240 " =    2.283
peak=   -3.160 closest distance to " NE2 GLN A 223 " =    1.607
peak=   -3.160 closest distance to " OE2 GLU A 152 " =    2.247
peak=   -3.155 closest distance to " O   HOH Z 357 " =    1.675
peak=   -3.155 closest distance to " O   HOH Z 128 " =    2.645
peak=   -3.153 closest distance to " NH2AARG A 275 " =    5.244
peak=   -3.150 closest distance to " CG2 VAL A 112 " =    2.749
peak=   -3.150 closest distance to " CA  LEU A 143 " =    0.889
peak=   -3.140 closest distance to " O   SER A 271 " =    1.204
peak=   -3.136 closest distance to " CD  GLN A 223 " =    0.713
peak=   -3.130 closest distance to " O   HOH Z 416 " =    0.986
peak=   -3.129 closest distance to " O   HOH Z 377 " =    1.924
peak=   -3.127 closest distance to " O   HOH Z 231 " =    1.971
peak=   -3.126 closest distance to " O   ALA A  34 " =    2.530
peak=   -3.126 closest distance to " ND2 ASN A  45 " =    2.660
peak=   -3.120 closest distance to " OE1 GLN A 183 " =    1.643
peak=   -3.118 closest distance to " CB  SER A  62 " =    5.317
peak=   -3.112 closest distance to " CB  ASN A  69 " =    1.703
peak=   -3.106 closest distance to " CG1BVAL A  72 " =    2.230
peak=   -3.105 closest distance to " OG BSER A  99 " =    1.147
peak=   -3.103 closest distance to " CD2 LEU A  25 " =    2.191
peak=   -3.102 closest distance to " OXT GLY A 302 " =    3.936
peak=   -3.097 closest distance to " O   HOH Z  25 " =    1.310
peak=   -3.092 closest distance to " CD1 TYR A 214 " =    1.435
peak=   -3.083 closest distance to " CZ  PHE A  38 " =    2.349
peak=   -3.071 closest distance to " CG  LEU A  83 " =    2.139
peak=   -3.068 closest distance to " CD  GLN A  88 " =    0.923
peak=   -3.066 closest distance to " O   HOH Z 181 " =    1.692
peak=   -3.049 closest distance to " O   HOH Z 356 " =    4.368

================= 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    :  0.4859 0.4891   6.298902e+00   6.289980e+00
   1_bss:  0.4751 0.4804   6.294259e+00   6.281867e+00
   1_xyz:  0.3992 0.4479   6.184806e+00   6.242893e+00
   1_adp:  0.3699 0.4528   6.155803e+00   6.250443e+00
   1_occ:  0.3694 0.4541   6.156259e+00   6.251285e+00
   2_bss:  0.3688 0.4523   6.159825e+00   6.252529e+00
   2_xyz:  0.3232 0.4118   6.064188e+00   6.193546e+00
   2_adp:  0.3117 0.4020   6.046679e+00   6.180264e+00
   2_occ:  0.3116 0.4021   6.046253e+00   6.180212e+00
   3_bss:  0.3119 0.4023   6.046205e+00   6.179928e+00
   3_xyz:  0.2571 0.3394   5.882982e+00   6.058537e+00
   3_adp:  0.2328 0.3226   5.822561e+00   6.022905e+00
   3_occ:  0.2326 0.3223   5.821890e+00   6.022006e+00
   4_bss:  0.2328 0.3214   5.820197e+00   6.020405e+00
   4_xyz:  0.1903 0.2549   5.619526e+00   5.841918e+00
   4_adp:  0.1719 0.2301   5.525033e+00   5.746512e+00
   4_occ:  0.1717 0.2299   5.523946e+00   5.745288e+00
   5_bss:  0.1716 0.2300   5.522115e+00   5.743901e+00
   5_xyz:  0.1428 0.1980   5.362438e+00   5.600102e+00
   5_adp:  0.1364 0.1862   5.314318e+00   5.544816e+00
   5_occ:  0.1364 0.1861   5.313862e+00   5.544427e+00
   5_bss:  0.1369 0.1861   5.314204e+00   5.543766e+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:  0.326  26.390  -3.380   1.213   3.549   0.000   0.000   0.000
   1_xyz:  0.326  26.390  -3.380   1.213   3.549   0.000   0.000   0.000
   1_adp:  0.326  26.390  -3.380   1.213   3.549   0.000   0.000   0.000
   1_occ:  0.326  26.390  -3.380   1.213   3.549   0.000   0.000   0.000
   2_bss:  0.337  67.610  -0.908   0.538   2.213   0.000   0.000   0.000
   2_xyz:  0.337  67.610  -0.908   0.538   2.213   0.000   0.000   0.000
   2_adp:  0.337  67.610  -0.908   0.538   2.213   0.000   0.000   0.000
   2_occ:  0.337  67.610  -0.908   0.538   2.213   0.000   0.000   0.000
   3_bss:  0.337  67.610  -0.359   0.651   2.308   0.000   0.000   0.000
   3_xyz:  0.337  67.610  -0.359   0.651   2.308   0.000   0.000   0.000
   3_adp:  0.337  67.610  -0.359   0.651   2.308   0.000   0.000   0.000
   3_occ:  0.337  67.610  -0.359   0.651   2.308   0.000   0.000   0.000
   4_bss:  0.334  67.610  -0.780  -0.295   1.557  -0.000   0.000   0.000
   4_xyz:  0.334  67.610  -0.780  -0.295   1.557  -0.000   0.000   0.000
   4_adp:  0.334  67.610  -0.780  -0.295   1.557  -0.000   0.000   0.000
   4_occ:  0.334  67.610  -0.780  -0.295   1.557  -0.000   0.000   0.000
   5_bss:  0.334  67.610  -1.145  -1.060   1.179  -0.000   0.000   0.000
   5_xyz:  0.334  67.610  -1.145  -1.060   1.179  -0.000   0.000   0.000
   5_adp:  0.334  67.610  -1.145  -1.060   1.179  -0.000   0.000   0.000
   5_occ:  0.334  67.610  -1.145  -1.060   1.179  -0.000   0.000   0.000
   5_bss:  0.319  57.179  -1.457  -1.478   0.878  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.353 0.3765  0.5241    80953.463
   1_bss:  60.136 0.3913  0.5569    78895.324
   1_xyz:  53.860 0.4707  0.6564    63794.370
   1_adp:  54.648 0.4602  0.6423    65597.281
   1_occ:  54.806 0.4582  0.6389    65933.929
   2_bss:  54.850 0.4576  0.6442    66150.438
   2_xyz:  47.235 0.5527  0.7690    50474.122
   2_adp:  45.559 0.5740  0.7837    48309.331
   2_occ:  45.550 0.5741  0.7837    48284.191
   3_bss:  45.528 0.5742  0.7899    48144.463
   3_xyz:  36.370 0.6844  0.9196    32058.059
   3_adp:  34.026 0.7119  0.9220    28801.631
   3_occ:  33.997 0.7122  0.9222    28736.336
   4_bss:  33.887 0.7133  0.9010    28517.103
   4_xyz:  26.188 0.7977  0.9702    17453.601
   4_adp:  22.900 0.8327  0.9808    14107.461
   4_occ:  22.862 0.8330  0.9809    14067.026
   5_bss:  22.787 0.8336  0.9636    13976.481
   5_xyz:  18.953 0.8711  0.9838    10194.738
   5_adp:  17.496 0.8851  0.9841     9202.487
   5_occ:  17.487 0.8852  0.9840     9185.745
   5_bss:  17.468 0.8853  0.9723     9159.494
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   2.0121e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   2.0121e-01
   1_xyz:   1.684  0.012  0.118 16.560  0.007  4.102   1.6123e-01
   1_adp:   1.684  0.012  0.118 16.560  0.007  4.102   1.6123e-01
   1_occ:   1.684  0.012  0.118 16.560  0.007  4.102   1.6123e-01
   2_bss:   1.684  0.012  0.118 16.560  0.007  4.102   1.6123e-01
   2_xyz:   1.268  0.008  0.091 15.679  0.005  4.107   9.0277e-02
   2_adp:   1.268  0.008  0.091 15.679  0.005  4.107   9.0277e-02
   2_occ:   1.268  0.008  0.091 15.679  0.005  4.107   9.0277e-02
   3_bss:   1.268  0.008  0.091 15.679  0.005  4.107   9.0277e-02
   3_xyz:   1.223  0.010  0.085 15.399  0.005  4.108   8.9457e-02
   3_adp:   1.223  0.010  0.085 15.399  0.005  4.108   8.9457e-02
   3_occ:   1.223  0.010  0.085 15.399  0.005  4.108   8.9457e-02
   4_bss:   1.223  0.010  0.085 15.399  0.005  4.108   8.9457e-02
   4_xyz:   1.072  0.007  0.077 14.912  0.004  4.122   6.6369e-02
   4_adp:   1.072  0.007  0.077 14.912  0.004  4.122   6.6369e-02
   4_occ:   1.072  0.007  0.077 14.912  0.004  4.122   6.6369e-02
   5_bss:   1.072  0.007  0.077 14.912  0.004  4.122   6.6369e-02
   5_xyz:   1.057  0.008  0.073 14.871  0.004  4.112   6.8747e-02
   5_adp:   1.057  0.008  0.073 14.871  0.004  4.112   6.8747e-02
   5_occ:   1.057  0.008  0.073 14.871  0.004  4.112   6.8747e-02
   5_bss:   1.057  0.008  0.073 14.871  0.004  4.112   6.8747e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.219   2.4210e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.219   2.4210e-01
   1_xyz:   9.156  0.073  0.444 78.516  0.054  1.913   1.0966e-01
   1_adp:   9.156  0.073  0.444 78.516  0.054  1.913   1.0966e-01
   1_occ:   9.156  0.073  0.444 78.516  0.054  1.913   1.0966e-01
   2_bss:   9.156  0.073  0.444 78.516  0.054  1.913   1.0966e-01
   2_xyz:   9.540  0.054  0.338 78.430  0.039  2.111   7.0630e-02
   2_adp:   9.540  0.054  0.338 78.430  0.039  2.111   7.0630e-02
   2_occ:   9.540  0.054  0.338 78.430  0.039  2.111   7.0630e-02
   3_bss:   9.540  0.054  0.338 78.430  0.039  2.111   7.0630e-02
   3_xyz:   8.522  0.059  0.308 81.596  0.027  2.118   8.0891e-02
   3_adp:   8.522  0.059  0.308 81.596  0.027  2.118   8.0891e-02
   3_occ:   8.522  0.059  0.308 81.596  0.027  2.118   8.0891e-02
   4_bss:   8.522  0.059  0.308 81.596  0.027  2.118   8.0891e-02
   4_xyz:   7.125  0.040  0.247 86.990  0.033  2.316   6.0981e-02
   4_adp:   7.125  0.040  0.247 86.990  0.033  2.316   6.0981e-02
   4_occ:   7.125  0.040  0.247 86.990  0.033  2.316   6.0981e-02
   5_bss:   7.125  0.040  0.247 86.990  0.033  2.316   6.0981e-02
   5_xyz:   6.118  0.048  0.233 85.475  0.034  2.307   1.0808e-01
   5_adp:   6.118  0.048  0.233 85.475  0.034  2.307   1.0808e-01
   5_occ:   6.118  0.048  0.233 85.475  0.034  2.307   1.0808e-01
   5_bss:   6.118  0.048  0.233 85.475  0.034  2.307   1.0808e-01
------------------------------------------------------------------------
           |-----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:  97.31   0.00  18.42  75.37   0.00  15.76  97.31   0.00  32.88
   1_occ:  97.31   0.00  18.42  75.37   0.00  15.76  97.31   0.00  32.88
   2_bss:  97.31   0.00  18.42  75.37   0.00  15.76  97.31   0.00  32.88
   2_xyz:  97.31   0.00  18.42  75.37   0.00  15.76  97.31   0.00  32.88
   2_adp:  96.42   0.00  18.02  71.10   0.00  15.22  96.42   0.00  33.28
   2_occ:  96.42   0.00  18.02  71.10   0.00  15.22  96.42   0.00  33.28
   3_bss:  96.42   0.00  18.02  71.10   0.00  15.22  96.42   0.00  33.28
   3_xyz:  96.42   0.00  18.02  71.10   0.00  15.22  96.42   0.00  33.28
   3_adp:  98.92   0.00  18.62  91.81   0.00  14.12  98.92   0.00  43.12
   3_occ:  98.92   0.00  18.62  91.81   0.00  14.12  98.92   0.00  43.12
   4_bss:  98.92   0.00  18.62  91.81   0.00  14.12  98.92   0.00  43.12
   4_xyz:  98.92   0.00  18.62  91.81   0.00  14.12  98.92   0.00  43.12
   4_adp: 106.08   0.00  17.85  95.47   0.00  12.68 106.08   3.13  45.96
   4_occ: 106.08   0.00  17.85  95.47   0.00  12.68 106.08   3.13  45.96
   5_bss: 106.08   0.00  17.85  95.47   0.00  12.68 106.08   3.13  45.96
   5_xyz: 106.08   0.00  17.85  95.47   0.00  12.68 106.08   3.13  45.96
   5_adp: 103.81   0.00  16.90  94.36   0.00  11.93 103.81   4.80  43.94
   5_occ: 103.81   0.00  16.90  94.36   0.00  11.93 103.81   4.80  43.94
   5_bss: 103.81   0.00  16.90  94.37   0.00  11.93 103.81   4.81  43.95
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.945    0.028    0.401
   1_adp:    2.945    0.028    0.401
   1_occ:    2.945    0.028    0.401
   2_bss:    2.945    0.028    0.401
   2_xyz:    2.271    0.014    0.527
   2_adp:    2.271    0.014    0.527
   2_occ:    2.271    0.014    0.527
   3_bss:    2.271    0.014    0.527
   3_xyz:    2.096    0.034    0.728
   3_adp:    2.096    0.034    0.728
   3_occ:    2.096    0.034    0.728
   4_bss:    2.096    0.034    0.728
   4_xyz:    1.973    0.087    0.847
   4_adp:    1.973    0.087    0.847
   4_occ:    1.973    0.087    0.847
   5_bss:    1.973    0.087    0.847
   5_xyz:    1.819    0.086    0.904
   5_adp:    1.819    0.086    0.904
   5_occ:    1.819    0.086    0.904
   5_bss:    1.819    0.086    0.904
------------------------------------------------------------------------

CPU time actual refinement: 325.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_494/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_494/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_494/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_494/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_494/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.24 
  Macro-tasks:
    bulk solvent and scale       = 37.66  
    individual site refinement   = 135.07 
    weights calculation          = 31.32  
    collect and process          = 6.49   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 210.64 
  Micro-tasks:
    mask                            = 3.07   
    f_calc                          = 102.00 
    alpha_beta                      = 8.45   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 110.21 
    fmodel                         = 6.46   
    r_factors                      = 0.20   
    phase_errors                   = 9.68   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 241.44 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.707 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    606 calls, 101.76 s
gradients_fft:          551 calls,  97.75 s

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

# Date 2008-01-16 Time 04:57:35 PST -0800 (1200488255.20 s)
Start R-work = 0.4859, R-free = 0.4891 (no bulk solvent and anisotropic scale)
Final R-work = 0.1546, R-free = 0.2020 (no bulk solvent and anisotropic scale)

Start R-work = 0.4751, R-free = 0.4804
Final R-work = 0.1369, R-free = 0.1861