# Date 2008-01-16 Time 06:10:03 PST -0800 (1200492603.60 s)
#phil __OFF__

Command line arguments: "../1028.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1914
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1028

-------------------------------------------------------------------------------
  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: (71.3037, 46.93, 86.39, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00038
Completeness in resolution range: 0.971869
Completeness with d_max=infinity: 0.968889

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   2.0004

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: (71.3037, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00038
Completeness in resolution range: 0.971869
Completeness with d_max=infinity: 0.968889

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2804 [2111/2136]  1901   210   9.9%
  bin  2:  4.2804 -  3.4102 [2037/2057]  1832   205  10.1%
  bin  3:  3.4102 -  2.9828 [2006/2025]  1803   203  10.1%
  bin  4:  2.9828 -  2.7118 [1988/2018]  1796   192   9.7%
  bin  5:  2.7118 -  2.5184 [1983/2002]  1786   197   9.9%
  bin  6:  2.5184 -  2.3705 [1964/1989]  1764   200  10.2%
  bin  7:  2.3705 -  2.2522 [1947/1975]  1747   200  10.3%
  bin  8:  2.2522 -  2.1544 [1959/1995]  1765   194   9.9%
  bin  9:  2.1544 -  2.0717 [1952/1994]  1762   190   9.7%
  bin 10:  2.0717 -  2.0004 [1642/1965]  1474   168  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1028/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2185
        3.04 -     3.66: 4603
        3.66 -     4.28: 9008
        4.28 -     4.90: 12263
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.948 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.304 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.318 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28063 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_1028/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1028/model_refine_001.geo

CPU time processing inputs: 8.77


============================ 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 = 71.30375 46.93 86.39 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: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2547   r_free= 0.2540   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| 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:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.851189                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7741 0.99   1380  154 0.2629 0.2429      6.2806      6.1959|
|  2:  4.7741 -  3.8092 0.99   1324  145 0.1966 0.1917      6.2195      6.1833|
|  3:  3.8092 -  3.3335 0.99   1289  143 0.2119 0.2081      6.0928      6.1772|
|  4:  3.3335 -  3.0314 0.99   1283  147 0.2197 0.2259      6.0021      5.9984|
|  5:  3.0314 -  2.8156 0.99   1291  140 0.2556 0.2707      5.9112      6.0506|
|  6:  2.8156 -  2.6505 0.99   1274  142 0.2514 0.2650      5.8444      5.7975|
|  7:  2.6505 -  2.5184 0.99   1277  136 0.2704 0.2610      5.8311      5.8725|
|  8:  2.5184 -  2.4092 0.98   1254  147 0.2731 0.2567      5.7844      5.7274|
|  9:  2.4092 -  2.3168 0.98   1256  137 0.2679 0.2719      5.7137      5.7365|
| 10:  2.3168 -  2.2371 1.00   1269  141 0.2726 0.2806      5.7119      5.7544|
| 11:  2.2371 -  2.1674 0.97   1248  137 0.2907 0.3031      5.7074      5.7947|
| 12:  2.1674 -  2.1056 0.98   1242  142 0.2905 0.2691      5.6371      5.6638|
| 13:  2.1056 -  2.0503 1.00   1258  136 0.2938 0.3170      5.5682      5.5328|
| 14:  2.0503 -  2.0004 0.77    985  112 0.2708 0.2685      5.4514      5.3734|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7741  1380   154  0.82  23.51   0.87     0.83      34941.57|
|  2:  4.7741 -  3.8092  1324   145  0.89  17.42   0.99     0.93      30439.80|
|  3:  3.8092 -  3.3335  1289   143  0.86  19.94   1.01     0.97      27530.13|
|  4:  3.3335 -  3.0314  1283   147  0.85  21.79   1.01     0.97      24475.65|
|  5:  3.0314 -  2.8156  1291   140  0.79  27.20   1.01     0.95      21995.72|
|  6:  2.8156 -  2.6505  1274   142  0.80  26.34   1.03     0.94      18580.33|
|  7:  2.6505 -  2.5184  1277   136  0.80  26.36   1.02     0.96      16672.50|
|  8:  2.5184 -  2.4092  1254   147  0.81  26.36   1.04     0.98      14902.33|
|  9:  2.4092 -  2.3168  1256   137  0.80  26.67   1.05     0.99      14379.67|
| 10:  2.3168 -  2.2371  1269   141  0.78  28.73   1.08     0.99      14313.56|
| 11:  2.2371 -  2.1674  1248   137  0.77  30.02   1.09     0.98      14246.22|
| 12:  2.1674 -  2.1056  1242   142  0.78  29.02   1.06     1.01      12825.32|
| 13:  2.1056 -  2.0503  1258   136  0.78  28.52   1.07     1.02      10165.47|
| 14:  2.0503 -  2.0004   985   112  0.83  24.59   1.07     1.01       6938.08|
|alpha:            min =        0.83 max =            1.02 mean =         0.96|
|beta:             min =     6938.08 max =        34941.57 mean =     19115.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.81|
|phase err.(work): min =        0.00 max =           89.96 mean =        25.42|
|phase err.(test): min =        0.00 max =           89.74 mean =        25.20|
|-----------------------------------------------------------------------------|

============================== 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 = 2.350177              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.331   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.433855              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.481   (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 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      180 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2005 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1821 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2782 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4645 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4363 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5577 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6686 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.139 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    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: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2547   r_free= 0.2540   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| 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:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.851189                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2370   r_free= 0.2378   ksol= 0.32   Bsol= 54.14   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.20,-2.99,-1.78,-0.00,-0.00,-0.00); trace/3= -1.53                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.817007                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.157316              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.658   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.237005              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.217   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2370      final r-factor (work) = 0.1596          |
| start r-factor (free) = 0.2378      final r-factor (free) = 0.1778          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4635 = 2.16 * 0.50 * 5.8431 + 1.00 * 0.1608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0513 = 2.16 * 0.50 * 5.5587 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1596      final r-factor (work) = 0.1471          |
| start r-factor (free) = 0.1778      final r-factor (free) = 0.1815          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3237 = 0.24 * 1.00 * 5.5587 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2877 = 0.24 * 1.00 * 5.3477 + 1.00 * 0.0202                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.81   16.63    None  None   None       |
|    all(noH): 2823   0      0.00    63.81   16.63    None  None   None       |
|    Sol.    : 438    0      5.08    63.81   37.33    None  None   None       |
|    Mac.    : 2385   0      0.00    54.50   12.83    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 -   6.381:  205   |   5:    31.904 -  38.285:   94        |
|      1:     6.381 -  12.762: 1275   |   6:    38.285 -  44.666:   99        |
|      2:    12.762 -  19.142:  674   |   7:    44.666 -  51.046:   79        |
|      3:    19.142 -  25.523:  206   |   8:    51.046 -  57.427:   57        |
|      4:    25.523 -  31.904:  116   |   9:    57.427 -  63.808:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1471 r_free = 0.1815             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1467 r_free = 0.1811             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1811   ksol= 0.32   Bsol= 54.14   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.20,-2.99,-1.78,-0.00,-0.00,-0.00); trace/3= -1.53                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.353623                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1457   r_free= 0.1795   ksol= 0.33   Bsol= 58.66   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-3.00,-1.84,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.348502                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.692914              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.856  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.173369              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.971   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1457      final r-factor (work) = 0.1231          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5836 = 1.69 * 0.50 * 5.3496 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5082 = 1.69 * 0.50 * 5.2639 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1610      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9505 = 0.17 * 1.00 * 5.2639 + 1.00 * 0.0379                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9068 = 0.17 * 1.00 * 5.1889 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.57    69.72   16.73    None  None   None       |
|    all(noH): 2823   0      1.57    69.72   16.73    None  None   None       |
|    Sol.    : 438    0      6.00    67.75   37.33    None  None   None       |
|    Mac.    : 2385   0      1.57    69.72   12.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.566 -   8.382:  554   |   5:    35.644 -  42.460:  105        |
|      1:     8.382 -  15.197: 1302   |   6:    42.460 -  49.275:   92        |
|      2:    15.197 -  22.013:  406   |   7:    49.275 -  56.091:   77        |
|      3:    22.013 -  28.829:  144   |   8:    56.091 -  62.907:   29        |
|      4:    28.829 -  35.644:  110   |   9:    62.907 -  69.722:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1194 r_free = 0.1574             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1193 r_free = 0.1574             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1574   ksol= 0.33   Bsol= 58.66   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.81,-3.00,-1.84,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.176978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1570   ksol= 0.33   Bsol= 58.66   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.68,-1.56,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175607                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.734351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.333  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.334849              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.655  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5516 = 1.73 * 0.50 * 5.1881 + 1.00 * 0.0526                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5291 = 1.73 * 0.50 * 5.1544 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7331 = 0.33 * 1.00 * 5.1544 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7296 = 0.33 * 1.00 * 5.1409 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.18    75.45   16.85    None  None   None       |
|    all(noH): 2823   0      1.18    75.45   16.85    None  None   None       |
|    Sol.    : 438    0      3.78    72.12   38.42    None  None   None       |
|    Mac.    : 2385   0      1.18    75.45   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.176 -   8.603:  656   |   5:    38.311 -  45.739:  115        |
|      1:     8.603 -  16.030: 1283   |   6:    45.739 -  53.166:   87        |
|      2:    16.030 -  23.457:  359   |   7:    53.166 -  60.593:   62        |
|      3:    23.457 -  30.884:  130   |   8:    60.593 -  68.020:   23        |
|      4:    30.884 -  38.311:  104   |   9:    68.020 -  75.447:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1557             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1557             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1557   ksol= 0.33   Bsol= 58.66   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.68,-1.56,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142064                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1552   ksol= 0.33   Bsol= 58.66   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.46,-1.37,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142634                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.441514              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.806  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.247429              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.223  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3362 = 2.44 * 0.50 * 5.1418 + 1.00 * 0.0593                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3263 = 2.44 * 0.50 * 5.1273 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1081          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4040 = 1.25 * 1.00 * 5.1273 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4016 = 1.25 * 1.00 * 5.1241 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.80   17.08    None  None   None       |
|    all(noH): 2823   0      0.00    85.80   17.08    None  None   None       |
|    Sol.    : 438    0      4.96    78.58   39.92    None  None   None       |
|    Mac.    : 2385   0      0.00    85.80   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.581:  714   |   5:    42.902 -  51.483:  103        |
|      1:     8.581 -  17.161: 1320   |   6:    51.483 -  60.063:   79        |
|      2:    17.161 -  25.742:  304   |   7:    60.063 -  68.644:   41        |
|      3:    25.742 -  34.322:  130   |   8:    68.644 -  77.224:   14        |
|      4:    34.322 -  42.902:  112   |   9:    77.224 -  85.805:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1081 r_free = 0.1576             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1577             target_work(ml) = 5.128         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1577   ksol= 0.33   Bsol= 58.66   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.46,-1.37,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127692                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1576   ksol= 0.33   Bsol= 58.66   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.19,-1.13,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127655                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.544632              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.024  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.343295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.381  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0254 = 1.54 * 0.50 * 5.1252 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0229 = 1.54 * 0.50 * 5.1396 + 1.00 * 0.0535                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7741 = 0.34 * 1.00 * 5.1396 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7761 = 0.34 * 1.00 * 5.1479 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    86.05   16.71    None  None   None       |
|    all(noH): 2823   0      0.49    86.05   16.71    None  None   None       |
|    Sol.    : 438    0      6.01    78.75   38.84    None  None   None       |
|    Mac.    : 2385   0      0.49    86.05   12.64    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:     0.493 -   9.049:  882   |   5:    43.273 -  51.829:   94        |
|      1:     9.049 -  17.605: 1197   |   6:    51.829 -  60.385:   77        |
|      2:    17.605 -  26.161:  270   |   7:    60.385 -  68.941:   29        |
|      3:    26.161 -  34.717:  140   |   8:    68.941 -  77.497:   13        |
|      4:    34.717 -  43.273:  116   |   9:    77.497 -  86.052:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1584             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1584             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1584   ksol= 0.33   Bsol= 58.66   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.19,-1.13,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146194                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7741 0.99   1380  154 0.0998 0.1284      5.3939      5.5211|
|  2:  4.7741 -  3.8092 0.99   1324  145 0.0865 0.1092      5.4439      5.6183|
|  3:  3.8092 -  3.3335 0.99   1289  143 0.1031 0.1500       5.468      5.8587|
|  4:  3.3335 -  3.0314 0.99   1283  147 0.1198 0.1575      5.4583      5.6008|
|  5:  3.0314 -  2.8156 0.99   1291  140 0.1341 0.1765      5.3393       5.574|
|  6:  2.8156 -  2.6505 0.99   1274  142 0.1186 0.1854      5.2136      5.4424|
|  7:  2.6505 -  2.5184 0.99   1277  136 0.1267 0.1587      5.1754      5.3683|
|  8:  2.5184 -  2.4092 0.98   1254  147 0.1149 0.1779      5.0558      5.3622|
|  9:  2.4092 -  2.3168 0.98   1256  137 0.1166 0.1663      5.0396      5.2608|
| 10:  2.3168 -  2.2371 1.00   1269  141 0.1105 0.1822      4.9604      5.2873|
| 11:  2.2371 -  2.1674 0.97   1248  137 0.1139 0.1730      4.9592      5.2487|
| 12:  2.1674 -  2.1056 0.98   1242  142 0.1121 0.1730      4.8899       5.212|
| 13:  2.1056 -  2.0503 1.00   1258  136 0.1131 0.1736      4.8054      5.0951|
| 14:  2.0503 -  2.0004 0.77    985  112 0.1080 0.1734      4.6789      4.9291|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7741  1380   154  0.94   9.31   0.97     0.94       7267.37|
|  2:  4.7741 -  3.8092  1324   145  0.95   7.90   1.00     0.99       9015.59|
|  3:  3.8092 -  3.3335  1289   143  0.94  11.02   1.02     1.01      10314.77|
|  4:  3.3335 -  3.0314  1283   147  0.92  13.48   1.00     0.98      10360.44|
|  5:  3.0314 -  2.8156  1291   140  0.90  16.26   0.99     0.96       8593.83|
|  6:  2.8156 -  2.6505  1274   142  0.90  15.62   0.98     0.96       7190.33|
|  7:  2.6505 -  2.5184  1277   136  0.91  15.61   0.98     0.96       6276.51|
|  8:  2.5184 -  2.4092  1254   147  0.91  14.89   0.99     0.97       5154.31|
|  9:  2.4092 -  2.3168  1256   137  0.91  15.04   0.99     0.96       4985.75|
| 10:  2.3168 -  2.2371  1269   141  0.91  15.21   0.99     0.94       4321.03|
| 11:  2.2371 -  2.1674  1248   137  0.89  16.82   0.98     0.95       4568.42|
| 12:  2.1674 -  2.1056  1242   142  0.92  14.84   0.99     0.97       3999.52|
| 13:  2.1056 -  2.0503  1258   136  0.90  15.95   0.98     0.97       3460.43|
| 14:  2.0503 -  2.0004   985   112  0.91  14.79   0.96     0.92       2588.47|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2588.47 max =        10360.44 mean =      6387.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.98|
|phase err.(test): min =        0.00 max =           88.14 mean =        13.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1584   ksol= 0.32   Bsol= 54.34   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-2.00,-0.94,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1584   ksol= 0.32   Bsol= 54.34   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-2.00,-0.94,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.146400                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7741 0.99   1380  154 0.0996 0.1282      5.3917      5.5193|
|  2:  4.7741 -  3.8092 0.99   1324  145 0.0862 0.1088      5.4415       5.616|
|  3:  3.8092 -  3.3335 0.99   1289  143 0.1030 0.1501      5.4671      5.8589|
|  4:  3.3335 -  3.0314 0.99   1283  147 0.1199 0.1575      5.4594      5.6017|
|  5:  3.0314 -  2.8156 0.99   1291  140 0.1343 0.1769      5.3409      5.5756|
|  6:  2.8156 -  2.6505 0.99   1274  142 0.1188 0.1857      5.2151      5.4439|
|  7:  2.6505 -  2.5184 0.99   1277  136 0.1268 0.1588      5.1765      5.3692|
|  8:  2.5184 -  2.4092 0.98   1254  147 0.1149 0.1782      5.0564      5.3631|
|  9:  2.4092 -  2.3168 0.98   1256  137 0.1167 0.1661        5.04      5.2604|
| 10:  2.3168 -  2.2371 1.00   1269  141 0.1106 0.1823       4.961      5.2878|
| 11:  2.2371 -  2.1674 0.97   1248  137 0.1140 0.1732      4.9598      5.2491|
| 12:  2.1674 -  2.1056 0.98   1242  142 0.1121 0.1732      4.8903      5.2129|
| 13:  2.1056 -  2.0503 1.00   1258  136 0.1132 0.1738      4.8057      5.0955|
| 14:  2.0503 -  2.0004 0.77    985  112 0.1080 0.1736      4.6793      4.9297|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1573 -  4.7741  1380   154  0.94   9.27   0.97     0.94       7224.16|
|  2:  4.7741 -  3.8092  1324   145  0.95   7.88   1.01     0.99       8983.16|
|  3:  3.8092 -  3.3335  1289   143  0.94  11.01   1.02     1.01      10299.50|
|  4:  3.3335 -  3.0314  1283   147  0.92  13.50   1.01     0.98      10375.91|
|  5:  3.0314 -  2.8156  1291   140  0.90  16.28   0.99     0.97       8615.53|
|  6:  2.8156 -  2.6505  1274   142  0.90  15.65   0.99     0.97       7213.96|
|  7:  2.6505 -  2.5184  1277   136  0.91  15.63   0.99     0.96       6291.61|
|  8:  2.5184 -  2.4092  1254   147  0.91  14.90   0.99     0.97       5161.65|
|  9:  2.4092 -  2.3168  1256   137  0.91  15.04   1.00     0.96       4987.30|
| 10:  2.3168 -  2.2371  1269   141  0.91  15.22   0.99     0.95       4324.41|
| 11:  2.2371 -  2.1674  1248   137  0.89  16.83   0.99     0.95       4573.89|
| 12:  2.1674 -  2.1056  1242   142  0.92  14.85   1.00     0.98       4004.81|
| 13:  2.1056 -  2.0503  1258   136  0.90  15.96   0.99     0.98       3464.20|
| 14:  2.0503 -  2.0004   985   112  0.91  14.80   0.97     0.93       2591.24|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2591.24 max =        10375.91 mean =      6387.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.99|
|phase err.(test): min =        0.00 max =           88.28 mean =        13.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.106)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    86.04   16.69    None  None   None       |
|    all(noH): 2823   0      0.48    86.04   16.69    None  None   None       |
|    Sol.    : 438    0      6.00    78.74   38.82    None  None   None       |
|    Mac.    : 2385   0      0.48    86.04   12.63    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:     0.477 -   9.033:  882   |   5:    43.257 -  51.813:   94        |
|      1:     9.033 -  17.589: 1197   |   6:    51.813 -  60.369:   77        |
|      2:    17.589 -  26.145:  270   |   7:    60.369 -  68.925:   29        |
|      3:    26.145 -  34.701:  140   |   8:    68.925 -  77.481:   13        |
|      4:    34.701 -  43.257:  116   |   9:    77.481 -  86.037:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.579 - 4.658
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 294
   mapped sites are within: 0.711 - 4.658

peak=    5.672 closest distance to " CG  PRO A  54 " =    1.333
peak=    5.661 closest distance to " CB  GLN A 223 " =    1.448
peak=    5.636 closest distance to " O   HOH Z 111 " =    2.249
peak=    5.093 closest distance to " O   HOH Z 232 " =    2.261
peak=    5.088 closest distance to " O   HOH Z 126 " =    1.899
peak=    5.027 closest distance to " CG  PRO A 213 " =    1.231
peak=    4.963 closest distance to " CB  SER A  63 " =    1.256
peak=    4.932 closest distance to " CB  PRO A  54 " =    0.962
peak=    4.861 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.785 closest distance to " CG  PRO A  90 " =    1.108
peak=    4.669 closest distance to " C   PRO A 198 " =    1.536
peak=    4.636 closest distance to " CG  PRO A 198 " =    1.268
peak=    4.625 closest distance to " O   HOH Z  78 " =    1.708
peak=    4.590 closest distance to " CB  LEU A 228 " =    1.085
peak=    4.584 closest distance to " O   HOH Z  15 " =    2.213
peak=    4.564 closest distance to " O   HOH Z 298 " =    1.967
peak=    4.545 closest distance to " CB  GLN A 183 " =    1.215
peak=    4.494 closest distance to " NE2 GLN A  11 " =    1.079
peak=    4.477 closest distance to " O   HOH Z 369 " =    2.107
peak=    4.473 closest distance to " CB  ASN A 187 " =    1.448
peak=    4.460 closest distance to " CA  TYR A  30 " =    0.941
peak=    4.450 closest distance to " CB  GLU A 128 " =    1.048
peak=    4.375 closest distance to " CB  ASN A 148 " =    1.371
peak=    4.344 closest distance to " CB  TYR A 169 " =    0.724
peak=    4.336 closest distance to " CG  PRO A 243 " =    1.072
peak=    4.303 closest distance to " O   HOH Z 236 " =    2.154
peak=    4.257 closest distance to " CZ  PHE A 218 " =    1.047
peak=    4.209 closest distance to " CB  ARG A 190 " =    1.598
peak=    4.195 closest distance to " CG2 VAL A 257 " =    0.958
peak=    4.189 closest distance to " OD1 ASN A  69 " =    2.542
peak=    4.189 closest distance to " CD1 LEU A 300 " =    1.214
peak=    4.183 closest distance to " O   HOH Z 261 " =    2.020
peak=    4.154 closest distance to " ND2 ASN A 187 " =    1.442
peak=    4.136 closest distance to " O   HOH Z 250 " =    1.511
peak=    4.114 closest distance to " O   HOH Z 142 " =    1.678
peak=    4.112 closest distance to " CB  ARG A  79 " =    1.346
peak=    4.099 closest distance to " O   HOH Z 234 " =    3.817
peak=    4.060 closest distance to " CB  GLU A 152 " =    1.192
peak=    4.041 closest distance to " O   HOH Z 189 " =    2.553
peak=    4.033 closest distance to " CB  TRP A 266 " =    0.954
peak=    4.032 closest distance to " CB  ASP A 124 " =    0.760
peak=    3.985 closest distance to " O   HOH Z 427 " =    3.084
peak=    3.982 closest distance to " CA  THR A 264 " =    0.863
peak=    3.976 closest distance to " O   HOH Z 209 " =    2.287
peak=    3.976 closest distance to " O   HOH Z 316 " =    3.159
peak=    3.966 closest distance to " NH2 ARG A 156 " =    1.207
peak=    3.960 closest distance to " CA  ASP A 124 " =    0.711
peak=    3.949 closest distance to " NH1AARG A 145 " =    1.211
peak=    3.946 closest distance to " O   HOH Z 158 " =    3.031
peak=    3.928 closest distance to " CD BLYS A 290 " =    1.016
peak=    3.908 closest distance to " O   HOH Z 303 " =    2.137
peak=    3.904 closest distance to " CB  VAL A 265 " =    1.257
peak=    3.900 closest distance to " CD  ARG A 159 " =    0.782
peak=    3.885 closest distance to " O   HOH Z 368 " =    1.982
peak=    3.884 closest distance to " CB  SER A   3 " =    1.322
peak=    3.878 closest distance to " O   HOH Z 214 " =    2.031
peak=    3.858 closest distance to " O   HOH Z 346 " =    1.660
peak=    3.856 closest distance to " O   HOH Z  61 " =    1.625
peak=    3.854 closest distance to " CG1 ILE A  33 " =    1.298
peak=    3.851 closest distance to " CB  ASP A 140 " =    0.925
peak=    3.841 closest distance to " CD  ARG A 269 " =    0.927
peak=    3.836 closest distance to " ND2 ASN A 249 " =    1.957
peak=    3.834 closest distance to " O   HOH Z  54 " =    2.345
peak=    3.816 closest distance to " CB  VAL A 202 " =    1.609
peak=    3.815 closest distance to " ND1 HIS A  86 " =    1.729
peak=    3.807 closest distance to " CE  LYS A  76 " =    0.837
peak=    3.807 closest distance to " CB  LEU A 143 " =    1.123
peak=    3.805 closest distance to " O   HOH Z  40 " =    1.739
peak=    3.804 closest distance to " CA  ASN A 215 " =    1.170
peak=    3.803 closest distance to " CA  TYR A  30 " =    1.063
peak=    3.791 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.784 closest distance to " O   HOH Z 193 " =    1.739
peak=    3.771 closest distance to " O   HOH Z 203 " =    1.848
peak=    3.770 closest distance to " O   HOH Z 180 " =    2.146
peak=    3.768 closest distance to " CG2 THR A 221 " =    1.040
peak=    3.765 closest distance to " NZ  LYS A 117 " =    3.253
peak=    3.761 closest distance to " CB  GLU A 277 " =    3.677
peak=    3.758 closest distance to " CB  SER A 212 " =    1.152
peak=    3.747 closest distance to " CD  ARG A  66 " =    2.346
peak=    3.746 closest distance to " CB  SER A 216 " =    0.819
peak=    3.746 closest distance to " O   HOH Z 272 " =    1.875
peak=    3.741 closest distance to " O   HOH Z   1 " =    2.008
peak=    3.733 closest distance to " O   HOH Z 133 " =    2.405
peak=    3.721 closest distance to " O   HOH Z  66 " =    2.179
peak=    3.720 closest distance to " CA  ALA A  51 " =    0.888
peak=    3.706 closest distance to " O   HOH Z 426 " =    1.656
peak=    3.703 closest distance to " O   HOH Z 193 " =    1.965
peak=    3.702 closest distance to " N   ARG A 156 " =    1.365
peak=    3.701 closest distance to " O   HOH Z 135 " =    1.677
peak=    3.694 closest distance to " CA  ARG A 195 " =    1.189
peak=    3.689 closest distance to " CB  MET A  47 " =    1.024
peak=    3.680 closest distance to " OD2 ASP A 286 " =    2.886
peak=    3.676 closest distance to " O   MET A 105 " =    1.857
peak=    3.675 closest distance to " CG  LEU A 167 " =    1.227
peak=    3.661 closest distance to " O   HOH Z 344 " =    3.215
peak=    3.659 closest distance to " CB  MET A  40 " =    0.806
peak=    3.654 closest distance to " N   ASN A 127 " =    1.256
peak=    3.636 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.630 closest distance to " CB  TRP A 179 " =    1.431
peak=    3.629 closest distance to " O   THR A 251 " =    1.200
peak=    3.627 closest distance to " O   HOH Z 305 " =    3.653
peak=    3.611 closest distance to " CG2 ILE A 120 " =    1.111
peak=    3.603 closest distance to " O   HOH Z 197 " =    3.173
peak=    3.602 closest distance to " O   HOH Z 132 " =    2.621
peak=    3.595 closest distance to " CG1 VAL A 153 " =    0.884
peak=    3.591 closest distance to " CA  MET A  40 " =    1.135
peak=    3.587 closest distance to " CA  ARG A  36 " =    1.142
peak=    3.587 closest distance to " CA  THR A 221 " =    0.972
peak=    3.583 closest distance to " CD  LYS A 166 " =    1.255
peak=    3.582 closest distance to " O   HOH Z 133 " =    1.672
peak=    3.581 closest distance to " CB  GLU A  46 " =    0.979
peak=    3.578 closest distance to " CB  ASN A 142 " =    1.007
peak=    3.576 closest distance to " O   SER A  87 " =    2.317
peak=    3.576 closest distance to " O   HOH Z 411 " =    3.772
peak=    3.574 closest distance to " CA  SER A  87 " =    1.042
peak=    3.569 closest distance to " O   HOH Z  10 " =    1.855
peak=    3.567 closest distance to " CB  ALA A 291 " =    1.340
peak=    3.565 closest distance to " CZ  PHE A 192 " =    0.896
peak=    3.564 closest distance to " O   HOH Z  88 " =    3.556
peak=    3.561 closest distance to " CB  ILE A 120 " =    1.194
peak=    3.557 closest distance to " CD  ARG A 219 " =    1.058
peak=    3.547 closest distance to " O   HOH Z 213 " =    1.949
peak=    3.541 closest distance to " CB  HIS A 108 " =    0.812
peak=    3.538 closest distance to " CA  ALA A  21 " =    1.182
peak=    3.537 closest distance to " CD2 LEU A 255 " =    1.641
peak=    3.534 closest distance to " ND2 ASN A 110 " =    1.712
peak=    3.532 closest distance to " O   HOH Z  21 " =    1.753
peak=    3.524 closest distance to " O   HOH Z 172 " =    3.463
peak=    3.518 closest distance to " CD1 LEU A  96 " =    0.758
peak=    3.515 closest distance to " O   HOH Z 126 " =    2.142
peak=    3.510 closest distance to " CB  TYR A 116 " =    0.827
peak=    3.510 closest distance to " O   HOH Z 403 " =    1.704
peak=    3.508 closest distance to " CD2 TRP A 179 " =    1.311
peak=    3.502 closest distance to " N   VAL A 126 " =    1.390
peak=    3.500 closest distance to " O   HOH Z 291 " =    1.587
peak=    3.498 closest distance to " O   HOH Z 219 " =    1.971
peak=    3.498 closest distance to " CD1 ILE A 106 " =    0.796
peak=    3.495 closest distance to " O   HOH Z 128 " =    2.129
peak=    3.494 closest distance to " CB  ALA A  34 " =    1.014
peak=    3.489 closest distance to " O   HOH Z  43 " =    1.847
peak=    3.483 closest distance to " N   ASN A  39 " =    1.338
peak=    3.482 closest distance to " O   TYR A 116 " =    1.271
peak=    3.480 closest distance to " O   HOH Z 425 " =    2.092
peak=    3.477 closest distance to " O   HOH Z 280 " =    3.051
peak=    3.468 closest distance to " CG1BVAL A  72 " =    1.643
peak=    3.456 closest distance to " O  BHOH Z 338 " =    2.357
peak=    3.451 closest distance to " CA  MET A 105 " =    0.996
peak=    3.447 closest distance to " CD2 LEU A 297 " =    0.876
peak=    3.447 closest distance to " CA  ALA A 154 " =    0.981
peak=    3.440 closest distance to " O   HOH Z 313 " =    1.888
peak=    3.438 closest distance to " O   HOH Z 108 " =    2.642
peak=    3.421 closest distance to " O   HOH Z 147 " =    1.766
peak=    3.416 closest distance to " CB  ALA A 242 " =    0.869
peak=    3.416 closest distance to " O   HOH Z 245 " =    1.274
peak=    3.416 closest distance to " NH2BARG A 145 " =    2.134
peak=    3.412 closest distance to " O   HOH Z 128 " =    2.324
peak=    3.408 closest distance to " O   HOH Z 273 " =    2.738
peak=    3.397 closest distance to " O   HOH Z 285 " =    2.921
peak=    3.387 closest distance to " ND1 HIS A  81 " =    1.644
peak=    3.385 closest distance to " O   HOH Z  53 " =    2.547
peak=    3.382 closest distance to " O   HOH Z 371 " =    3.072
peak=    3.375 closest distance to " O   THR A 220 " =    1.277
peak=    3.371 closest distance to " O   HOH Z 403 " =    1.353
peak=    3.367 closest distance to " CB  ARG A 139 " =    0.881
peak=    3.365 closest distance to " ND2 ASN A 249 " =    0.830
peak=    3.364 closest distance to " CA  ALA A 233 " =    1.475
peak=    3.364 closest distance to " CZ  PHE A 208 " =    1.130
peak=    3.363 closest distance to " O   HOH Z 425 " =    1.271
peak=    3.363 closest distance to " CA  ASP A 191 " =    0.793
peak=    3.361 closest distance to " O   HOH Z 227 " =    1.668
peak=    3.360 closest distance to " OG  SER A  22 " =    2.778
peak=    3.336 closest distance to " O   HOH Z 402 " =    1.417
peak=    3.335 closest distance to " O   HOH Z 234 " =    1.751
peak=    3.333 closest distance to " O   HOH Z  59 " =    1.989
peak=    3.326 closest distance to " CB  ALA A 248 " =    1.038
peak=    3.326 closest distance to " CA  ALA A 158 " =    1.191
peak=    3.321 closest distance to " O   HOH Z 295 " =    1.504
peak=    3.320 closest distance to " O   HOH Z 290 " =    1.072
peak=    3.309 closest distance to " CZ  PHE A  38 " =    1.286
peak=    3.309 closest distance to " O   HOH Z 437 " =    1.297
peak=    3.307 closest distance to " O   HOH Z 419 " =    1.969
peak=    3.306 closest distance to " O   HOH Z 185 " =    1.792
peak=    3.305 closest distance to " CB  SER A 141 " =    0.966
peak=    3.305 closest distance to " CB  ALA A   1 " =    4.658
peak=    3.294 closest distance to " CG  ARG A 159 " =    0.909
peak=    3.290 closest distance to " O   ALA A 165 " =    1.478
peak=    3.290 closest distance to " CB  PHE A  16 " =    0.987
peak=    3.287 closest distance to " OD1BASN A 224 " =    2.303
peak=    3.282 closest distance to " O   HOH Z 406 " =    1.633
peak=    3.279 closest distance to " CD  LYS A 119 " =    1.200
peak=    3.278 closest distance to " O   HOH Z  20 " =    1.608
peak=    3.275 closest distance to " CZ2 TRP A 179 " =    1.726
peak=    3.275 closest distance to " O   HOH Z 271 " =    2.253
peak=    3.271 closest distance to " CA  GLY A 267 " =    1.140
peak=    3.269 closest distance to " O   HOH Z 171 " =    2.138
peak=    3.267 closest distance to " C   TYR A 214 " =    1.559
peak=    3.266 closest distance to " O   TRP A 274 " =    1.840
peak=    3.265 closest distance to " CB  LYS A 193 " =    0.965
peak=    3.263 closest distance to " O   HOH Z 409 " =    2.982
peak=    3.262 closest distance to " CG  MET A 113 " =    1.359
peak=    3.260 closest distance to " OG BSER A 164 " =    2.423
peak=    3.260 closest distance to " CB  LEU A  83 " =    0.800
peak=    3.258 closest distance to " O   HOH Z 329 " =    3.780
peak=    3.258 closest distance to " N   GLY A  98 " =    1.083
peak=    3.258 closest distance to " N   TYR A  15 " =    0.732
peak=    3.257 closest distance to " CA  ASP A 140 " =    1.242
peak=    3.256 closest distance to " NE2 HIS A 207 " =    1.321
peak=    3.255 closest distance to " CB  TYR A 169 " =    1.227
peak=    3.250 closest distance to " O   HOH Z 353 " =    2.712
peak=    3.249 closest distance to " O   HOH Z 166 " =    3.793
peak=    3.249 closest distance to " O   HOH Z 391 " =    2.883
peak=    3.248 closest distance to " CA  ALA A 291 " =    0.847
peak=    3.247 closest distance to " CB  PRO A 198 " =    1.003
peak=    3.245 closest distance to " O   HOH Z 109 " =    2.660
peak=    3.244 closest distance to " O   HOH Z 359 " =    1.381
peak=    3.243 closest distance to " O   HOH Z 345 " =    3.524
peak=    3.242 closest distance to " O   HOH Z  96 " =    1.977
peak=    3.238 closest distance to " CG  GLN A  11 " =    1.526
peak=    3.235 closest distance to " CA  ASN A 127 " =    1.074
peak=    3.233 closest distance to " O   HOH Z  66 " =    2.079
peak=    3.231 closest distance to " O   HOH Z 359 " =    3.891
peak=    3.228 closest distance to " CB  ASN A 110 " =    1.138
peak=    3.228 closest distance to " CG1 ILE A 151 " =    0.983
peak=    3.226 closest distance to " CA  ARG A 102 " =    1.147
peak=    3.224 closest distance to " CB  ALA A   9 " =    1.555
peak=    3.224 closest distance to " O   HOH Z 193 " =    1.995
peak=    3.222 closest distance to " CB  THR A 157 " =    1.102
peak=    3.222 closest distance to " CA  ASN A 217 " =    1.255
peak=    3.217 closest distance to " CB  GLN A  88 " =    1.254
peak=    3.217 closest distance to " CB  SER A 210 " =    0.818
peak=    3.214 closest distance to " OG  SER A 206 " =    1.276
peak=    3.212 closest distance to " O   HOH Z 294 " =    1.548
peak=    3.211 closest distance to " N   GLN A 278 " =    1.098
peak=    3.210 closest distance to " CB  ALA A 248 " =    1.282
peak=    3.208 closest distance to " CB  GLN A  89 " =    1.249
peak=    3.205 closest distance to " O   ALA A 158 " =    1.270
peak=    3.203 closest distance to " O   HOH Z  93 " =    2.843
peak=    3.202 closest distance to " CB  ASP A 200 " =    1.050
peak=    3.202 closest distance to " O   HOH Z  88 " =    1.878
peak=    3.201 closest distance to " O   HOH Z 383 " =    1.924
peak=    3.195 closest distance to " CG BARG A 102 " =    1.869
peak=    3.195 closest distance to " O   HOH Z  44 " =    3.171
peak=    3.194 closest distance to " O   HOH Z  88 " =    2.973
peak=    3.192 closest distance to " O   HOH Z 148 " =    3.356
peak=    3.190 closest distance to " OD1 ASP A 171 " =    1.251
peak=    3.188 closest distance to " CG2BVAL A  41 " =    0.851
peak=    3.186 closest distance to " CB  LYS A 117 " =    1.188
peak=    3.183 closest distance to " O   HOH Z 423 " =    1.731
peak=    3.183 closest distance to " N   PHE A 130 " =    1.204
peak=    3.182 closest distance to " CA  ALA A  84 " =    1.389
peak=    3.181 closest distance to " CG  MET A 185 " =    1.203
peak=    3.179 closest distance to " CA  ILE A  33 " =    1.540
peak=    3.175 closest distance to " O   HOH Z  61 " =    1.491
peak=    3.174 closest distance to " CB  SER A 273 " =    0.891
peak=    3.170 closest distance to " CA  LEU A 282 " =    1.079
peak=    3.165 closest distance to " CB  ARG A 138 " =    1.003
peak=    3.156 closest distance to " CB  ALA A 114 " =    1.042
peak=    3.155 closest distance to " CB  ASN A 215 " =    1.150
peak=    3.151 closest distance to " O   HOH Z 133 " =    3.212
peak=    3.151 closest distance to " O   HOH Z 411 " =    1.775
peak=    3.148 closest distance to " CG  MET A 185 " =    1.013
peak=    3.147 closest distance to " CB  GLU A 152 " =    1.416
peak=    3.147 closest distance to " CA  GLN A 223 " =    0.939
peak=    3.146 closest distance to " CA  ILE A 234 " =    0.945
peak=    3.142 closest distance to " CA  VAL A 125 " =    1.098
peak=    3.141 closest distance to " NE2 GLN A  58 " =    3.623
peak=    3.128 closest distance to " O   HOH Z  44 " =    1.603
peak=    3.128 closest distance to " N   ASN A 252 " =    1.399
peak=    3.127 closest distance to " CA  GLU A  46 " =    0.748
peak=    3.127 closest distance to " CB  TRP A 150 " =    1.369
peak=    3.126 closest distance to " O   HOH Z  49 " =    2.948
peak=    3.123 closest distance to " CA  ASN A 176 " =    1.861
peak=    3.122 closest distance to " CG BARG A 275 " =    1.458
peak=    3.120 closest distance to " O   HOH Z  49 " =    2.215
peak=    3.120 closest distance to " O   HOH Z  97 " =    1.965
peak=    3.109 closest distance to " OD1 ASP A 238 " =    0.984
peak=    3.107 closest distance to " NZ  LYS A  76 " =    1.509
peak=    3.106 closest distance to " O  BHOH Z  74 " =    1.303
peak=    3.104 closest distance to " CA  TYR A 116 " =    1.394
peak=    3.103 closest distance to " N   SER A 135 " =    1.355
peak=    3.100 closest distance to " CA  GLN A  88 " =    1.460
peak=    3.098 closest distance to " CG  GLN A 278 " =    1.356
peak=    3.096 closest distance to " O   HOH Z 183 " =    1.361
peak=    3.085 closest distance to " CD1AILE A 234 " =    0.970
peak=    3.080 closest distance to " CB  SER A  62 " =    1.206
peak=    3.077 closest distance to " N   ALA A 154 " =    0.970
peak=    3.073 closest distance to " NH1BARG A 145 " =    1.006
peak=    3.072 closest distance to " O   HOH Z 201 " =    3.239
peak=    3.072 closest distance to " CB  ALA A 137 " =    1.066
peak=    3.041 closest distance to " O   ASN A 209 " =    1.346

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.754 - 5.605
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.754 - 5.605

peak=   -4.495 closest distance to " CB  PRO A 243 " =    2.637
peak=   -4.364 closest distance to " CD  ARG A 156 " =    2.042
peak=   -4.351 closest distance to " O   HOH Z 266 " =    5.166
peak=   -4.283 closest distance to " CG1 VAL A 112 " =    2.614
peak=   -4.264 closest distance to " O   HOH Z 377 " =    1.904
peak=   -4.251 closest distance to " CG  GLN A 223 " =    1.993
peak=   -4.228 closest distance to " CD  ARG A  14 " =    3.364
peak=   -4.200 closest distance to " O   VAL A  67 " =    2.705
peak=   -4.106 closest distance to " O   HOH Z 231 " =    2.195
peak=   -4.102 closest distance to " CZ3 TRP A 179 " =    1.146
peak=   -4.060 closest distance to " O   ILE A 109 " =    2.573
peak=   -4.013 closest distance to " O   HOH Z 118 " =    3.359
peak=   -4.003 closest distance to " CE2 TYR A  30 " =    2.803
peak=   -3.968 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.967 closest distance to " O   HOH Z 389 " =    1.948
peak=   -3.953 closest distance to " O   HOH Z 290 " =    1.166
peak=   -3.936 closest distance to " O   HOH Z  10 " =    1.570
peak=   -3.926 closest distance to " CD  GLN A  58 " =    1.010
peak=   -3.910 closest distance to " O   HOH Z 372 " =    2.456
peak=   -3.908 closest distance to " N   ALA A  43 " =    2.601
peak=   -3.894 closest distance to " C   HIS A 108 " =    1.086
peak=   -3.892 closest distance to " CB  ALA A 291 " =    2.277
peak=   -3.867 closest distance to " O   HOH Z 126 " =    1.869
peak=   -3.794 closest distance to " O   HOH Z 198 " =    2.120
peak=   -3.792 closest distance to " OG BSER A 134 " =    1.174
peak=   -3.791 closest distance to " O   HOH Z  38 " =    1.330
peak=   -3.784 closest distance to " CG1 VAL A 112 " =    2.921
peak=   -3.783 closest distance to " NH2AARG A 275 " =    5.508
peak=   -3.781 closest distance to " O   HOH Z 435 " =    2.771
peak=   -3.778 closest distance to " O   HOH Z 313 " =    1.946
peak=   -3.765 closest distance to " ND2 ASN A  45 " =    1.531
peak=   -3.753 closest distance to " O   HOH Z 351 " =    1.468
peak=   -3.744 closest distance to " CG  PHE A 283 " =    2.804
peak=   -3.741 closest distance to " CG1 VAL A 250 " =    2.655
peak=   -3.732 closest distance to " CE  MET A 105 " =    2.321
peak=   -3.710 closest distance to " O   HOH Z 353 " =    2.123
peak=   -3.696 closest distance to " O   HOH Z  43 " =    1.586
peak=   -3.691 closest distance to " C   ASN A 285 " =    2.546
peak=   -3.681 closest distance to " OG  SER A  97 " =    2.232
peak=   -3.680 closest distance to " CG2 ILE A 263 " =    2.382
peak=   -3.680 closest distance to " ND2 ASN A  45 " =    1.062
peak=   -3.678 closest distance to " O   HOH Z  52 " =    1.327
peak=   -3.676 closest distance to " O   HOH Z 407 " =    3.296
peak=   -3.669 closest distance to " O   HOH Z  73 " =    2.150
peak=   -3.669 closest distance to " O   HOH Z 185 " =    2.317
peak=   -3.662 closest distance to " CG  MET A 105 " =    0.962
peak=   -3.658 closest distance to " C   ALA A 158 " =    1.400
peak=   -3.638 closest distance to " CG  ARG A 269 " =    2.541
peak=   -3.629 closest distance to " CD  ARG A 139 " =    1.575
peak=   -3.623 closest distance to " O   HOH Z 196 " =    2.067
peak=   -3.623 closest distance to " CG  ASP A 231 " =    0.793
peak=   -3.621 closest distance to " CA  GLY A 241 " =    3.143
peak=   -3.613 closest distance to " CB  ASN A  39 " =    2.306
peak=   -3.591 closest distance to " OE1 GLN A  88 " =    1.157
peak=   -3.589 closest distance to " CA  GLY A 241 " =    2.337
peak=   -3.587 closest distance to " CA  GLY A 203 " =    2.421
peak=   -3.586 closest distance to " CZ  TYR A 169 " =    1.723
peak=   -3.585 closest distance to " CB  ALA A  43 " =    2.612
peak=   -3.583 closest distance to " OD2 ASP A 171 " =    1.841
peak=   -3.582 closest distance to " CD1 PHE A  59 " =    1.857
peak=   -3.580 closest distance to " CZ  PHE A  59 " =    1.631
peak=   -3.566 closest distance to " O   GLY A 211 " =    1.408
peak=   -3.560 closest distance to " OD1 ASN A 148 " =    1.576
peak=   -3.551 closest distance to " OXT GLY A 302 " =    2.945
peak=   -3.549 closest distance to " O   HOH Z  93 " =    2.476
peak=   -3.546 closest distance to " ND2 ASN A 249 " =    2.186
peak=   -3.541 closest distance to " CD2 PHE A 192 " =    2.017
peak=   -3.539 closest distance to " O   VAL A  67 " =    2.805
peak=   -3.537 closest distance to " CD2 TYR A 293 " =    1.989
peak=   -3.535 closest distance to " CD1 LEU A 228 " =    2.386
peak=   -3.530 closest distance to " O   VAL A 189 " =    2.552
peak=   -3.529 closest distance to " O   HOH Z 394 " =    1.445
peak=   -3.507 closest distance to " O   HOH Z  60 " =    2.542
peak=   -3.505 closest distance to " CB  ALA A 291 " =    2.238
peak=   -3.500 closest distance to " O   PRO A 163 " =    2.084
peak=   -3.490 closest distance to " O   HOH Z  11 " =    1.783
peak=   -3.489 closest distance to " O   HOH Z 298 " =    2.496
peak=   -3.488 closest distance to " O   HOH Z 426 " =    1.659
peak=   -3.485 closest distance to " CE2 PHE A 218 " =    2.474
peak=   -3.476 closest distance to " O   HOH Z  51 " =    1.641
peak=   -3.472 closest distance to " CA  ASP A 298 " =    1.082
peak=   -3.464 closest distance to " O   HOH Z 198 " =    1.423
peak=   -3.463 closest distance to " C   LEU A 143 " =    1.218
peak=   -3.458 closest distance to " O   HOH Z 253 " =    4.046
peak=   -3.458 closest distance to " O   GLY A 203 " =    2.437
peak=   -3.451 closest distance to " O   HOH Z 311 " =    3.726
peak=   -3.450 closest distance to " N   SER A 212 " =    1.842
peak=   -3.439 closest distance to " NE2 GLN A  88 " =    1.948
peak=   -3.437 closest distance to " CD2 PHE A  61 " =    2.549
peak=   -3.434 closest distance to " O   HOH Z 211 " =    1.614
peak=   -3.422 closest distance to " CD1 LEU A 101 " =    2.423
peak=   -3.409 closest distance to " O   HOH Z 292 " =    4.666
peak=   -3.408 closest distance to " NH1 ARG A 195 " =    2.597
peak=   -3.397 closest distance to " CD  ARG A 195 " =    5.161
peak=   -3.397 closest distance to " CB  TYR A  15 " =    2.191
peak=   -3.396 closest distance to " CD2 LEU A 237 " =    2.880
peak=   -3.394 closest distance to " OD1 ASP A 171 " =    1.572
peak=   -3.393 closest distance to " N   THR A 157 " =    1.557
peak=   -3.393 closest distance to " OD1 ASN A 187 " =    1.516
peak=   -3.392 closest distance to " O   HOH Z 102 " =    1.618
peak=   -3.387 closest distance to " N   ALA A 226 " =    2.227
peak=   -3.385 closest distance to " O   ALA A  10 " =    1.647
peak=   -3.385 closest distance to " C   PHE A  59 " =    1.333
peak=   -3.379 closest distance to " CB  ALA A 248 " =    2.048
peak=   -3.379 closest distance to " CB  CYS A 201 " =    2.675
peak=   -3.366 closest distance to " O   HOH Z  44 " =    2.204
peak=   -3.362 closest distance to " O   HOH Z 243 " =    2.137
peak=   -3.358 closest distance to " NH2 ARG A  79 " =    1.528
peak=   -3.356 closest distance to " OD1 ASP A 191 " =    1.652
peak=   -3.345 closest distance to " C   GLY A  17 " =    1.291
peak=   -3.343 closest distance to " O   HOH Z 111 " =    2.044
peak=   -3.341 closest distance to " N   MET A 105 " =    2.806
peak=   -3.336 closest distance to " O   HOH Z 348 " =    2.275
peak=   -3.320 closest distance to " CE BMET A  47 " =    1.831
peak=   -3.318 closest distance to " OG  SER A  62 " =    1.719
peak=   -3.318 closest distance to " CG1 VAL A 197 " =    2.281
peak=   -3.318 closest distance to " O   HOH Z  13 " =    1.539
peak=   -3.313 closest distance to " CA  GLY A 241 " =    2.821
peak=   -3.309 closest distance to " CB  ALA A 248 " =    2.482
peak=   -3.308 closest distance to " CD  GLU A 236 " =    1.062
peak=   -3.307 closest distance to " CG  GLU A 277 " =    1.132
peak=   -3.307 closest distance to " CB  PRO A 163 " =    2.543
peak=   -3.304 closest distance to " O   HOH Z 114 " =    1.606
peak=   -3.301 closest distance to " O   HOH Z 298 " =    1.223
peak=   -3.300 closest distance to " CB  ASP A 132 " =    2.317
peak=   -3.299 closest distance to " O   HOH Z 275 " =    1.532
peak=   -3.295 closest distance to " O   HOH Z 393 " =    1.433
peak=   -3.292 closest distance to " SG ACYS A 201 " =    2.043
peak=   -3.289 closest distance to " NE2 GLN A 278 " =    1.768
peak=   -3.288 closest distance to " NH2 ARG A  79 " =    1.989
peak=   -3.279 closest distance to " CE  MET A 105 " =    2.289
peak=   -3.277 closest distance to " CZ BARG A 275 " =    1.877
peak=   -3.260 closest distance to " C   LEU A 222 " =    0.754
peak=   -3.256 closest distance to " CA  ASP A  27 " =    2.482
peak=   -3.255 closest distance to " CG  TRP A 266 " =    1.837
peak=   -3.253 closest distance to " N   GLN A  58 " =    1.745
peak=   -3.249 closest distance to " O   PHE A 218 " =    1.573
peak=   -3.246 closest distance to " CE  LYS A  76 " =    2.714
peak=   -3.245 closest distance to " O   HOH Z  51 " =    1.368
peak=   -3.244 closest distance to " O   HOH Z 252 " =    4.284
peak=   -3.240 closest distance to " N   THR A 235 " =    1.284
peak=   -3.236 closest distance to " CD1 ILE A 239 " =    2.114
peak=   -3.233 closest distance to " ND2BASN A 224 " =    1.723
peak=   -3.232 closest distance to " CG1 VAL A 125 " =    1.938
peak=   -3.227 closest distance to " O   HOH Z 377 " =    0.883
peak=   -3.226 closest distance to " OG BSER A 134 " =    1.817
peak=   -3.226 closest distance to " C   GLY A  13 " =    0.980
peak=   -3.226 closest distance to " ND2 ASN A  60 " =    1.396
peak=   -3.224 closest distance to " CB  ASP A 286 " =    2.062
peak=   -3.223 closest distance to " O   GLY A 196 " =    1.155
peak=   -3.223 closest distance to " CB  TRP A  85 " =    2.365
peak=   -3.222 closest distance to " CA  GLY A  98 " =    1.973
peak=   -3.221 closest distance to " O   HOH Z 281 " =    2.631
peak=   -3.220 closest distance to " O   HOH Z 241 " =    1.369
peak=   -3.218 closest distance to " CD1 LEU A 297 " =    2.489
peak=   -3.217 closest distance to " O   ALA A 180 " =    1.385
peak=   -3.213 closest distance to " O   HOH Z 322 " =    1.523
peak=   -3.210 closest distance to " CE1 TYR A 169 " =    2.565
peak=   -3.208 closest distance to " O   HOH Z 295 " =    1.554
peak=   -3.206 closest distance to " O   SER A 135 " =    1.453
peak=   -3.204 closest distance to " O   HOH Z 191 " =    5.605
peak=   -3.201 closest distance to " O   HOH Z 222 " =    1.193
peak=   -3.201 closest distance to " O   HOH Z  37 " =    1.886
peak=   -3.194 closest distance to " NE2 GLN A 194 " =    1.769
peak=   -3.191 closest distance to " NH2 ARG A  66 " =    2.121
peak=   -3.181 closest distance to " O   HOH Z 166 " =    1.911
peak=   -3.178 closest distance to " CG2 VAL A 189 " =    2.096
peak=   -3.168 closest distance to " CG  ARG A  66 " =    2.316
peak=   -3.166 closest distance to " N   SER A 276 " =    1.271
peak=   -3.165 closest distance to " CE3 TRP A 150 " =    1.656
peak=   -3.156 closest distance to " CD2 TYR A 247 " =    2.516
peak=   -3.156 closest distance to " O   HOH Z 423 " =    1.159
peak=   -3.153 closest distance to " O   HOH Z 350 " =    1.846
peak=   -3.148 closest distance to " CG2 THR A 221 " =    2.222
peak=   -3.147 closest distance to " OD2 ASP A 191 " =    1.558
peak=   -3.146 closest distance to " CE  LYS A  76 " =    2.670
peak=   -3.146 closest distance to " CB  CYS A 254 " =    2.321
peak=   -3.140 closest distance to " CG  PRO A 163 " =    2.484
peak=   -3.133 closest distance to " O   HOH Z 317 " =    1.569
peak=   -3.128 closest distance to " O   HOH Z 123 " =    2.323
peak=   -3.128 closest distance to " O   HOH Z 128 " =    2.595
peak=   -3.126 closest distance to " O   HOH Z   6 " =    1.493
peak=   -3.125 closest distance to " CD2 LEU A 237 " =    2.243
peak=   -3.123 closest distance to " O   HOH Z 207 " =    2.213
peak=   -3.122 closest distance to " O   ALA A 292 " =    2.047
peak=   -3.121 closest distance to " CD1 ILE A 151 " =    2.387
peak=   -3.118 closest distance to " CG  GLN A  88 " =    0.919
peak=   -3.118 closest distance to " N   ALA A 248 " =    1.602
peak=   -3.100 closest distance to " CD2 PHE A  59 " =    2.554
peak=   -3.098 closest distance to " SD  MET A 188 " =    2.371
peak=   -3.093 closest distance to " O   GLN A 240 " =    2.423
peak=   -3.082 closest distance to " CB  ASP A 132 " =    2.363
peak=   -3.082 closest distance to " O   TRP A  70 " =    1.491
peak=   -3.080 closest distance to " C   MET A 188 " =    1.413
peak=   -3.074 closest distance to " CG  ASN A 301 " =    1.982
peak=   -3.069 closest distance to " CD1 ILE A 199 " =    2.631
peak=   -3.053 closest distance to " O   HOH Z 184 " =    1.825
peak=   -3.040 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.034 closest distance to " O   HOH Z 244 " =    2.082
peak=   -3.029 closest distance to " O   HOH Z 417 " =    2.543
peak=   -3.024 closest distance to " CE3 TRP A  70 " =    1.854

================= 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    :  0.2547 0.2540   5.851189e+00   5.858338e+00
   1_bss:  0.2370 0.2378   5.817007e+00   5.822222e+00
   1_xyz:  0.1596 0.1778   5.410213e+00   5.505393e+00
   1_adp:  0.1471 0.1815   5.356291e+00   5.527869e+00
   1_occ:  0.1467 0.1811   5.353623e+00   5.525970e+00
   2_bss:  0.1457 0.1795   5.348502e+00   5.519839e+00
   2_xyz:  0.1231 0.1610   5.205366e+00   5.414595e+00
   2_adp:  0.1194 0.1574   5.177166e+00   5.393698e+00
   2_occ:  0.1193 0.1574   5.176978e+00   5.393756e+00
   3_bss:  0.1191 0.1570   5.175607e+00   5.392191e+00
   3_xyz:  0.1137 0.1552   5.147551e+00   5.379830e+00
   3_adp:  0.1125 0.1557   5.142079e+00   5.379587e+00
   3_occ:  0.1124 0.1557   5.142064e+00   5.379748e+00
   4_bss:  0.1126 0.1552   5.142634e+00   5.377966e+00
   4_xyz:  0.1090 0.1567   5.129214e+00   5.381724e+00
   4_adp:  0.1081 0.1576   5.127446e+00   5.384259e+00
   4_occ:  0.1081 0.1577   5.127692e+00   5.384766e+00
   5_bss:  0.1080 0.1576   5.127655e+00   5.384688e+00
   5_xyz:  0.1110 0.1592   5.147639e+00   5.397826e+00
   5_adp:  0.1113 0.1584   5.146065e+00   5.394287e+00
   5_occ:  0.1113 0.1584   5.146194e+00   5.394561e+00
   5_bss:  0.1112 0.1584   5.146400e+00   5.394829e+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:  0.319  54.142   0.197  -2.995  -1.780  -0.000  -0.000  -0.000
   1_xyz:  0.319  54.142   0.197  -2.995  -1.780  -0.000  -0.000  -0.000
   1_adp:  0.319  54.142   0.197  -2.995  -1.780  -0.000  -0.000  -0.000
   1_occ:  0.319  54.142   0.197  -2.995  -1.780  -0.000  -0.000  -0.000
   2_bss:  0.333  58.662  -1.808  -3.001  -1.838  -0.000  -0.000  -0.000
   2_xyz:  0.333  58.662  -1.808  -3.001  -1.838  -0.000  -0.000  -0.000
   2_adp:  0.333  58.662  -1.808  -3.001  -1.838  -0.000  -0.000  -0.000
   2_occ:  0.333  58.662  -1.808  -3.001  -1.838  -0.000  -0.000  -0.000
   3_bss:  0.330  58.662  -2.224  -2.684  -1.557  -0.000  -0.000  -0.000
   3_xyz:  0.330  58.662  -2.224  -2.684  -1.557  -0.000  -0.000  -0.000
   3_adp:  0.330  58.662  -2.224  -2.684  -1.557  -0.000  -0.000  -0.000
   3_occ:  0.330  58.662  -2.224  -2.684  -1.557  -0.000  -0.000  -0.000
   4_bss:  0.330  58.662  -2.228  -2.456  -1.374  -0.000  -0.000  -0.000
   4_xyz:  0.330  58.662  -2.228  -2.456  -1.374  -0.000  -0.000  -0.000
   4_adp:  0.330  58.662  -2.228  -2.456  -1.374  -0.000  -0.000  -0.000
   4_occ:  0.330  58.662  -2.228  -2.456  -1.374  -0.000  -0.000  -0.000
   5_bss:  0.325  58.662  -2.020  -2.187  -1.130  -0.000  -0.000  -0.000
   5_xyz:  0.325  58.662  -2.020  -2.187  -1.130  -0.000  -0.000  -0.000
   5_adp:  0.325  58.662  -2.020  -2.187  -1.130  -0.000  -0.000  -0.000
   5_occ:  0.325  58.662  -2.020  -2.187  -1.130  -0.000  -0.000  -0.000
   5_bss:  0.320  54.343  -1.877  -2.001  -0.943  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  25.395 0.8116  0.9640    19114.697
   1_bss:  24.238 0.8220  0.9285    16580.763
   1_xyz:  16.153 0.8985  0.9859     8121.147
   1_adp:  16.710 0.8932  0.9848     8406.265
   1_occ:  16.662 0.8935  0.9847     8342.636
   2_bss:  16.516 0.8948  0.9617     8248.869
   2_xyz:  14.398 0.9121  0.9707     6676.646
   2_adp:  13.915 0.9160  0.9695     6380.816
   2_occ:  13.918 0.9160  0.9693     6379.086
   3_bss:  13.890 0.9162  0.9714     6359.040
   3_xyz:  13.643 0.9182  0.9718     6221.617
   3_adp:  13.628 0.9184  0.9662     6202.619
   3_occ:  13.632 0.9184  0.9661     6204.643
   4_bss:  13.625 0.9183  0.9702     6162.497
   4_xyz:  13.687 0.9178  0.9705     6224.329
   4_adp:  13.764 0.9172  0.9634     6240.524
   4_occ:  13.774 0.9171  0.9633     6245.804
   5_bss:  13.773 0.9172  0.9716     6243.210
   5_xyz:  13.999 0.9155  0.9700     6412.201
   5_adp:  13.929 0.9160  0.9637     6385.617
   5_occ:  13.936 0.9160  0.9637     6386.808
   5_bss:  13.941 0.9159  0.9690     6387.449
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6082e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6082e-01
   1_xyz:   0.955  0.007  0.066 14.989  0.004  4.114   5.5380e-02
   1_adp:   0.955  0.007  0.066 14.989  0.004  4.114   5.5380e-02
   1_occ:   0.955  0.007  0.066 14.989  0.004  4.114   5.5380e-02
   2_bss:   0.955  0.007  0.066 14.989  0.004  4.114   5.5380e-02
   2_xyz:   0.940  0.006  0.072 14.363  0.004  4.123   5.2569e-02
   2_adp:   0.940  0.006  0.072 14.363  0.004  4.123   5.2569e-02
   2_occ:   0.940  0.006  0.072 14.363  0.004  4.123   5.2569e-02
   3_bss:   0.940  0.006  0.072 14.363  0.004  4.123   5.2569e-02
   3_xyz:   0.984  0.008  0.076 14.474  0.004  4.114   5.9293e-02
   3_adp:   0.984  0.008  0.076 14.474  0.004  4.114   5.9293e-02
   3_occ:   0.984  0.008  0.076 14.474  0.004  4.114   5.9293e-02
   4_bss:   0.984  0.008  0.076 14.474  0.004  4.114   5.9293e-02
   4_xyz:   1.052  0.009  0.081 14.681  0.004  4.117   6.7138e-02
   4_adp:   1.052  0.009  0.081 14.681  0.004  4.117   6.7138e-02
   4_occ:   1.052  0.009  0.081 14.681  0.004  4.117   6.7138e-02
   5_bss:   1.052  0.009  0.081 14.681  0.004  4.117   6.7138e-02
   5_xyz:   0.931  0.007  0.072 14.427  0.004  4.116   5.3477e-02
   5_adp:   0.931  0.007  0.072 14.427  0.004  4.116   5.3477e-02
   5_occ:   0.931  0.007  0.072 14.427  0.004  4.116   5.3477e-02
   5_bss:   0.931  0.007  0.072 14.427  0.004  4.116   5.3477e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4244e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4244e-01
   1_xyz:   8.603  0.046  0.231 83.779  0.032  2.363   5.5334e-02
   1_adp:   8.603  0.046  0.231 83.779  0.032  2.363   5.5334e-02
   1_occ:   8.603  0.046  0.231 83.779  0.032  2.363   5.5334e-02
   2_bss:   8.603  0.046  0.231 83.779  0.032  2.363   5.5334e-02
   2_xyz:   7.581  0.043  0.216 82.838  0.038  2.390   3.5199e-02
   2_adp:   7.581  0.043  0.216 82.838  0.038  2.390   3.5199e-02
   2_occ:   7.581  0.043  0.216 82.838  0.038  2.390   3.5199e-02
   3_bss:   7.581  0.043  0.216 82.838  0.038  2.390   3.5199e-02
   3_xyz:   7.302  0.047  0.223 83.309  0.034  2.363   4.0741e-02
   3_adp:   7.302  0.047  0.223 83.309  0.034  2.363   4.0741e-02
   3_occ:   7.302  0.047  0.223 83.309  0.034  2.363   4.0741e-02
   4_bss:   7.302  0.047  0.223 83.309  0.034  2.363   4.0741e-02
   4_xyz:   7.339  0.043  0.252 83.712  0.037  2.324   5.2114e-02
   4_adp:   7.339  0.043  0.252 83.712  0.037  2.324   5.2114e-02
   4_occ:   7.339  0.043  0.252 83.712  0.037  2.324   5.2114e-02
   5_bss:   7.339  0.043  0.252 83.712  0.037  2.324   5.2114e-02
   5_xyz:   7.412  0.041  0.228 83.342  0.035  2.386   3.4256e-02
   5_adp:   7.412  0.041  0.228 83.342  0.035  2.386   3.4256e-02
   5_occ:   7.412  0.041  0.228 83.342  0.035  2.386   3.4256e-02
   5_bss:   7.412  0.041  0.228 83.342  0.035  2.386   3.4256e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  63.81   0.00  16.63  54.50   0.00  12.83  63.81   5.08  37.33
   1_occ:  63.81   0.00  16.63  54.50   0.00  12.83  63.81   5.08  37.33
   2_bss:  63.81   0.00  16.63  54.50   0.00  12.83  63.81   5.08  37.33
   2_xyz:  63.81   0.00  16.63  54.50   0.00  12.83  63.81   5.08  37.33
   2_adp:  69.72   1.57  16.73  69.72   1.57  12.94  67.75   6.00  37.33
   2_occ:  69.72   1.57  16.73  69.72   1.57  12.94  67.75   6.00  37.33
   3_bss:  69.72   1.57  16.73  69.72   1.57  12.94  67.75   6.00  37.33
   3_xyz:  69.72   1.57  16.73  69.72   1.57  12.94  67.75   6.00  37.33
   3_adp:  75.45   1.18  16.85  75.45   1.18  12.89  72.12   3.78  38.42
   3_occ:  75.45   1.18  16.85  75.45   1.18  12.89  72.12   3.78  38.42
   4_bss:  75.45   1.18  16.85  75.45   1.18  12.89  72.12   3.78  38.42
   4_xyz:  75.45   1.18  16.85  75.45   1.18  12.89  72.12   3.78  38.42
   4_adp:  85.80   0.00  17.08  85.80   0.00  12.89  78.58   4.96  39.92
   4_occ:  85.80   0.00  17.08  85.80   0.00  12.89  78.58   4.96  39.92
   5_bss:  85.80   0.00  17.08  85.80   0.00  12.89  78.58   4.96  39.92
   5_xyz:  85.80   0.00  17.08  85.80   0.00  12.89  78.58   4.96  39.92
   5_adp:  86.05   0.49  16.71  86.05   0.49  12.64  78.75   6.01  38.84
   5_occ:  86.05   0.49  16.71  86.05   0.49  12.64  78.75   6.01  38.84
   5_bss:  86.04   0.48  16.69  86.04   0.48  12.63  78.74   6.00  38.82
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.991    0.006    0.199
   1_adp:    0.991    0.006    0.199
   1_occ:    0.991    0.006    0.199
   2_bss:    0.991    0.006    0.199
   2_xyz:    0.733    0.014    0.246
   2_adp:    0.733    0.014    0.246
   2_occ:    0.733    0.014    0.246
   3_bss:    0.733    0.014    0.246
   3_xyz:    0.749    0.015    0.258
   3_adp:    0.749    0.015    0.258
   3_occ:    0.749    0.015    0.258
   4_bss:    0.749    0.015    0.258
   4_xyz:    0.827    0.007    0.278
   4_adp:    0.827    0.007    0.278
   4_occ:    0.827    0.007    0.278
   5_bss:    0.827    0.007    0.278
   5_xyz:    0.889    0.007    0.279
   5_adp:    0.889    0.007    0.279
   5_occ:    0.889    0.007    0.279
   5_bss:    0.889    0.007    0.279
------------------------------------------------------------------------

CPU time actual refinement: 319.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1028/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_1028/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1028/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1028/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1028/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.59 
  Macro-tasks:
    bulk solvent and scale       = 42.03  
    individual site refinement   = 124.81 
    weights calculation          = 29.28  
    collect and process          = 6.80   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 203.02 
  Micro-tasks:
    mask                            = 1.13   
    f_calc                          = 100.68 
    alpha_beta                      = 8.51   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 103.75 
    fmodel                         = 6.62   
    r_factors                      = 0.15   
    phase_errors                   = 12.31  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 234.60 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.602 micro seconds
Total CPU time: 5.54 minutes
from_scatterers_fft:    626 calls, 100.29 s
gradients_fft:          571 calls,  92.65 s

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

# Date 2008-01-16 Time 06:15:37 PST -0800 (1200492937.33 s)
Start R-work = 0.2547, R-free = 0.2540 (no bulk solvent and anisotropic scale)
Final R-work = 0.1337, R-free = 0.1767 (no bulk solvent and anisotropic scale)

Start R-work = 0.2370, R-free = 0.2378
Final R-work = 0.1112, R-free = 0.1584