# Date 2008-01-16 Time 05:31:22 PST -0800 (1200490282.30 s)
#phil __OFF__

Command line arguments: "../768.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22541
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 768

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.4607, 88.1178, 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: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 1.98283
Completeness in resolution range: 0.94674
Completeness with d_max=infinity: 0.943912

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1289
                             d_min =   1.9828

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1289 1.98283
Completeness in resolution range: 0.94674
Completeness with d_max=infinity: 0.943912

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1294 -  4.2434 [2171/2196]  1951   220  10.1%
  bin  2:  4.2434 -  3.3805 [2084/2104]  1879   205   9.8%
  bin  3:  3.3805 -  2.9568 [2077/2096]  1869   208  10.0%
  bin  4:  2.9568 -  2.6881 [2026/2056]  1822   204  10.1%
  bin  5:  2.6881 -  2.4963 [2032/2051]  1831   201   9.9%
  bin  6:  2.4963 -  2.3497 [2013/2038]  1810   203  10.1%
  bin  7:  2.3497 -  2.2324 [2026/2054]  1821   205  10.1%
  bin  8:  2.2324 -  2.1355 [1989/2025]  1791   198  10.0%
  bin  9:  2.1355 -  2.0535 [1997/2039]  1803   194   9.7%
  bin 10:  2.0535 -  1.9828 [1174/2032]  1053   121  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_768/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: 0.11 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:
        1.79 -     2.41: 22
        2.41 -     3.04: 2122
        3.04 -     3.66: 4639
        3.66 -     4.28: 8965
        4.28 -     4.90: 12361
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.792 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.907 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.965 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.965 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28104 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_768/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_768/model_refine_001.geo

CPU time processing inputs: 8.01


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.4607 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3878   r_free= 0.3795   ksol= 0.00   Bsol= 0.00   scale= 0.934    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.177027                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7332 0.99   1413  156 0.3160 0.2899      6.4568      6.3306|
|  2:  4.7332 -  3.7761 0.99   1363  153 0.3056 0.3255      6.5983      6.5985|
|  3:  3.7761 -  3.3044 0.99   1324  143 0.3397 0.3008      6.5082      6.4682|
|  4:  3.3044 -  3.0049 0.99   1331  152 0.3722 0.3890      6.3886      6.4257|
|  5:  3.0049 -  2.7909 0.99   1313  147 0.4128 0.3514      6.2494       6.185|
|  6:  2.7909 -  2.6273 0.99   1310  143 0.3981 0.4379      6.1341       6.112|
|  7:  2.6273 -  2.4963 0.99   1298  144 0.4102 0.3916      6.1289      6.0824|
|  8:  2.4963 -  2.3881 0.98   1294  147 0.4469 0.4491      6.1183      6.1236|
|  9:  2.3881 -  2.2965 0.98   1293  137 0.4359 0.4277      6.0402      6.0464|
| 10:  2.2965 -  2.2175 1.00   1273  150 0.4535 0.4326      6.0422      5.9817|
| 11:  2.2175 -  2.1484 0.98   1307  141 0.4550 0.4578      5.9859      6.0101|
| 12:  2.1484 -  2.0871 0.98   1270  145 0.4578 0.4134      5.9155       5.912|
| 13:  2.0871 -  2.0323 0.99   1281  140 0.4433 0.4736      5.8091      5.7666|
| 14:  2.0323 -  1.9828 0.42    560   61 0.4570 0.4336       5.841      5.7637|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1294 -  4.7332  1413   156  0.80  25.11   0.85     0.83      41708.76|
|  2:  4.7332 -  3.7761  1363   153  0.81  24.80   0.94     0.90      59315.06|
|  3:  3.7761 -  3.3044  1324   143  0.75  31.28   0.96     0.90      63592.75|
|  4:  3.3044 -  3.0049  1331   152  0.69  36.63   0.94     0.85      58179.50|
|  5:  3.0049 -  2.7909  1313   147  0.63  41.83   0.95     0.80      46974.79|
|  6:  2.7909 -  2.6273  1310   143  0.60  43.71   0.95     0.76      42465.07|
|  7:  2.6273 -  2.4963  1298   144  0.59  44.60   0.96     0.76      40243.67|
|  8:  2.4963 -  2.3881  1294   147  0.57  46.32   0.94     0.76      37714.18|
|  9:  2.3881 -  2.2965  1293   137  0.57  46.64   0.97     0.77      35161.59|
| 10:  2.2965 -  2.2175  1273   150  0.56  47.69   0.98     0.76      32750.82|
| 11:  2.2175 -  2.1484  1307   141  0.54  49.44   0.96     0.77      33568.57|
| 12:  2.1484 -  2.0871  1270   145  0.52  50.63   0.98     0.76      30941.57|
| 13:  2.0871 -  2.0323  1281   140  0.51  51.93   0.97     0.76      26977.55|
| 14:  2.0323 -  1.9828   560    61  0.57  47.07   1.00     0.76      20797.63|
|alpha:            min =        0.76 max =            0.90 mean =         0.80|
|beta:             min =    20797.63 max =        63592.75 mean =     41763.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.54|
|phase err.(test): min =        0.00 max =           89.98 mean =        41.37|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.215105              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.990   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.084229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.620   (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 |  1.792 -  2.103:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.103 -  2.414:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.414 -  2.724:      165 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.724 -  3.035:     1957 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.035 -  3.346:     1853 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.346 -  3.657:     2786 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.657 -  3.968:     4617 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.968 -  4.278:     4348 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.278 -  4.589:     5630 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.589 -  4.900:     6731 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| 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  1.792 |       0.208 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3878   r_free= 0.3795   ksol= 0.00   Bsol= 0.00   scale= 0.934    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.177027                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3746   r_free= 0.3706   ksol= 0.32   Bsol= 57.20   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-0.64,4.06,-0.00,0.00,0.00); trace/3= 0.16                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.161234                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.788260              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.937   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.547851              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.401   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3746      final r-factor (work) = 0.2035          |
| start r-factor (free) = 0.3706      final r-factor (free) = 0.2336          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1357 = 7.79 * 0.50 * 6.1555 + 1.00 * 0.1653                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0048 = 7.79 * 0.50 * 5.8808 + 1.00 * 0.1041                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2035      final r-factor (work) = 0.1832          |
| start r-factor (free) = 0.2336      final r-factor (free) = 0.2398          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2281 = 0.55 * 1.00 * 5.8808 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0529 = 0.55 * 1.00 * 5.5521 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    86.35   17.61    None  None   None       |
|    all(noH): 2823   0      0.76    86.35   17.61    None  None   None       |
|    Sol.    : 438    0      2.46    86.35   42.10    None  None   None       |
|    Mac.    : 2385   0      0.76    72.24   13.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.756 -   9.315:  846   |   5:    43.553 -  52.112:  100        |
|      1:     9.315 -  17.874: 1166   |   6:    52.112 -  60.672:   85        |
|      2:    17.874 -  26.434:  315   |   7:    60.672 -  69.231:   46        |
|      3:    26.434 -  34.993:  137   |   8:    69.231 -  77.790:   11        |
|      4:    34.993 -  43.553:  110   |   9:    77.790 -  86.350:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1832 r_free = 0.2398             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1831 r_free = 0.2397             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1831   r_free= 0.2397   ksol= 0.32   Bsol= 57.20   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-0.64,4.06,-0.00,0.00,0.00); trace/3= 0.16                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.564611                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1795   r_free= 0.2351   ksol= 0.33   Bsol= 70.07   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.13,0.45,-0.00,0.00,0.00); trace/3= -1.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.553792                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.040743              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.192   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.243746              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.918  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1795      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.2351      final r-factor (free) = 0.1862          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5637 = 3.04 * 0.50 * 5.5641 + 1.00 * 0.1041                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3443 = 3.04 * 0.50 * 5.4488 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1380      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.1862      final r-factor (free) = 0.1770          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3393 = 0.24 * 1.00 * 5.4488 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2999 = 0.24 * 1.00 * 5.2967 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.46   17.28    None  None   None       |
|    all(noH): 2823   0      0.00    83.46   17.28    None  None   None       |
|    Sol.    : 438    0      5.33    83.46   41.17    None  None   None       |
|    Mac.    : 2385   0      0.00    72.13   12.90    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 -   8.346:  626   |   5:    41.730 -  50.076:   96        |
|      1:     8.346 -  16.692: 1356   |   6:    50.076 -  58.422:   91        |
|      2:    16.692 -  25.038:  336   |   7:    58.422 -  66.768:   50        |
|      3:    25.038 -  33.384:  137   |   8:    66.768 -  75.114:   17        |
|      4:    33.384 -  41.730:  106   |   9:    75.114 -  83.460:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1315 r_free = 0.1770             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1313 r_free = 0.1768             target_work(ml) = 5.270         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1313   r_free= 0.1768   ksol= 0.33   Bsol= 70.07   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.13,0.45,-0.00,0.00,0.00); trace/3= -1.51                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.270313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1763   ksol= 0.34   Bsol= 70.07   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.42,-0.29,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.267850                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.204899              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.171  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.684392              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.067  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1311      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1763      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5467 = 3.20 * 0.50 * 5.2961 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4338 = 3.20 * 0.50 * 5.2184 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5803 = 0.68 * 1.00 * 5.2184 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5439 = 0.68 * 1.00 * 5.1639 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.34    83.73   17.31    None  None   None       |
|    all(noH): 2823   0      0.34    83.73   17.31    None  None   None       |
|    Sol.    : 438    0      5.45    83.73   41.52    None  None   None       |
|    Mac.    : 2385   0      0.34    76.85   12.86    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:     0.339 -   8.679:  748   |   5:    42.037 -  50.376:   79        |
|      1:     8.679 -  17.018: 1262   |   6:    50.376 -  58.716:  100        |
|      2:    17.018 -  25.358:  314   |   7:    58.716 -  67.056:   49        |
|      3:    25.358 -  33.697:  129   |   8:    67.056 -  75.395:   22        |
|      4:    33.697 -  42.037:  110   |   9:    75.395 -  83.735:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1608             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1608             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1608   ksol= 0.34   Bsol= 70.07   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.42,-0.29,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161170                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1607   ksol= 0.34   Bsol= 70.07   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.39,-0.40,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.160879                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.410908              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.516  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.186148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.268  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2962 = 2.41 * 0.50 * 5.1637 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2814 = 2.41 * 0.50 * 5.1584 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2866 = 2.19 * 1.00 * 5.1584 + 1.00 * 0.0097                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2835 = 2.19 * 1.00 * 5.1563 + 1.00 * 0.0109                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.51   17.37    None  None   None       |
|    all(noH): 2823   0      0.00    90.51   17.37    None  None   None       |
|    Sol.    : 438    0      5.59    90.51   42.03    None  None   None       |
|    Mac.    : 2385   0      0.00    89.84   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.051:  895   |   5:    45.253 -  54.303:   82        |
|      1:     9.051 -  18.101: 1197   |   6:    54.303 -  63.354:   82        |
|      2:    18.101 -  27.152:  263   |   7:    63.354 -  72.404:   39        |
|      3:    27.152 -  36.202:  130   |   8:    72.404 -  81.455:   24        |
|      4:    36.202 -  45.253:  103   |   9:    81.455 -  90.506:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1612             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1120 r_free = 0.1613             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1613   ksol= 0.34   Bsol= 70.07   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.39,-0.40,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159699                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1612   ksol= 0.32   Bsol= 62.76   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.19,-0.25,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.159653                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.708869              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.209  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.744905              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.158  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1612      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4694 = 1.71 * 0.50 * 5.1569 + 1.00 * 0.0632                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4683 = 1.71 * 0.50 * 5.1655 + 1.00 * 0.0547                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8587 = 0.74 * 1.00 * 5.1655 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8608 = 0.74 * 1.00 * 5.1686 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.85   17.14    None  None   None       |
|    all(noH): 2823   0      0.00    90.85   17.14    None  None   None       |
|    Sol.    : 438    0      5.36    90.85   41.67    None  None   None       |
|    Mac.    : 2385   0      0.00    90.35   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:     0.000 -   9.085:  942   |   5:    45.424 -  54.509:   87        |
|      1:     9.085 -  18.170: 1170   |   6:    54.509 -  63.594:   75        |
|      2:    18.170 -  27.255:  246   |   7:    63.594 -  72.679:   39        |
|      3:    27.255 -  36.339:  136   |   8:    72.679 -  81.763:   22        |
|      4:    36.339 -  45.424:   98   |   9:    81.763 -  90.848:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1615             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1615             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1615   ksol= 0.32   Bsol= 62.76   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.19,-0.25,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.167123                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7332 0.99   1413  156 0.0977 0.1297      5.3922      5.5653|
|  2:  4.7332 -  3.7761 0.99   1363  153 0.0852 0.1123      5.4357      5.6205|
|  3:  3.7761 -  3.3044 0.99   1324  143 0.1060 0.1537      5.4792      5.8578|
|  4:  3.3044 -  3.0049 0.99   1331  152 0.1225 0.1707      5.4615      5.6221|
|  5:  3.0049 -  2.7909 0.99   1313  147 0.1346 0.1743      5.3424      5.5872|
|  6:  2.7909 -  2.6273 0.99   1310  143 0.1244 0.2004      5.2303      5.5231|
|  7:  2.6273 -  2.4963 0.99   1298  144 0.1313 0.1635      5.2009      5.3375|
|  8:  2.4963 -  2.3881 0.98   1294  147 0.1171 0.1579       5.083      5.3092|
|  9:  2.3881 -  2.2965 0.98   1293  137 0.1199 0.1928      5.0505      5.3628|
| 10:  2.2965 -  2.2175 1.00   1273  150 0.1154 0.1718      4.9643        5.22|
| 11:  2.2175 -  2.1484 0.98   1307  141 0.1144 0.1773      4.9611      5.2832|
| 12:  2.1484 -  2.0871 0.98   1270  145 0.1194 0.1810      4.9135      5.2239|
| 13:  2.0871 -  2.0323 0.99   1281  140 0.1145 0.1832      4.8087      5.0642|
| 14:  2.0323 -  1.9828 0.42    560   61 0.0979 0.1558      4.6713      4.8997|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1294 -  4.7332  1413   156  0.94   9.19   0.97     0.94       7335.35|
|  2:  4.7332 -  3.7761  1363   153  0.95   8.05   1.01     0.99       9208.35|
|  3:  3.7761 -  3.3044  1324   143  0.93  11.42   1.02     1.02      10464.57|
|  4:  3.3044 -  3.0049  1331   152  0.91  14.28   1.01     0.98      10600.11|
|  5:  3.0049 -  2.7909  1313   147  0.90  16.05   1.00     0.98       8672.94|
|  6:  2.7909 -  2.6273  1310   143  0.89  16.83   0.98     0.95       7475.78|
|  7:  2.6273 -  2.4963  1298   144  0.90  16.09   0.99     0.95       6674.45|
|  8:  2.4963 -  2.3881  1294   147  0.90  15.84   0.99     0.96       5590.56|
|  9:  2.3881 -  2.2965  1293   137  0.90  15.89   0.99     0.95       5217.49|
| 10:  2.2965 -  2.2175  1273   150  0.90  15.81   0.99     0.96       4458.46|
| 11:  2.2175 -  2.1484  1307   141  0.90  16.42   0.97     0.92       4454.37|
| 12:  2.1484 -  2.0871  1270   145  0.90  16.37   1.00     0.99       4241.98|
| 13:  2.0871 -  2.0323  1281   140  0.89  17.01   0.98     0.96       3603.93|
| 14:  2.0323 -  1.9828   560    61  0.92  13.92   0.96     0.93       2656.98|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2656.98 max =        10600.11 mean =      6675.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.47|
|phase err.(test): min =        0.00 max =           88.07 mean =        13.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1614   ksol= 0.32   Bsol= 62.77   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.05,-0.11,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.167214                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.13 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1614   ksol= 0.32   Bsol= 62.77   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.05,-0.11,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.167214                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1294 -  4.7332 0.99   1413  156 0.0977 0.1299      5.3929      5.5666|
|  2:  4.7332 -  3.7761 0.99   1363  153 0.0852 0.1123      5.4361      5.6204|
|  3:  3.7761 -  3.3044 0.99   1324  143 0.1060 0.1538      5.4792      5.8582|
|  4:  3.3044 -  3.0049 0.99   1331  152 0.1225 0.1707      5.4616      5.6221|
|  5:  3.0049 -  2.7909 0.99   1313  147 0.1346 0.1742      5.3423      5.5867|
|  6:  2.7909 -  2.6273 0.99   1310  143 0.1243 0.2004      5.2303      5.5233|
|  7:  2.6273 -  2.4963 0.99   1298  144 0.1313 0.1635       5.201      5.3378|
|  8:  2.4963 -  2.3881 0.98   1294  147 0.1171 0.1578      5.0831      5.3087|
|  9:  2.3881 -  2.2965 0.98   1293  137 0.1199 0.1927      5.0505      5.3629|
| 10:  2.2965 -  2.2175 1.00   1273  150 0.1154 0.1717      4.9644      5.2197|
| 11:  2.2175 -  2.1484 0.98   1307  141 0.1144 0.1772      4.9611      5.2831|
| 12:  2.1484 -  2.0871 0.98   1270  145 0.1194 0.1809      4.9133      5.2237|
| 13:  2.0871 -  2.0323 0.99   1281  140 0.1145 0.1832      4.8086      5.0638|
| 14:  2.0323 -  1.9828 0.42    560   61 0.0979 0.1558      4.6714      4.8997|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1294 -  4.7332  1413   156  0.94   9.20   0.97     0.94       7349.75|
|  2:  4.7332 -  3.7761  1363   153  0.95   8.05   1.01     1.00       9218.74|
|  3:  3.7761 -  3.3044  1324   143  0.93  11.42   1.02     1.02      10468.01|
|  4:  3.3044 -  3.0049  1331   152  0.91  14.28   1.01     0.99      10601.73|
|  5:  3.0049 -  2.7909  1313   147  0.90  16.05   1.00     0.98       8672.14|
|  6:  2.7909 -  2.6273  1310   143  0.89  16.83   0.98     0.95       7474.30|
|  7:  2.6273 -  2.4963  1298   144  0.90  16.09   0.99     0.96       6674.62|
|  8:  2.4963 -  2.3881  1294   147  0.90  15.85   0.99     0.97       5590.42|
|  9:  2.3881 -  2.2965  1293   137  0.90  15.89   1.00     0.96       5218.70|
| 10:  2.2965 -  2.2175  1273   150  0.90  15.81   1.00     0.96       4457.72|
| 11:  2.2175 -  2.1484  1307   141  0.90  16.42   0.98     0.93       4453.41|
| 12:  2.1484 -  2.0871  1270   145  0.90  16.37   1.00     1.00       4240.75|
| 13:  2.0871 -  2.0323  1281   140  0.89  17.01   0.99     0.97       3602.87|
| 14:  2.0323 -  1.9828   560    61  0.92  13.92   0.97     0.94       2656.43|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2656.43 max =        10601.73 mean =      6677.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.47|
|phase err.(test): min =        0.00 max =           88.07 mean =        13.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.034)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.85   17.14    None  None   None       |
|    all(noH): 2823   0      0.00    90.85   17.14    None  None   None       |
|    Sol.    : 438    0      5.36    90.85   41.67    None  None   None       |
|    Mac.    : 2385   0      0.00    90.35   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:     0.003 -   9.088:  942   |   5:    45.427 -  54.512:   87        |
|      1:     9.088 -  18.173: 1170   |   6:    54.512 -  63.597:   75        |
|      2:    18.173 -  27.258:  246   |   7:    63.597 -  72.682:   39        |
|      3:    27.258 -  36.342:  136   |   8:    72.682 -  81.766:   22        |
|      4:    36.342 -  45.427:   98   |   9:    81.766 -  90.851:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.512 - 4.704
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 303
   mapped sites are within: 0.705 - 4.704

peak=    5.503 closest distance to " NE2 GLN A  11 " =    1.168
peak=    5.457 closest distance to " CG  PRO A  54 " =    1.349
peak=    5.280 closest distance to " NH2 ARG A  56 " =    2.156
peak=    5.140 closest distance to " O   HOH Z 144 " =    1.859
peak=    5.139 closest distance to " CB  GLN A 223 " =    1.452
peak=    5.057 closest distance to " CG  PRO A 280 " =    0.957
peak=    4.821 closest distance to " CG  PRO A 198 " =    1.245
peak=    4.799 closest distance to " CG  PRO A 213 " =    1.228
peak=    4.788 closest distance to " CB  PRO A  54 " =    1.024
peak=    4.754 closest distance to " CZ  PHE A 218 " =    1.065
peak=    4.705 closest distance to " O   HOH Z 232 " =    2.346
peak=    4.666 closest distance to " CB  ARG A  79 " =    1.454
peak=    4.638 closest distance to " CB  ARG A 275 " =    0.935
peak=    4.622 closest distance to " O   HOH Z 126 " =    1.992
peak=    4.597 closest distance to " O   HOH Z  78 " =    1.852
peak=    4.532 closest distance to " CB  GLN A 183 " =    1.251
peak=    4.528 closest distance to " O   HOH Z 298 " =    1.957
peak=    4.528 closest distance to " O   HOH Z 287 " =    2.013
peak=    4.505 closest distance to " CB  ASN A 148 " =    1.417
peak=    4.499 closest distance to " CB  ARG A 190 " =    1.626
peak=    4.478 closest distance to " CG2 VAL A 257 " =    0.912
peak=    4.460 closest distance to " CD  ARG A 159 " =    0.767
peak=    4.343 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.338 closest distance to " ND2 ASN A 187 " =    1.548
peak=    4.322 closest distance to " O   HOH Z 369 " =    2.071
peak=    4.302 closest distance to " CB  LEU A 228 " =    1.116
peak=    4.301 closest distance to " O   HOH Z 188 " =    2.776
peak=    4.274 closest distance to " O   HOH Z 427 " =    2.912
peak=    4.254 closest distance to " CG  LEU A 167 " =    1.266
peak=    4.226 closest distance to " O   HOH Z 423 " =    1.357
peak=    4.218 closest distance to " CE  LYS A  76 " =    0.884
peak=    4.215 closest distance to " CB  SER A  63 " =    1.207
peak=    4.190 closest distance to " CG  PRO A 243 " =    1.088
peak=    4.171 closest distance to " CB  VAL A 265 " =    1.303
peak=    4.168 closest distance to " O   HOH Z 303 " =    2.205
peak=    4.145 closest distance to " CD2 TRP A 179 " =    1.311
peak=    4.107 closest distance to " O   HOH Z   9 " =    1.985
peak=    4.095 closest distance to " CB  ASN A 142 " =    1.002
peak=    4.087 closest distance to " O   HOH Z 406 " =    1.704
peak=    4.051 closest distance to " O   HOH Z 180 " =    2.108
peak=    4.023 closest distance to " CA  ARG A 195 " =    1.242
peak=    3.996 closest distance to " CB  ASN A  39 " =    0.916
peak=    3.991 closest distance to " O   PRO A 198 " =    1.574
peak=    3.990 closest distance to " CZ3 TRP A 266 " =    1.143
peak=    3.979 closest distance to " O   HOH Z 234 " =    3.738
peak=    3.977 closest distance to " CB  TRP A 266 " =    1.056
peak=    3.938 closest distance to " ND2 ASN A 249 " =    0.837
peak=    3.903 closest distance to " CA  ALA A 158 " =    1.220
peak=    3.896 closest distance to " O   HOH Z 316 " =    3.068
peak=    3.890 closest distance to " CD  ARG A  66 " =    2.275
peak=    3.884 closest distance to " CB  SER A 210 " =    0.760
peak=    3.872 closest distance to " O   HOH Z 158 " =    3.106
peak=    3.870 closest distance to " O   HOH Z 133 " =    2.618
peak=    3.864 closest distance to " O   HOH Z 371 " =    1.930
peak=    3.863 closest distance to " O   HOH Z 126 " =    1.877
peak=    3.854 closest distance to " CB  GLU A 128 " =    0.910
peak=    3.847 closest distance to " O   HOH Z   1 " =    1.991
peak=    3.846 closest distance to " CB  GLU A  46 " =    0.977
peak=    3.846 closest distance to " O   HOH Z 272 " =    1.807
peak=    3.843 closest distance to " O   HOH Z 368 " =    3.683
peak=    3.842 closest distance to " O   HOH Z 353 " =    2.629
peak=    3.839 closest distance to " CB  PRO A  90 " =    1.113
peak=    3.836 closest distance to " O   HOH Z  57 " =    2.193
peak=    3.831 closest distance to " O   HOH Z  53 " =    2.535
peak=    3.829 closest distance to " NH1AARG A 145 " =    1.295
peak=    3.815 closest distance to " CB  ASP A 124 " =    0.802
peak=    3.805 closest distance to " CB  VAL A 202 " =    1.643
peak=    3.805 closest distance to " CD  ARG A 269 " =    0.945
peak=    3.803 closest distance to " NZ  LYS A 117 " =    3.160
peak=    3.798 closest distance to " CA  THR A 264 " =    0.877
peak=    3.783 closest distance to " O   HOH Z 214 " =    2.195
peak=    3.782 closest distance to " OD1 ASN A  69 " =    2.589
peak=    3.760 closest distance to " CA  SER A  87 " =    1.001
peak=    3.753 closest distance to " O   ASN A  74 " =    1.426
peak=    3.748 closest distance to " O   HOH Z 394 " =    4.052
peak=    3.746 closest distance to " O   HOH Z 285 " =    2.247
peak=    3.742 closest distance to " O   HOH Z 290 " =    1.014
peak=    3.740 closest distance to " CD1 LEU A 300 " =    1.132
peak=    3.723 closest distance to " O   HOH Z 250 " =    1.411
peak=    3.710 closest distance to " CA  ARG A  36 " =    1.047
peak=    3.707 closest distance to " CB  SER A 216 " =    0.912
peak=    3.698 closest distance to " CB  MET A  40 " =    0.801
peak=    3.697 closest distance to " O   HOH Z  21 " =    1.767
peak=    3.695 closest distance to " O   HOH Z 422 " =    2.725
peak=    3.695 closest distance to " O   HOH Z 411 " =    3.820
peak=    3.689 closest distance to " CB  GLU A 277 " =    3.702
peak=    3.689 closest distance to " O   HOH Z  61 " =    1.664
peak=    3.689 closest distance to " O   HOH Z 313 " =    2.049
peak=    3.676 closest distance to " O   HOH Z 405 " =    1.250
peak=    3.675 closest distance to " CB  SER A 212 " =    1.164
peak=    3.674 closest distance to " O   HOH Z 286 " =    2.388
peak=    3.672 closest distance to " CB  ASN A 110 " =    1.102
peak=    3.671 closest distance to " O   HOH Z 346 " =    1.661
peak=    3.669 closest distance to " O   HOH Z  10 " =    1.731
peak=    3.664 closest distance to " CB  TYR A 116 " =    0.841
peak=    3.663 closest distance to " O   HOH Z 261 " =    1.854
peak=    3.657 closest distance to " NE2 HIS A 207 " =    1.163
peak=    3.654 closest distance to " O   HOH Z  40 " =    1.954
peak=    3.649 closest distance to " O   HOH Z 421 " =    2.182
peak=    3.649 closest distance to " CA  ASN A 215 " =    1.124
peak=    3.648 closest distance to " CA  ALA A  51 " =    0.985
peak=    3.640 closest distance to " CA  ALA A 160 " =    0.957
peak=    3.620 closest distance to " CG2 THR A 221 " =    1.033
peak=    3.618 closest distance to " CB  ALA A 114 " =    0.759
peak=    3.616 closest distance to " N   PHE A 130 " =    1.201
peak=    3.612 closest distance to " O   TYR A 116 " =    1.332
peak=    3.598 closest distance to " O   HOH Z 167 " =    1.783
peak=    3.597 closest distance to " OG BSER A 164 " =    2.369
peak=    3.596 closest distance to " O   HOH Z 126 " =    1.526
peak=    3.593 closest distance to " N   ASN A 127 " =    1.347
peak=    3.589 closest distance to " CB  TYR A 169 " =    0.828
peak=    3.586 closest distance to " O   HOH Z 265 " =    2.173
peak=    3.582 closest distance to " CB  LYS A 117 " =    1.229
peak=    3.575 closest distance to " O   HOH Z 371 " =    2.930
peak=    3.574 closest distance to " CB  GLU A 152 " =    1.183
peak=    3.551 closest distance to " O   HOH Z 386 " =    3.045
peak=    3.547 closest distance to " CB  GLN A  88 " =    1.232
peak=    3.546 closest distance to " O   HOH Z 345 " =    1.760
peak=    3.544 closest distance to " CA  ALA A 154 " =    1.073
peak=    3.538 closest distance to " CE1 TYR A 186 " =    1.369
peak=    3.536 closest distance to " CA  ARG A 102 " =    1.138
peak=    3.526 closest distance to " O   THR A 251 " =    1.116
peak=    3.526 closest distance to " O   HOH Z 327 " =    1.657
peak=    3.519 closest distance to " O   HOH Z 329 " =    4.154
peak=    3.508 closest distance to " O  BHOH Z 338 " =    2.386
peak=    3.506 closest distance to " O   THR A 220 " =    1.256
peak=    3.501 closest distance to " O   HOH Z 128 " =    2.303
peak=    3.501 closest distance to " CD BLYS A 290 " =    1.023
peak=    3.499 closest distance to " CA  TYR A 116 " =    1.337
peak=    3.497 closest distance to " CZ  PHE A  38 " =    1.213
peak=    3.495 closest distance to " O   HOH Z   9 " =    1.295
peak=    3.491 closest distance to " CB  THR A  31 " =    1.562
peak=    3.489 closest distance to " O   HOH Z 209 " =    2.242
peak=    3.476 closest distance to " CD1 LEU A  96 " =    0.767
peak=    3.475 closest distance to " O   HOH Z 172 " =    2.955
peak=    3.465 closest distance to " O   HOH Z 132 " =    2.522
peak=    3.461 closest distance to " CA  VAL A 125 " =    1.118
peak=    3.460 closest distance to " O   HOH Z 325 " =    2.423
peak=    3.455 closest distance to " CB  SER A   3 " =    1.345
peak=    3.455 closest distance to " O   SER A  87 " =    2.142
peak=    3.454 closest distance to " O   HOH Z 359 " =    1.480
peak=    3.453 closest distance to " CG2 ILE A 120 " =    1.308
peak=    3.452 closest distance to " CA  ASP A 124 " =    0.740
peak=    3.451 closest distance to " O   HOH Z 116 " =    3.102
peak=    3.450 closest distance to " O   HOH Z 294 " =    1.567
peak=    3.448 closest distance to " CD2 LEU A 297 " =    0.897
peak=    3.445 closest distance to " O   HOH Z 280 " =    3.053
peak=    3.443 closest distance to " O   HOH Z  88 " =    3.918
peak=    3.441 closest distance to " O   HOH Z 389 " =    1.881
peak=    3.433 closest distance to " CA  ALA A 233 " =    1.227
peak=    3.431 closest distance to " CA  ASN A 127 " =    1.095
peak=    3.429 closest distance to " CB  ASN A 187 " =    1.248
peak=    3.426 closest distance to " CB  ASP A 140 " =    1.012
peak=    3.419 closest distance to " N   ASN A  39 " =    1.317
peak=    3.415 closest distance to " CD  LYS A 166 " =    1.279
peak=    3.413 closest distance to " CG  GLU A  37 " =    0.887
peak=    3.411 closest distance to " O   HOH Z 391 " =    2.913
peak=    3.411 closest distance to " O   HOH Z 368 " =    2.073
peak=    3.410 closest distance to " O   HOH Z  43 " =    1.844
peak=    3.404 closest distance to " O   HOH Z 258 " =    2.009
peak=    3.404 closest distance to " O   HOH Z   3 " =    2.058
peak=    3.404 closest distance to " CB  ARG A 138 " =    0.999
peak=    3.402 closest distance to " O   HOH Z  88 " =    3.211
peak=    3.395 closest distance to " O   HOH Z 426 " =    1.999
peak=    3.394 closest distance to " CA  THR A 221 " =    1.035
peak=    3.391 closest distance to " O   HOH Z 285 " =    2.021
peak=    3.389 closest distance to " O   HOH Z 185 " =    1.927
peak=    3.379 closest distance to " NH2BARG A 145 " =    2.112
peak=    3.368 closest distance to " CB  MET A  47 " =    1.151
peak=    3.357 closest distance to " O   HOH Z 380 " =    1.668
peak=    3.351 closest distance to " CA  PRO A 280 " =    1.252
peak=    3.345 closest distance to " OD2 ASP A 286 " =    3.269
peak=    3.344 closest distance to " CA  GLU A  46 " =    0.932
peak=    3.343 closest distance to " O   HOH Z 365 " =    2.878
peak=    3.339 closest distance to " CD1AILE A 234 " =    0.934
peak=    3.334 closest distance to " OG BSER A 134 " =    2.855
peak=    3.332 closest distance to " CG1 ILE A  33 " =    1.259
peak=    3.327 closest distance to " CA  MET A 105 " =    1.001
peak=    3.324 closest distance to " CG2AVAL A  72 " =    1.594
peak=    3.323 closest distance to " O   HOH Z 171 " =    4.175
peak=    3.323 closest distance to " CB  VAL A 265 " =    1.961
peak=    3.321 closest distance to " CB  ASN A 215 " =    1.155
peak=    3.321 closest distance to " CB  TRP A 179 " =    1.454
peak=    3.318 closest distance to " CA  ASN A 217 " =    1.241
peak=    3.312 closest distance to " O   HOH Z   1 " =    1.639
peak=    3.310 closest distance to " CD  LYS A  76 " =    2.078
peak=    3.310 closest distance to " O   HOH Z 291 " =    1.511
peak=    3.307 closest distance to " CB  SER A 273 " =    0.883
peak=    3.307 closest distance to " CA  ALA A 100 " =    1.029
peak=    3.306 closest distance to " O   HOH Z 273 " =    2.839
peak=    3.305 closest distance to " CA  ILE A 263 " =    1.112
peak=    3.303 closest distance to " CB  ILE A 120 " =    1.312
peak=    3.303 closest distance to " O   HOH Z 310 " =    2.201
peak=    3.299 closest distance to " CB  GLN A  89 " =    1.344
peak=    3.298 closest distance to " CG1 ILE A 151 " =    1.074
peak=    3.292 closest distance to " C   ILE A 106 " =    1.932
peak=    3.290 closest distance to " O   HOH Z 437 " =    1.191
peak=    3.286 closest distance to " CA  ALA A 160 " =    1.300
peak=    3.283 closest distance to " CG2 VAL A 197 " =    1.091
peak=    3.282 closest distance to " NH1 ARG A 138 " =    1.091
peak=    3.279 closest distance to " CB  VAL A 268 " =    0.821
peak=    3.275 closest distance to " O   HOH Z  40 " =    2.090
peak=    3.270 closest distance to " O   HOH Z 402 " =    1.369
peak=    3.266 closest distance to " CB  ALA A   1 " =    4.704
peak=    3.262 closest distance to " CG  PHE A 204 " =    0.856
peak=    3.262 closest distance to " O   HOH Z 425 " =    1.994
peak=    3.261 closest distance to " O   HOH Z 193 " =    2.070
peak=    3.260 closest distance to " CG2 ILE A 239 " =    0.739
peak=    3.255 closest distance to " NH2AARG A 275 " =    3.662
peak=    3.253 closest distance to " NE2 GLN A  73 " =    3.929
peak=    3.253 closest distance to " O   HOH Z 425 " =    1.274
peak=    3.253 closest distance to " CB  LEU A  83 " =    0.705
peak=    3.248 closest distance to " CG  ARG A 138 " =    1.198
peak=    3.246 closest distance to " CG1 VAL A 189 " =    1.971
peak=    3.242 closest distance to " O   HOH Z 148 " =    3.483
peak=    3.241 closest distance to " CG1 VAL A 153 " =    0.969
peak=    3.241 closest distance to " O   HOH Z  61 " =    1.508
peak=    3.240 closest distance to " O   ASN A 209 " =    1.209
peak=    3.238 closest distance to " CE  LYS A  48 " =    1.182
peak=    3.233 closest distance to " O   HOH Z 116 " =    1.813
peak=    3.231 closest distance to " CG AARG A 275 " =    1.164
peak=    3.231 closest distance to " O   HOH Z 352 " =    1.855
peak=    3.230 closest distance to " CA  ALA A 299 " =    0.943
peak=    3.230 closest distance to " CG  ARG A 159 " =    0.879
peak=    3.228 closest distance to " CB  GLN A 103 " =    0.857
peak=    3.224 closest distance to " CA  LYS A 117 " =    1.177
peak=    3.221 closest distance to " O   THR A 182 " =    1.425
peak=    3.221 closest distance to " CB  SER A  62 " =    1.038
peak=    3.220 closest distance to " O   HOH Z 345 " =    3.437
peak=    3.219 closest distance to " O   HOH Z 369 " =    1.679
peak=    3.215 closest distance to " N   ARG A 156 " =    1.353
peak=    3.214 closest distance to " N   GLN A 278 " =    1.374
peak=    3.213 closest distance to " CA  ILE A 106 " =    0.860
peak=    3.211 closest distance to " OG  SER A 135 " =    1.238
peak=    3.208 closest distance to " CG  MET A 113 " =    1.140
peak=    3.206 closest distance to " O   HOH Z 368 " =    4.193
peak=    3.206 closest distance to " O   HOH Z   9 " =    3.306
peak=    3.204 closest distance to " N   ASP A 162 " =    1.181
peak=    3.202 closest distance to " CG  GLN A 144 " =    0.849
peak=    3.201 closest distance to " O   HOH Z 305 " =    3.657
peak=    3.201 closest distance to " O   HOH Z 124 " =    2.069
peak=    3.199 closest distance to " O   HOH Z 409 " =    2.465
peak=    3.199 closest distance to " O   HOH Z 213 " =    2.833
peak=    3.195 closest distance to " CB  ALA A 291 " =    1.203
peak=    3.191 closest distance to " CA  ILE A 234 " =    0.993
peak=    3.188 closest distance to " CB  ASN A 173 " =    1.106
peak=    3.188 closest distance to " O   HOH Z 193 " =    1.686
peak=    3.187 closest distance to " O   HOH Z 218 " =    4.578
peak=    3.186 closest distance to " O   HOH Z 340 " =    2.126
peak=    3.185 closest distance to " O   HOH Z 373 " =    1.522
peak=    3.184 closest distance to " O   HOH Z 336 " =    1.806
peak=    3.183 closest distance to " CB  ALA A 248 " =    0.957
peak=    3.181 closest distance to " CG1 ILE A 120 " =    1.058
peak=    3.180 closest distance to " O   HOH Z 344 " =    3.202
peak=    3.177 closest distance to " NZ  LYS A  48 " =    1.198
peak=    3.176 closest distance to " CG2 ILE A  20 " =    1.489
peak=    3.171 closest distance to " O   HOH Z  59 " =    1.662
peak=    3.167 closest distance to " CA  SER A  95 " =    0.984
peak=    3.166 closest distance to " CB  ARG A 139 " =    0.991
peak=    3.162 closest distance to " CG  GLN A  89 " =    1.506
peak=    3.161 closest distance to " O   HOH Z 234 " =    2.220
peak=    3.160 closest distance to " O   HOH Z 227 " =    1.864
peak=    3.160 closest distance to " CA  ARG A 156 " =    1.039
peak=    3.158 closest distance to " O   HOH Z 245 " =    1.263
peak=    3.145 closest distance to " CB  PHE A 204 " =    0.797
peak=    3.140 closest distance to " OG  SER A  62 " =    2.952
peak=    3.140 closest distance to " O   HOH Z 299 " =    4.435
peak=    3.136 closest distance to " CG1 ILE A  49 " =    1.539
peak=    3.132 closest distance to " OG  SER A  22 " =    2.821
peak=    3.130 closest distance to " CB  LEU A  96 " =    1.318
peak=    3.129 closest distance to " O   HOH Z 147 " =    1.789
peak=    3.128 closest distance to " O   HOH Z 248 " =    1.600
peak=    3.127 closest distance to " CD1 ILE A 263 " =    1.289
peak=    3.126 closest distance to " CG  GLN A  55 " =    2.313
peak=    3.123 closest distance to " N   VAL A 296 " =    1.735
peak=    3.118 closest distance to " O   HOH Z 233 " =    1.616
peak=    3.116 closest distance to " CD  ARG A 195 " =    3.425
peak=    3.116 closest distance to " CB  ALA A 114 " =    1.002
peak=    3.113 closest distance to " O   HOH Z 153 " =    3.847
peak=    3.107 closest distance to " CB  HIS A 108 " =    0.785
peak=    3.105 closest distance to " O   HOH Z 423 " =    2.540
peak=    3.103 closest distance to " CG  MET A 185 " =    1.189
peak=    3.103 closest distance to " CB  ALA A 227 " =    1.100
peak=    3.103 closest distance to " OE2 GLU A  53 " =    1.941
peak=    3.103 closest distance to " NH1BARG A 145 " =    1.053
peak=    3.098 closest distance to " CB  PRO A 243 " =    1.471
peak=    3.088 closest distance to " CB  ALA A 180 " =    1.224
peak=    3.087 closest distance to " O   HOH Z 251 " =    1.682
peak=    3.086 closest distance to " CB  ALA A 291 " =    0.805
peak=    3.083 closest distance to " CA  LYS A 290 " =    1.233
peak=    3.079 closest distance to " CG  GLU A 277 " =    4.391
peak=    3.079 closest distance to " CG2 ILE A 151 " =    0.922
peak=    3.078 closest distance to " O   HOH Z 282 " =    1.916
peak=    3.075 closest distance to " CG BARG A 102 " =    1.844
peak=    3.075 closest distance to " OE2 GLU A  53 " =    1.391
peak=    3.069 closest distance to " O   HOH Z 188 " =    1.896
peak=    3.054 closest distance to " O   HOH Z 188 " =    2.242
peak=    3.049 closest distance to " CG2BVAL A  41 " =    0.923
peak=    3.014 closest distance to " CA  GLY A  35 " =    1.026

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.741 - 5.680
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 209
   mapped sites are within: 0.741 - 5.680

peak=   -4.645 closest distance to " O   HOH Z 377 " =    2.061
peak=   -4.587 closest distance to " CD  ARG A  14 " =    3.481
peak=   -4.403 closest distance to " CD  ARG A 156 " =    2.116
peak=   -4.402 closest distance to " OG BSER A 134 " =    1.299
peak=   -4.395 closest distance to " O   HOH Z 231 " =    2.276
peak=   -4.244 closest distance to " CB  PRO A 243 " =    2.686
peak=   -4.228 closest distance to " O   PRO A 198 " =    1.217
peak=   -4.165 closest distance to " CG2 ILE A  49 " =    2.743
peak=   -4.071 closest distance to " CD2 TYR A 293 " =    1.900
peak=   -4.036 closest distance to " O   HOH Z 266 " =    5.502
peak=   -4.025 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -4.023 closest distance to " O   HOH Z 351 " =    1.481
peak=   -3.976 closest distance to " N   ALA A  43 " =    2.635
peak=   -3.947 closest distance to " CB  ALA A  43 " =    2.623
peak=   -3.936 closest distance to " ND2 ASN A 249 " =    2.248
peak=   -3.926 closest distance to " C   HIS A 108 " =    1.147
peak=   -3.916 closest distance to " CZ3 TRP A 179 " =    1.208
peak=   -3.912 closest distance to " O   VAL A  67 " =    2.639
peak=   -3.908 closest distance to " CD  GLN A  58 " =    1.014
peak=   -3.881 closest distance to " CG1 VAL A 112 " =    3.040
peak=   -3.856 closest distance to " O   HOH Z  73 " =    2.156
peak=   -3.843 closest distance to " CB  PHE A 192 " =    2.061
peak=   -3.841 closest distance to " CE BMET A  47 " =    1.352
peak=   -3.817 closest distance to " O   HOH Z 198 " =    1.896
peak=   -3.802 closest distance to " O   HOH Z 185 " =    2.292
peak=   -3.801 closest distance to " CE  MET A 105 " =    2.424
peak=   -3.789 closest distance to " O   ALA A  10 " =    1.668
peak=   -3.785 closest distance to " CG  GLN A 223 " =    2.113
peak=   -3.779 closest distance to " CE2 TYR A  30 " =    2.720
peak=   -3.755 closest distance to " N   THR A 157 " =    1.627
peak=   -3.739 closest distance to " O   HOH Z 389 " =    2.080
peak=   -3.734 closest distance to " NH2AARG A 275 " =    5.478
peak=   -3.728 closest distance to " O   PRO A 163 " =    2.043
peak=   -3.727 closest distance to " O   HOH Z  38 " =    1.570
peak=   -3.722 closest distance to " O   HOH Z 211 " =    1.278
peak=   -3.715 closest distance to " O   HOH Z 394 " =    1.532
peak=   -3.707 closest distance to " CB  ASN A  39 " =    2.255
peak=   -3.695 closest distance to " O   HOH Z  52 " =    1.415
peak=   -3.695 closest distance to " CD2 PHE A  61 " =    2.100
peak=   -3.672 closest distance to " CD1 PHE A  59 " =    1.997
peak=   -3.666 closest distance to " ND2 ASN A  45 " =    1.979
peak=   -3.662 closest distance to " OXT GLY A 302 " =    3.053
peak=   -3.659 closest distance to " O   HOH Z 290 " =    1.210
peak=   -3.653 closest distance to " CG2 THR A 178 " =    2.341
peak=   -3.647 closest distance to " O   HOH Z 407 " =    3.176
peak=   -3.640 closest distance to " OH  TYR A 172 " =    1.825
peak=   -3.635 closest distance to " O   TYR A 247 " =    2.814
peak=   -3.634 closest distance to " CB  ALA A 291 " =    2.292
peak=   -3.621 closest distance to " CA  GLY A 241 " =    2.296
peak=   -3.608 closest distance to " ND2 ASN A  45 " =    1.164
peak=   -3.607 closest distance to " O   HOH Z 357 " =    2.070
peak=   -3.596 closest distance to " CG2 ILE A  20 " =    3.010
peak=   -3.596 closest distance to " O   HOH Z 102 " =    1.573
peak=   -3.592 closest distance to " CG1 VAL A 250 " =    2.650
peak=   -3.586 closest distance to " CE3 TRP A 150 " =    2.225
peak=   -3.576 closest distance to " O   HOH Z 372 " =    2.489
peak=   -3.570 closest distance to " ND2 ASN A 187 " =    1.513
peak=   -3.560 closest distance to " OE1 GLN A  88 " =    1.087
peak=   -3.546 closest distance to " O   HOH Z   9 " =    1.645
peak=   -3.544 closest distance to " O   PHE A 218 " =    1.469
peak=   -3.539 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.532 closest distance to " O   HOH Z 131 " =    4.068
peak=   -3.509 closest distance to " O   HOH Z  10 " =    1.496
peak=   -3.507 closest distance to " O   HOH Z 111 " =    1.741
peak=   -3.505 closest distance to " O   HOH Z  60 " =    2.434
peak=   -3.504 closest distance to " CA  ASP A  27 " =    2.481
peak=   -3.503 closest distance to " OD1 ASP A 171 " =    1.629
peak=   -3.499 closest distance to " O   HOH Z 174 " =    2.627
peak=   -3.499 closest distance to " O   GLU A 152 " =    1.385
peak=   -3.498 closest distance to " CG  MET A 105 " =    0.978
peak=   -3.492 closest distance to " OG  SER A  97 " =    2.211
peak=   -3.483 closest distance to " CA  GLY A 241 " =    3.358
peak=   -3.479 closest distance to " CD1 LEU A 255 " =    2.926
peak=   -3.470 closest distance to " CD1 LEU A 101 " =    2.311
peak=   -3.464 closest distance to " N   SER A 212 " =    2.010
peak=   -3.462 closest distance to " O   TYR A 186 " =    1.656
peak=   -3.461 closest distance to " O   HOH Z  51 " =    1.666
peak=   -3.460 closest distance to " O   HOH Z 318 " =    2.032
peak=   -3.451 closest distance to " OD1 ASN A 148 " =    1.456
peak=   -3.449 closest distance to " CB  ALA A 100 " =    2.259
peak=   -3.447 closest distance to " O   HOH Z 313 " =    1.850
peak=   -3.445 closest distance to " O   HOH Z 191 " =    5.680
peak=   -3.437 closest distance to " CB  ASP A 286 " =    2.189
peak=   -3.437 closest distance to " ND2 ASN A  60 " =    4.094
peak=   -3.429 closest distance to " CB  TRP A  85 " =    2.426
peak=   -3.427 closest distance to " CB  TYR A  15 " =    2.271
peak=   -3.427 closest distance to " CE2 PHE A 218 " =    2.413
peak=   -3.424 closest distance to " OD1 ASP A 191 " =    1.711
peak=   -3.423 closest distance to " CE2 TYR A 116 " =    3.192
peak=   -3.418 closest distance to " CG  ARG A 269 " =    2.551
peak=   -3.417 closest distance to " CB  ALA A 291 " =    1.997
peak=   -3.410 closest distance to " CG2 ILE A 263 " =    2.311
peak=   -3.406 closest distance to " O   GLY A  17 " =    1.165
peak=   -3.393 closest distance to " CB  GLN A  11 " =    1.689
peak=   -3.392 closest distance to " O   ARG A 145 " =    1.531
peak=   -3.390 closest distance to " CE2 PHE A  61 " =    2.665
peak=   -3.390 closest distance to " CB  ALA A 161 " =    2.570
peak=   -3.390 closest distance to " O   HOH Z 348 " =    2.236
peak=   -3.389 closest distance to " O   HOH Z 196 " =    2.133
peak=   -3.382 closest distance to " O   HOH Z 253 " =    3.924
peak=   -3.378 closest distance to " O   TRP A  70 " =    1.412
peak=   -3.371 closest distance to " N   THR A  52 " =    1.745
peak=   -3.369 closest distance to " O   HOH Z 166 " =    2.031
peak=   -3.361 closest distance to " O   HOH Z 281 " =    2.700
peak=   -3.360 closest distance to " O   VAL A 189 " =    1.689
peak=   -3.357 closest distance to " CB  ALA A   9 " =    2.439
peak=   -3.354 closest distance to " O   HOH Z 128 " =    2.666
peak=   -3.353 closest distance to " O   HOH Z 359 " =    3.224
peak=   -3.350 closest distance to " O   VAL A 189 " =    2.568
peak=   -3.347 closest distance to " CD2 TYR A 247 " =    2.456
peak=   -3.346 closest distance to " OD2 ASP A 191 " =    1.376
peak=   -3.345 closest distance to " CG  HIS A  86 " =    1.117
peak=   -3.344 closest distance to " ND2 ASN A  60 " =    1.409
peak=   -3.337 closest distance to " O   HOH Z 295 " =    1.621
peak=   -3.337 closest distance to " O   HOH Z  65 " =    1.330
peak=   -3.335 closest distance to " O   ILE A 106 " =    1.977
peak=   -3.333 closest distance to " O   HOH Z 103 " =    1.818
peak=   -3.331 closest distance to " CA  GLY A 203 " =    2.413
peak=   -3.330 closest distance to " O   HOH Z 298 " =    2.509
peak=   -3.330 closest distance to " O   HOH Z 189 " =    2.093
peak=   -3.328 closest distance to " CG1BVAL A  41 " =    2.809
peak=   -3.322 closest distance to " NE2 GLN A 278 " =    1.581
peak=   -3.315 closest distance to " O   HOH Z 252 " =    4.240
peak=   -3.313 closest distance to " O   HOH Z 114 " =    2.902
peak=   -3.303 closest distance to " O   HOH Z 412 " =    4.348
peak=   -3.297 closest distance to " N   SER A 276 " =    1.310
peak=   -3.294 closest distance to " CB  ALA A   7 " =    2.208
peak=   -3.293 closest distance to " CA  GLY A 133 " =    2.037
peak=   -3.286 closest distance to " O   HOH Z 275 " =    1.699
peak=   -3.284 closest distance to " O   HOH Z 429 " =    1.890
peak=   -3.276 closest distance to " O   SER A 135 " =    1.423
peak=   -3.274 closest distance to " CG  PRO A 198 " =    1.917
peak=   -3.272 closest distance to " CE3 TRP A 274 " =    2.314
peak=   -3.271 closest distance to " O   HOH Z 216 " =    1.361
peak=   -3.270 closest distance to " CB  ALA A 248 " =    2.406
peak=   -3.266 closest distance to " O   HOH Z 275 " =    1.514
peak=   -3.265 closest distance to " CG  PRO A 243 " =    1.768
peak=   -3.265 closest distance to " CD1 LEU A   5 " =    2.485
peak=   -3.263 closest distance to " CD  GLU A 236 " =    1.139
peak=   -3.260 closest distance to " CA  GLY A  57 " =    2.165
peak=   -3.260 closest distance to " CZ  PHE A  59 " =    1.642
peak=   -3.255 closest distance to " CD  ARG A  79 " =    1.145
peak=   -3.255 closest distance to " CA  GLY A  98 " =    1.912
peak=   -3.255 closest distance to " OG BSER A 134 " =    1.830
peak=   -3.255 closest distance to " N   ASP A 286 " =    2.350
peak=   -3.250 closest distance to " O   HOH Z 395 " =    5.188
peak=   -3.248 closest distance to " CD2 PHE A 225 " =    1.104
peak=   -3.247 closest distance to " O   HOH Z 140 " =    1.508
peak=   -3.247 closest distance to " O   HOH Z 298 " =    1.253
peak=   -3.244 closest distance to " O   HOH Z 368 " =    1.738
peak=   -3.244 closest distance to " O   GLN A 240 " =    2.400
peak=   -3.243 closest distance to " CG  PHE A 283 " =    2.667
peak=   -3.241 closest distance to " ND2 ASN A 285 " =    2.144
peak=   -3.241 closest distance to " CG1 VAL A 125 " =    1.839
peak=   -3.239 closest distance to " O   HOH Z  71 " =    2.262
peak=   -3.235 closest distance to " O   HOH Z 426 " =    1.600
peak=   -3.234 closest distance to " N   ASP A 171 " =    2.400
peak=   -3.233 closest distance to " CG  GLU A 277 " =    1.300
peak=   -3.233 closest distance to " CE1 TYR A 247 " =    2.757
peak=   -3.227 closest distance to " CZ  TYR A 169 " =    1.784
peak=   -3.225 closest distance to " CA  ASN A 127 " =    1.153
peak=   -3.224 closest distance to " NE2 GLN A 194 " =    1.857
peak=   -3.217 closest distance to " O   HOH Z 176 " =    0.822
peak=   -3.215 closest distance to " NH2BARG A 275 " =    1.907
peak=   -3.212 closest distance to " OG  SER A  87 " =    1.414
peak=   -3.210 closest distance to " O   HOH Z  22 " =    2.421
peak=   -3.202 closest distance to " O   ARG A  56 " =    1.837
peak=   -3.202 closest distance to " CD2 HIS A 207 " =    2.168
peak=   -3.195 closest distance to " O   HOH Z 134 " =    3.413
peak=   -3.191 closest distance to " O   ALA A 292 " =    2.126
peak=   -3.189 closest distance to " CB  PRO A  54 " =    2.535
peak=   -3.188 closest distance to " OD2 ASP A  50 " =    1.728
peak=   -3.186 closest distance to " CG  LEU A  83 " =    1.991
peak=   -3.186 closest distance to " CB  ALA A  10 " =    2.271
peak=   -3.178 closest distance to " C   PHE A  59 " =    1.261
peak=   -3.174 closest distance to " O   HOH Z  11 " =    1.778
peak=   -3.173 closest distance to " NH2 ARG A  79 " =    1.550
peak=   -3.167 closest distance to " CG2 VAL A 189 " =    2.027
peak=   -3.166 closest distance to " NH2 ARG A 219 " =    1.667
peak=   -3.164 closest distance to " C   LEU A 143 " =    1.192
peak=   -3.162 closest distance to " O   HOH Z 350 " =    1.846
peak=   -3.162 closest distance to " O   ALA A  51 " =    1.336
peak=   -3.160 closest distance to " O   HOH Z 108 " =    1.610
peak=   -3.156 closest distance to " OD1AASN A 224 " =    1.856
peak=   -3.153 closest distance to " O   HOH Z 278 " =    1.688
peak=   -3.146 closest distance to " CD1 LEU A 297 " =    2.675
peak=   -3.145 closest distance to " CB  ASP A 132 " =    2.412
peak=   -3.139 closest distance to " N   LYS A 166 " =    1.873
peak=   -3.138 closest distance to " O   SER A  22 " =    2.511
peak=   -3.132 closest distance to " O   ALA A  34 " =    2.440
peak=   -3.124 closest distance to " OH  TYR A 247 " =    2.157
peak=   -3.120 closest distance to " O   HOH Z  63 " =    1.898
peak=   -3.106 closest distance to " N   ALA A 248 " =    1.565
peak=   -3.102 closest distance to " C   LEU A 222 " =    0.741
peak=   -3.102 closest distance to " CB  ALA A 114 " =    2.603
peak=   -3.098 closest distance to " CA  GLY A 133 " =    2.267
peak=   -3.097 closest distance to " O   SER A 276 " =    1.763
peak=   -3.092 closest distance to " CD1 ILE A 199 " =    2.565
peak=   -3.088 closest distance to " CG  TRP A 266 " =    1.847
peak=   -3.087 closest distance to " O   HOH Z 166 " =    1.458
peak=   -3.085 closest distance to " O   HOH Z 353 " =    2.239
peak=   -3.083 closest distance to " CA  SER A 135 " =    1.274
peak=   -3.082 closest distance to " CD1 TRP A  70 " =    1.126
peak=   -3.073 closest distance to " O   PRO A 198 " =    1.372
peak=   -3.055 closest distance to " O   HOH Z 323 " =    1.506
peak=   -3.040 closest distance to " CD2 PHE A  59 " =    2.486
peak=   -3.020 closest distance to " CA  GLY A 241 " =    2.886
peak=   -3.017 closest distance to " CD  GLN A  77 " =    1.609
peak=   -3.016 closest distance to " CG1AVAL A  41 " =    2.817

================= 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    :  0.3878 0.3795   6.177027e+00   6.149673e+00
   1_bss:  0.3746 0.3706   6.161234e+00   6.130557e+00
   1_xyz:  0.2035 0.2336   5.620053e+00   5.720077e+00
   1_adp:  0.1832 0.2398   5.565357e+00   5.756713e+00
   1_occ:  0.1831 0.2397   5.564611e+00   5.756153e+00
   2_bss:  0.1795 0.2351   5.553792e+00   5.746183e+00
   2_xyz:  0.1380 0.1862   5.317848e+00   5.536692e+00
   2_adp:  0.1315 0.1770   5.271081e+00   5.485980e+00
   2_occ:  0.1313 0.1768   5.270313e+00   5.485626e+00
   3_bss:  0.1311 0.1763   5.267850e+00   5.482207e+00
   3_xyz:  0.1164 0.1616   5.174507e+00   5.410900e+00
   3_adp:  0.1138 0.1608   5.161025e+00   5.404334e+00
   3_occ:  0.1138 0.1608   5.161170e+00   5.404723e+00
   4_bss:  0.1137 0.1607   5.160879e+00   5.404602e+00
   4_xyz:  0.1129 0.1607   5.160653e+00   5.407985e+00
   4_adp:  0.1121 0.1612   5.159476e+00   5.411608e+00
   4_occ:  0.1120 0.1613   5.159699e+00   5.412110e+00
   5_bss:  0.1119 0.1612   5.159653e+00   5.412281e+00
   5_xyz:  0.1134 0.1620   5.169668e+00   5.418652e+00
   5_adp:  0.1133 0.1615   5.167056e+00   5.415071e+00
   5_occ:  0.1133 0.1615   5.167123e+00   5.415245e+00
   5_bss:  0.1132 0.1614   5.167214e+00   5.415296e+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:  0.325  57.202  -2.941  -0.640   4.063  -0.000   0.000   0.000
   1_xyz:  0.325  57.202  -2.941  -0.640   4.063  -0.000   0.000   0.000
   1_adp:  0.325  57.202  -2.941  -0.640   4.063  -0.000   0.000   0.000
   1_occ:  0.325  57.202  -2.941  -0.640   4.063  -0.000   0.000   0.000
   2_bss:  0.333  70.067  -2.855  -2.134   0.447  -0.000   0.000   0.000
   2_xyz:  0.333  70.067  -2.855  -2.134   0.447  -0.000   0.000   0.000
   2_adp:  0.333  70.067  -2.855  -2.134   0.447  -0.000   0.000   0.000
   2_occ:  0.333  70.067  -2.855  -2.134   0.447  -0.000   0.000   0.000
   3_bss:  0.335  70.067  -2.704  -2.423  -0.285  -0.000  -0.000  -0.000
   3_xyz:  0.335  70.067  -2.704  -2.423  -0.285  -0.000  -0.000  -0.000
   3_adp:  0.335  70.067  -2.704  -2.423  -0.285  -0.000  -0.000  -0.000
   3_occ:  0.335  70.067  -2.704  -2.423  -0.285  -0.000  -0.000  -0.000
   4_bss:  0.335  70.067  -2.475  -2.388  -0.404  -0.000  -0.000  -0.000
   4_xyz:  0.335  70.067  -2.475  -2.388  -0.404  -0.000  -0.000  -0.000
   4_adp:  0.335  70.067  -2.475  -2.388  -0.404  -0.000  -0.000  -0.000
   4_occ:  0.335  70.067  -2.475  -2.388  -0.404  -0.000  -0.000  -0.000
   5_bss:  0.322  62.763  -2.203  -2.193  -0.248  -0.000  -0.000  -0.000
   5_xyz:  0.322  62.763  -2.203  -2.193  -0.248  -0.000  -0.000  -0.000
   5_adp:  0.322  62.763  -2.203  -2.193  -0.248  -0.000  -0.000  -0.000
   5_occ:  0.322  62.763  -2.203  -2.193  -0.248  -0.000  -0.000  -0.000
   5_bss:  0.322  62.766  -2.022  -2.048  -0.113  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.521 0.6263  0.7975    41764.327
   1_bss:  40.368 0.6386  0.8199    38918.038
   1_xyz:  22.084 0.8421  1.0067    13271.691
   1_adp:  23.058 0.8316  0.9993    14137.872
   1_occ:  23.062 0.8315  0.9991    14117.119
   2_bss:  22.585 0.8367  0.9491    13826.770
   2_xyz:  17.326 0.8861  0.9793     8591.222
   2_adp:  16.156 0.8969  0.9788     7883.068
   2_occ:  16.150 0.8969  0.9786     7870.829
   3_bss:  16.077 0.8975  0.9692     7808.227
   3_xyz:  14.441 0.9112  0.9767     6639.161
   3_adp:  14.263 0.9129  0.9717     6522.660
   3_occ:  14.271 0.9128  0.9715     6526.727
   4_bss:  14.266 0.9129  0.9734     6527.804
   4_xyz:  14.288 0.9130  0.9725     6597.091
   4_adp:  14.355 0.9125  0.9649     6610.468
   4_occ:  14.364 0.9124  0.9649     6618.116
   5_bss:  14.370 0.9124  0.9718     6618.361
   5_xyz:  14.489 0.9114  0.9715     6719.114
   5_adp:  14.416 0.9120  0.9650     6672.975
   5_occ:  14.420 0.9120  0.9650     6675.929
   5_bss:  14.423 0.9120  0.9703     6677.880
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6535e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6535e-01
   1_xyz:   1.347  0.012  0.089 15.820  0.006  4.116   1.0412e-01
   1_adp:   1.347  0.012  0.089 15.820  0.006  4.116   1.0412e-01
   1_occ:   1.347  0.012  0.089 15.820  0.006  4.116   1.0412e-01
   2_bss:   1.347  0.012  0.089 15.820  0.006  4.116   1.0412e-01
   2_xyz:   1.018  0.007  0.074 14.879  0.004  4.124   6.0070e-02
   2_adp:   1.018  0.007  0.074 14.879  0.004  4.124   6.0070e-02
   2_occ:   1.018  0.007  0.074 14.879  0.004  4.124   6.0070e-02
   3_bss:   1.018  0.007  0.074 14.879  0.004  4.124   6.0070e-02
   3_xyz:   1.089  0.010  0.082 14.973  0.004  4.114   7.1571e-02
   3_adp:   1.089  0.010  0.082 14.973  0.004  4.114   7.1571e-02
   3_occ:   1.089  0.010  0.082 14.973  0.004  4.114   7.1571e-02
   4_bss:   1.089  0.010  0.082 14.973  0.004  4.114   7.1571e-02
   4_xyz:   1.014  0.009  0.078 14.728  0.004  4.116   6.3223e-02
   4_adp:   1.014  0.009  0.078 14.728  0.004  4.116   6.3223e-02
   4_occ:   1.014  0.009  0.078 14.728  0.004  4.116   6.3223e-02
   5_bss:   1.014  0.009  0.078 14.728  0.004  4.116   6.3223e-02
   5_xyz:   0.946  0.007  0.073 14.513  0.003  4.117   5.4745e-02
   5_adp:   0.946  0.007  0.073 14.513  0.003  4.117   5.4745e-02
   5_occ:   0.946  0.007  0.073 14.513  0.003  4.117   5.4745e-02
   5_bss:   0.946  0.007  0.073 14.513  0.003  4.117   5.4745e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.792   2.4224e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.792   2.4224e-01
   1_xyz:  10.334  0.067  0.268 82.710  0.055  2.191   1.7273e-01
   1_adp:  10.334  0.067  0.268 82.710  0.055  2.191   1.7273e-01
   1_occ:  10.334  0.067  0.268 82.710  0.055  2.191   1.7273e-01
   2_bss:  10.334  0.067  0.268 82.710  0.055  2.191   1.7273e-01
   2_xyz:   7.186  0.041  0.211 82.204  0.027  2.365   4.6131e-02
   2_adp:   7.186  0.041  0.211 82.204  0.027  2.365   4.6131e-02
   2_occ:   7.186  0.041  0.211 82.204  0.027  2.365   4.6131e-02
   3_bss:   7.186  0.041  0.211 82.204  0.027  2.365   4.6131e-02
   3_xyz:   6.966  0.051  0.286 84.280  0.030  2.330   5.4649e-02
   3_adp:   6.966  0.051  0.286 84.280  0.030  2.330   5.4649e-02
   3_occ:   6.966  0.051  0.286 84.280  0.030  2.330   5.4649e-02
   4_bss:   6.966  0.051  0.286 84.280  0.030  2.330   5.4649e-02
   4_xyz:   6.888  0.044  0.257 83.077  0.030  2.363   4.6207e-02
   4_adp:   6.888  0.044  0.257 83.077  0.030  2.363   4.6207e-02
   4_occ:   6.888  0.044  0.257 83.077  0.030  2.363   4.6207e-02
   5_bss:   6.888  0.044  0.257 83.077  0.030  2.363   4.6207e-02
   5_xyz:   7.039  0.043  0.225 83.818  0.030  2.400   3.2872e-02
   5_adp:   7.039  0.043  0.225 83.818  0.030  2.400   3.2872e-02
   5_occ:   7.039  0.043  0.225 83.818  0.030  2.400   3.2872e-02
   5_bss:   7.039  0.043  0.225 83.818  0.030  2.400   3.2872e-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:  86.35   0.76  17.61  72.24   0.76  13.12  86.35   2.46  42.10
   1_occ:  86.35   0.76  17.61  72.24   0.76  13.12  86.35   2.46  42.10
   2_bss:  86.35   0.76  17.61  72.24   0.76  13.12  86.35   2.46  42.10
   2_xyz:  86.35   0.76  17.61  72.24   0.76  13.12  86.35   2.46  42.10
   2_adp:  83.46   0.00  17.28  72.13   0.00  12.90  83.46   5.33  41.17
   2_occ:  83.46   0.00  17.28  72.13   0.00  12.90  83.46   5.33  41.17
   3_bss:  83.46   0.00  17.28  72.13   0.00  12.90  83.46   5.33  41.17
   3_xyz:  83.46   0.00  17.28  72.13   0.00  12.90  83.46   5.33  41.17
   3_adp:  83.73   0.34  17.31  76.85   0.34  12.86  83.73   5.45  41.52
   3_occ:  83.73   0.34  17.31  76.85   0.34  12.86  83.73   5.45  41.52
   4_bss:  83.73   0.34  17.31  76.85   0.34  12.86  83.73   5.45  41.52
   4_xyz:  83.73   0.34  17.31  76.85   0.34  12.86  83.73   5.45  41.52
   4_adp:  90.51   0.00  17.37  89.84   0.00  12.84  90.51   5.59  42.03
   4_occ:  90.51   0.00  17.37  89.84   0.00  12.84  90.51   5.59  42.03
   5_bss:  90.51   0.00  17.37  89.84   0.00  12.84  90.51   5.59  42.03
   5_xyz:  90.51   0.00  17.37  89.84   0.00  12.84  90.51   5.59  42.03
   5_adp:  90.85   0.00  17.14  90.35   0.00  12.64  90.85   5.36  41.67
   5_occ:  90.85   0.00  17.14  90.35   0.00  12.64  90.85   5.36  41.67
   5_bss:  90.85   0.00  17.14  90.35   0.00  12.64  90.85   5.36  41.67
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.402    0.020    0.443
   1_adp:    1.402    0.020    0.443
   1_occ:    1.402    0.020    0.443
   2_bss:    1.402    0.020    0.443
   2_xyz:    1.096    0.039    0.472
   2_adp:    1.096    0.039    0.472
   2_occ:    1.096    0.039    0.472
   3_bss:    1.096    0.039    0.472
   3_xyz:    1.211    0.062    0.514
   3_adp:    1.211    0.062    0.514
   3_occ:    1.211    0.062    0.514
   4_bss:    1.211    0.062    0.514
   4_xyz:    1.510    0.073    0.525
   4_adp:    1.510    0.073    0.525
   4_occ:    1.510    0.073    0.525
   5_bss:    1.510    0.073    0.525
   5_xyz:    1.578    0.069    0.532
   5_adp:    1.578    0.069    0.532
   5_occ:    1.578    0.069    0.532
   5_bss:    1.578    0.069    0.532
------------------------------------------------------------------------

CPU time actual refinement: 277.07


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_768/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_768/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_768/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_768/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_768/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 276.94 
  Macro-tasks:
    bulk solvent and scale       = 30.27  
    individual site refinement   = 109.90 
    weights calculation          = 24.26  
    collect and process          = 5.51   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 170.03 
  Micro-tasks:
    mask                            = 1.00   
    f_calc                          = 90.13  
    alpha_beta                      = 6.82   
    target                          = 0.96   
    gradients_wrt_atomic_parameters = 97.40  
    fmodel                         = 5.59   
    r_factors                      = 0.18   
    phase_errors                   = 9.10   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 211.38 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.948 micro seconds
Total CPU time: 4.81 minutes
from_scatterers_fft:    673 calls, 89.93 s
gradients_fft:          618 calls, 86.15 s

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

# Date 2008-01-16 Time 05:36:10 PST -0800 (1200490570.50 s)
Start R-work = 0.3878, R-free = 0.3795 (no bulk solvent and anisotropic scale)
Final R-work = 0.1345, R-free = 0.1788 (no bulk solvent and anisotropic scale)

Start R-work = 0.3746, R-free = 0.3706
Final R-work = 0.1132, R-free = 0.1614