# Date 2008-01-16 Time 04:32:07 PST -0800 (1200486727.25 s)
#phil __OFF__

Command line arguments: "../355.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25961
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 355

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 48.1033, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0137 1.97064
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941915

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0137
                             d_min =   1.9706

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0137 1.97064
Completeness in resolution range: 0.944777
Completeness with d_max=infinity: 0.941915

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0141 -  4.2172 [2180/2209]  1960   220  10.1%
  bin  2:  4.2172 -  3.3597 [2089/2112]  1881   208  10.0%
  bin  3:  3.3597 -  2.9386 [2063/2088]  1855   208  10.1%
  bin  4:  2.9386 -  2.6716 [2030/2047]  1834   196   9.7%
  bin  5:  2.6716 -  2.4810 [2032/2075]  1820   212  10.4%
  bin  6:  2.4810 -  2.3353 [2026/2054]  1834   192   9.5%
  bin  7:  2.3353 -  2.2187 [2008/2044]  1802   206  10.3%
  bin  8:  2.2187 -  2.1224 [1991/2033]  1800   191   9.6%
  bin  9:  2.1224 -  2.0409 [1983/2039]  1779   204  10.3%
  bin 10:  2.0409 -  1.9706 [1187/2033]  1065   122  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_355/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.48 -     2.17: 19
        2.17 -     2.85: 1116
        2.85 -     3.53: 4430
        3.53 -     4.22: 9272
        4.22 -     4.90: 13527
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.484 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.531 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.766 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.804 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28359 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_355/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_355/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 48.10325 85.5261 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: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4577   r_free= 0.4459   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.271166                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.7039 0.99   1414  159 0.3725 0.4086      6.5667      6.6193|
|  2:  4.7039 -  3.7528 0.99   1360  151 0.4041 0.3974      6.8201      6.8055|
|  3:  3.7528 -  3.2841 0.99   1332  147 0.4267 0.4066      6.6621      6.6804|
|  4:  3.2841 -  2.9864 0.99   1326  139 0.4380 0.3925      6.5034      6.4027|
|  5:  2.9864 -  2.7738 0.99   1316  151 0.4910 0.4402      6.3614      6.3428|
|  6:  2.7738 -  2.6111 0.99   1305  148 0.4925 0.4554      6.2705      6.1208|
|  7:  2.6111 -  2.4810 0.98   1297  149 0.4967 0.4447      6.2473       6.156|
|  8:  2.4810 -  2.3734 0.98   1319  136 0.4946 0.5204      6.1612      6.2206|
|  9:  2.3734 -  2.2824 0.99   1288  144 0.5176 0.4888      6.1181      6.1115|
| 10:  2.2824 -  2.2039 0.98   1300  145 0.4940 0.5246      6.0981      6.1263|
| 11:  2.2039 -  2.1352 0.97   1268  145 0.4955 0.4907      6.0153      6.0071|
| 12:  2.1352 -  2.0743 0.98   1281  147 0.5015 0.4760      5.9423      5.9816|
| 13:  2.0743 -  2.0198 0.93   1225  129 0.4890 0.4989      5.8646      5.8498|
| 14:  2.0198 -  1.9706 0.46    599   69 0.4978 0.5057      5.8216      5.6815|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0141 -  4.7039  1414   159  0.65  38.49   0.83     0.68      85353.28|
|  2:  4.7039 -  3.7528  1360   151  0.70  35.11   0.91     0.79     104300.58|
|  3:  3.7528 -  3.2841  1332   147  0.63  41.04   0.92     0.82     102320.80|
|  4:  3.2841 -  2.9864  1326   139  0.60  44.21   0.92     0.79      81662.88|
|  5:  2.9864 -  2.7738  1316   151  0.52  50.18   0.88     0.73      66544.04|
|  6:  2.7738 -  2.6111  1305   148  0.50  52.01   0.90     0.68      56932.17|
|  7:  2.6111 -  2.4810  1297   149  0.47  54.47   0.91     0.63      55734.33|
|  8:  2.4810 -  2.3734  1319   136  0.41  58.83   0.91     0.58      54046.27|
|  9:  2.3734 -  2.2824  1288   144  0.39  60.47   0.92     0.58      51579.33|
| 10:  2.2824 -  2.2039  1300   145  0.41  59.32   0.95     0.58      45660.77|
| 11:  2.2039 -  2.1352  1268   145  0.43  58.04   0.94     0.64      41151.57|
| 12:  2.1352 -  2.0743  1281   147  0.41  59.19   0.96     0.64      37760.71|
| 13:  2.0743 -  2.0198  1225   129  0.39  60.74   0.96     0.59      33601.97|
| 14:  2.0198 -  1.9706   599    69  0.32  65.68   0.95     0.46      29748.49|
|alpha:            min =        0.46 max =            0.82 mean =         0.67|
|beta:             min =    29748.49 max =       104300.58 mean =     62273.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.96 mean =        51.94|
|phase err.(test): min =        0.00 max =           89.98 mean =        51.80|
|-----------------------------------------------------------------------------|

============================== 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 = 8.335035              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.529   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.738957              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.302   (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 |  1.484 -  1.826:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.826 -  2.167:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.167 -  2.509:       34 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.509 -  2.851:     1082 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.851 -  3.192:     1952 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.192 -  3.534:     2478 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.534 -  3.875:     4649 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.875 -  4.217:     4623 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.217 -  4.558:     6116 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.558 -  4.900:     7411 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.484 |       0.486 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    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: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4577   r_free= 0.4459   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.271166                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4489   r_free= 0.4340   ksol= 0.30   Bsol= 20.00   scale= 0.931   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,4.89,-1.13,0.00,-0.00,-0.00); trace/3= 0.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.261403                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.508828              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.121   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.988404              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.126   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4489      final r-factor (work) = 0.3664          |
| start r-factor (free) = 0.4340      final r-factor (free) = 0.3900          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6946 = 7.51 * 0.50 * 6.2623 + 1.00 * 0.1831                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.2335 = 7.51 * 0.50 * 6.1602 + 1.00 * 0.1055                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3664      final r-factor (work) = 0.3357          |
| start r-factor (free) = 0.3900      final r-factor (free) = 0.3963          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0948 = 0.99 * 1.00 * 6.1602 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0347 = 0.99 * 1.00 * 6.0875 + 1.00 * 0.0178                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.41   19.05    None  None   None       |
|    all(noH): 2823   0      0.00    92.41   19.05    None  None   None       |
|    Sol.    : 438    0      0.00    92.41   36.00    None  None   None       |
|    Mac.    : 2385   0      0.00    80.05   15.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.241:  824   |   5:    46.203 -  55.444:   90        |
|      1:     9.241 -  18.481:  871   |   6:    55.444 -  64.685:   63        |
|      2:    18.481 -  27.722:  509   |   7:    64.685 -  73.925:   21        |
|      3:    27.722 -  36.963:  276   |   8:    73.925 -  83.166:    8        |
|      4:    36.963 -  46.203:  155   |   9:    83.166 -  92.407:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3357 r_free = 0.3963             target_work(ml) = 6.089         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3352 r_free = 0.3970             target_work(ml) = 6.088         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3352   r_free= 0.3970   ksol= 0.30   Bsol= 20.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,4.89,-1.13,0.00,-0.00,-0.00); trace/3= 0.56                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.088186                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3349   r_free= 0.3951   ksol= 0.29   Bsol= 34.25   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,3.50,-0.26,0.00,-0.00,-0.00); trace/3= 0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.089204                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.966481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.383   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.606001              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.598  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3349      final r-factor (work) = 0.2850          |
| start r-factor (free) = 0.3951      final r-factor (free) = 0.3470          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2712 = 5.97 * 0.50 * 6.0892 + 1.00 * 0.1055                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0412 = 5.97 * 0.50 * 6.0170 + 1.00 * 0.0910                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2850      final r-factor (work) = 0.2743          |
| start r-factor (free) = 0.3470      final r-factor (free) = 0.3407          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6641 = 0.61 * 1.00 * 6.0170 + 1.00 * 0.0178                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6161 = 0.61 * 1.00 * 5.9454 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.82   18.29    None  None   None       |
|    all(noH): 2823   0      0.00    94.82   18.29    None  None   None       |
|    Sol.    : 438    0      2.39    92.36   35.25    None  None   None       |
|    Mac.    : 2385   0      0.00    94.82   15.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.482:  897   |   5:    47.409 -  56.890:   72        |
|      1:     9.482 -  18.963:  926   |   6:    56.890 -  66.372:   51        |
|      2:    18.963 -  28.445:  457   |   7:    66.372 -  75.854:   15        |
|      3:    28.445 -  37.927:  241   |   8:    75.854 -  85.335:    8        |
|      4:    37.927 -  47.409:  148   |   9:    85.335 -  94.817:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2743 r_free = 0.3407             target_work(ml) = 5.941         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2741 r_free = 0.3407             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2741   r_free= 0.3407   ksol= 0.29   Bsol= 34.25   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,3.50,-0.26,0.00,-0.00,-0.00); trace/3= 0.54                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.940301                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2742   r_free= 0.3402   ksol= 0.31   Bsol= 41.16   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.30,2.55,-0.06,0.00,-0.00,-0.00); trace/3= 0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.941579                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.299453              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.995   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.634853              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.295  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2742      final r-factor (work) = 0.2132          |
| start r-factor (free) = 0.3402      final r-factor (free) = 0.2690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7667 = 8.30 * 0.50 * 5.9464 + 1.00 * 0.0910                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.3296 = 8.30 * 0.50 * 5.8400 + 1.00 * 0.0953                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2132      final r-factor (work) = 0.1909          |
| start r-factor (free) = 0.2690      final r-factor (free) = 0.2476          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7208 = 0.63 * 1.00 * 5.8400 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5997 = 0.63 * 1.00 * 5.6506 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.63   17.84    None  None   None       |
|    all(noH): 2823   0      0.00    96.63   17.84    None  None   None       |
|    Sol.    : 438    0      4.04    96.63   40.50    None  None   None       |
|    Mac.    : 2385   0      0.00    90.12   13.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.663: 1059   |   5:    48.314 -  57.977:   98        |
|      1:     9.663 -  19.326:  966   |   6:    57.977 -  67.639:   41        |
|      2:    19.326 -  28.988:  303   |   7:    67.639 -  77.302:   31        |
|      3:    28.988 -  38.651:  179   |   8:    77.302 -  86.965:   13        |
|      4:    38.651 -  48.314:  126   |   9:    86.965 -  96.628:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1909 r_free = 0.2476             target_work(ml) = 5.614         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1907 r_free = 0.2478             target_work(ml) = 5.613         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1907   r_free= 0.2478   ksol= 0.31   Bsol= 41.16   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.30,2.55,-0.06,0.00,-0.00,-0.00); trace/3= 0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.613382                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1902   r_free= 0.2468   ksol= 0.32   Bsol= 57.28   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,0.59,-0.65,0.00,-0.00,-0.00); trace/3= -0.66                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.611010                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.433060              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.730  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.304716              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.902  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1902      final r-factor (work) = 0.1532          |
| start r-factor (free) = 0.2468      final r-factor (free) = 0.2006          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8028 = 3.43 * 0.50 * 5.6553 + 1.00 * 0.0953                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5438 = 3.43 * 0.50 * 5.5215 + 1.00 * 0.0660                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1532      final r-factor (work) = 0.1429          |
| start r-factor (free) = 0.2006      final r-factor (free) = 0.1876          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6948 = 0.30 * 1.00 * 5.5215 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6491 = 0.30 * 1.00 * 5.3790 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    97.42   17.20    None  None   None       |
|    all(noH): 2823   0      1.01    97.42   17.20    None  None   None       |
|    Sol.    : 438    0      3.81    92.72   41.06    None  None   None       |
|    Mac.    : 2385   0      1.01    97.42   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.008 -  10.649: 1283   |   5:    49.216 -  58.857:   88        |
|      1:    10.649 -  20.291:  899   |   6:    58.857 -  68.499:   44        |
|      2:    20.291 -  29.932:  206   |   7:    68.499 -  78.141:   24        |
|      3:    29.932 -  39.574:  125   |   8:    78.141 -  87.782:    9        |
|      4:    39.574 -  49.216:  137   |   9:    87.782 -  97.424:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1429 r_free = 0.1876             target_work(ml) = 5.343         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1427 r_free = 0.1875             target_work(ml) = 5.343         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1427   r_free= 0.1875   ksol= 0.32   Bsol= 57.28   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,0.59,-0.65,0.00,-0.00,-0.00); trace/3= -0.66                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.342534                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1428   r_free= 0.1875   ksol= 0.33   Bsol= 57.28   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-0.29,-0.83,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.344271                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.427051              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.671  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.168611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.613  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1428      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1875      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2871 = 3.43 * 0.50 * 5.3813 + 1.00 * 0.0660                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1210 = 3.43 * 0.50 * 5.2791 + 1.00 * 0.0752                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9001 = 0.17 * 1.00 * 5.2791 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8918 = 0.17 * 1.00 * 5.2156 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.11   16.53    None  None   None       |
|    all(noH): 2823   0      0.00    95.11   16.53    None  None   None       |
|    Sol.    : 438    0      4.92    92.44   39.16    None  None   None       |
|    Mac.    : 2385   0      0.00    95.11   12.38    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 -   9.511: 1047   |   5:    47.556 -  57.067:   92        |
|      1:     9.511 -  19.022: 1147   |   6:    57.067 -  66.578:   43        |
|      2:    19.022 -  28.533:  212   |   7:    66.578 -  76.089:   18        |
|      3:    28.533 -  38.045:  124   |   8:    76.089 -  85.600:    9        |
|      4:    38.045 -  47.556:  126   |   9:    85.600 -  95.111:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1202 r_free = 0.1656             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1201 r_free = 0.1654             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1654   ksol= 0.33   Bsol= 57.28   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-0.29,-0.83,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.200774                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.7039 0.99   1414  159 0.0981 0.1370      5.3873      5.6034|
|  2:  4.7039 -  3.7528 0.99   1360  151 0.0881 0.1135       5.476      5.6838|
|  3:  3.7528 -  3.2841 0.99   1332  147 0.1147 0.1662      5.5397      5.8839|
|  4:  3.2841 -  2.9864 0.99   1326  139 0.1324 0.1724      5.5088      5.6958|
|  5:  2.9864 -  2.7738 0.99   1316  151 0.1442 0.1824      5.3918      5.5553|
|  6:  2.7738 -  2.6111 0.99   1305  148 0.1403 0.2042      5.3028      5.5063|
|  7:  2.6111 -  2.4810 0.98   1297  149 0.1305 0.1733      5.2248      5.4385|
|  8:  2.4810 -  2.3734 0.98   1319  136 0.1302 0.1784      5.1494      5.3753|
|  9:  2.3734 -  2.2824 0.99   1288  144 0.1256 0.1871      5.0683       5.344|
| 10:  2.2824 -  2.2039 0.98   1300  145 0.1255 0.1694      5.0415      5.2226|
| 11:  2.2039 -  2.1352 0.97   1268  145 0.1218 0.1912        4.96       5.282|
| 12:  2.1352 -  2.0743 0.98   1281  147 0.1218 0.1614      4.8989      5.1142|
| 13:  2.0743 -  2.0198 0.93   1225  129 0.1191 0.1797      4.8105      5.0886|
| 14:  2.0198 -  1.9706 0.46    599   69 0.1155 0.1735      4.7032      4.9118|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0141 -  4.7039  1414   159  0.94   9.71   0.97     0.95       7729.02|
|  2:  4.7039 -  3.7528  1360   151  0.95   8.73   1.02     1.01      10163.60|
|  3:  3.7528 -  3.2841  1332   147  0.92  12.64   1.03     1.01      12017.26|
|  4:  3.2841 -  2.9864  1326   139  0.91  14.83   1.01     1.00      11422.92|
|  5:  2.9864 -  2.7738  1316   151  0.89  17.51   1.00     0.98       9520.05|
|  6:  2.7738 -  2.6111  1305   148  0.89  17.49   0.98     0.95       8016.21|
|  7:  2.6111 -  2.4810  1297   149  0.90  16.67   0.99     0.95       6947.60|
|  8:  2.4810 -  2.3734  1319   136  0.90  16.80   1.01     0.98       6275.23|
|  9:  2.3734 -  2.2824  1288   144  0.89  16.96   1.00     0.97       5471.35|
| 10:  2.2824 -  2.2039  1300   145  0.89  16.86   1.00     0.97       5073.76|
| 11:  2.2039 -  2.1352  1268   145  0.90  16.56   1.01     0.98       4490.88|
| 12:  2.1352 -  2.0743  1281   147  0.91  15.85   1.01     0.98       3916.63|
| 13:  2.0743 -  2.0198  1225   129  0.90  16.28   1.01     1.01       3355.33|
| 14:  2.0198 -  1.9706   599    69  0.90  15.49   0.98     0.94       2674.15|
|alpha:            min =        0.94 max =            1.01 mean =         0.98|
|beta:             min =     2674.15 max =        12017.26 mean =      7161.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.09|
|phase err.(test): min =        0.00 max =           89.22 mean =        14.62|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1646   ksol= 0.33   Bsol= 57.29   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-0.74,-0.90,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201330                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1646   ksol= 0.33   Bsol= 57.29   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-0.74,-0.90,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.201330                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0141 -  4.7039 0.99   1414  159 0.1002 0.1318      5.3933      5.5861|
|  2:  4.7039 -  3.7528 0.99   1360  151 0.0896 0.1119      5.4802      5.6909|
|  3:  3.7528 -  3.2841 0.99   1332  147 0.1151 0.1658      5.5421        5.88|
|  4:  3.2841 -  2.9864 0.99   1326  139 0.1330 0.1726      5.5089      5.6931|
|  5:  2.9864 -  2.7738 0.99   1316  151 0.1441 0.1820      5.3904      5.5546|
|  6:  2.7738 -  2.6111 0.99   1305  148 0.1403 0.2043      5.3024      5.5057|
|  7:  2.6111 -  2.4810 0.98   1297  149 0.1305 0.1739      5.2238      5.4398|
|  8:  2.4810 -  2.3734 0.98   1319  136 0.1297 0.1778      5.1483      5.3755|
|  9:  2.3734 -  2.2824 0.99   1288  144 0.1252 0.1870      5.0668      5.3431|
| 10:  2.2824 -  2.2039 0.98   1300  145 0.1254 0.1701      5.0406      5.2243|
| 11:  2.2039 -  2.1352 0.97   1268  145 0.1215 0.1908      4.9593      5.2821|
| 12:  2.1352 -  2.0743 0.98   1281  147 0.1217 0.1613      4.8992      5.1151|
| 13:  2.0743 -  2.0198 0.93   1225  129 0.1194 0.1796      4.8116       5.087|
| 14:  2.0198 -  1.9706 0.46    599   69 0.1154 0.1734      4.7025       4.911|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0141 -  4.7039  1414   159  0.94   9.64   0.97     0.95       7543.76|
|  2:  4.7039 -  3.7528  1360   151  0.95   8.69   1.01     1.01      10075.15|
|  3:  3.7528 -  3.2841  1332   147  0.92  12.60   1.02     1.01      12007.39|
|  4:  3.2841 -  2.9864  1326   139  0.91  14.79   1.01     1.00      11362.85|
|  5:  2.9864 -  2.7738  1316   151  0.89  17.46   1.00     0.97       9477.63|
|  6:  2.7738 -  2.6111  1305   148  0.89  17.49   0.98     0.94       8030.72|
|  7:  2.6111 -  2.4810  1297   149  0.90  16.67   0.98     0.94       6946.23|
|  8:  2.4810 -  2.3734  1319   136  0.90  16.79   1.00     0.97       6277.42|
|  9:  2.3734 -  2.2824  1288   144  0.89  16.96   1.00     0.96       5472.40|
| 10:  2.2824 -  2.2039  1300   145  0.89  16.85   0.99     0.96       5066.97|
| 11:  2.2039 -  2.1352  1268   145  0.90  16.55   1.00     0.97       4491.83|
| 12:  2.1352 -  2.0743  1281   147  0.91  15.85   1.00     0.97       3925.21|
| 13:  2.0743 -  2.0198  1225   129  0.90  16.28   0.99     1.00       3354.12|
| 14:  2.0198 -  1.9706   599    69  0.90  15.47   0.97     0.93       2660.63|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2660.63 max =        12007.39 mean =      7131.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.07|
|phase err.(test): min =        0.00 max =           89.79 mean =        14.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.798)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.11   16.53    None  None   None       |
|    all(noH): 2823   0      0.00    95.11   16.53    None  None   None       |
|    Sol.    : 438    0      4.92    92.44   39.16    None  None   None       |
|    Mac.    : 2385   0      0.00    95.11   12.38    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 -   9.514: 1047   |   5:    47.559 -  57.070:   92        |
|      1:     9.514 -  19.025: 1147   |   6:    57.070 -  66.581:   43        |
|      2:    19.025 -  28.536:  212   |   7:    66.581 -  76.092:   18        |
|      3:    28.536 -  38.048:  124   |   8:    76.092 -  85.603:    9        |
|      4:    38.048 -  47.559:  126   |   9:    85.603 -  95.114:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.557 - 5.163
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 315
   mapped sites are within: 0.707 - 5.163

peak=    6.039 closest distance to " O   HOH Z 120 " =    1.207
peak=    5.291 closest distance to " O   HOH Z 210 " =    1.340
peak=    5.259 closest distance to " O   HOH Z 113 " =    2.348
peak=    5.154 closest distance to " CB  SER A  63 " =    1.139
peak=    5.101 closest distance to " C   PRO A 198 " =    1.508
peak=    5.028 closest distance to " O   HOH Z 124 " =    1.376
peak=    5.018 closest distance to " O   HOH Z 403 " =    1.973
peak=    4.989 closest distance to " CA  TYR A  30 " =    0.926
peak=    4.643 closest distance to " CG1 ILE A  33 " =    1.251
peak=    4.639 closest distance to " CB  GLN A 223 " =    1.450
peak=    4.630 closest distance to " O   HOH Z 102 " =    1.401
peak=    4.627 closest distance to " O   HOH Z 389 " =    2.002
peak=    4.600 closest distance to " O   HOH Z  43 " =    1.768
peak=    4.596 closest distance to " O   HOH Z  80 " =    1.932
peak=    4.590 closest distance to " O   HOH Z 134 " =    2.036
peak=    4.561 closest distance to " O   HOH Z  15 " =    2.187
peak=    4.555 closest distance to " O   HOH Z 189 " =    2.076
peak=    4.500 closest distance to " O   HOH Z  59 " =    2.362
peak=    4.460 closest distance to " CB  ARG A 275 " =    0.834
peak=    4.456 closest distance to " O   HOH Z 406 " =    1.644
peak=    4.453 closest distance to " O   HOH Z 209 " =    2.378
peak=    4.437 closest distance to " O   HOH Z  97 " =    1.906
peak=    4.430 closest distance to " O   HOH Z 272 " =    1.938
peak=    4.420 closest distance to " CB  GLN A 183 " =    1.264
peak=    4.418 closest distance to " O   HOH Z   7 " =    1.091
peak=    4.407 closest distance to " O   HOH Z 433 " =    1.660
peak=    4.404 closest distance to " O   HOH Z  49 " =    1.290
peak=    4.377 closest distance to " O   HOH Z 428 " =    1.244
peak=    4.370 closest distance to " ND2 ASN A 187 " =    1.708
peak=    4.353 closest distance to " O   HOH Z 154 " =    1.697
peak=    4.291 closest distance to " O   HOH Z  40 " =    1.821
peak=    4.283 closest distance to " O   HOH Z 402 " =    1.711
peak=    4.253 closest distance to " O   GLY A  23 " =    2.421
peak=    4.249 closest distance to " NH2BARG A 145 " =    1.989
peak=    4.248 closest distance to " O   HOH Z  63 " =    2.128
peak=    4.244 closest distance to " O   HOH Z 357 " =    2.029
peak=    4.240 closest distance to " CB  SER A 141 " =    1.046
peak=    4.237 closest distance to " O   HOH Z 130 " =    2.432
peak=    4.218 closest distance to " CD  ARG A 195 " =    1.074
peak=    4.214 closest distance to " O   HOH Z  44 " =    1.989
peak=    4.202 closest distance to " O   HOH Z 130 " =    1.216
peak=    4.185 closest distance to " O   HOH Z 126 " =    1.624
peak=    4.179 closest distance to " O   HOH Z 142 " =    1.439
peak=    4.157 closest distance to " CD2 TRP A 179 " =    1.402
peak=    4.150 closest distance to " CG  PRO A 213 " =    1.225
peak=    4.133 closest distance to " O   HOH Z 247 " =    1.473
peak=    4.133 closest distance to " O   HOH Z 234 " =    3.686
peak=    4.129 closest distance to " O   HOH Z 414 " =    2.044
peak=    4.126 closest distance to " CD  LYS A 166 " =    1.506
peak=    4.103 closest distance to " O   HOH Z 422 " =    0.875
peak=    4.079 closest distance to " CB  ARG A  79 " =    1.422
peak=    4.075 closest distance to " O   SER A  87 " =    2.183
peak=    4.075 closest distance to " OG BSER A 210 " =    1.175
peak=    4.055 closest distance to " NE2 GLN A  11 " =    1.047
peak=    4.042 closest distance to " CB  GLU A 277 " =    3.688
peak=    4.042 closest distance to " O   HOH Z 265 " =    2.155
peak=    4.034 closest distance to " O   HOH Z 361 " =    3.343
peak=    4.023 closest distance to " O   HOH Z 352 " =    1.892
peak=    4.019 closest distance to " CG  PRO A  90 " =    1.235
peak=    3.983 closest distance to " O   HOH Z 334 " =    1.594
peak=    3.967 closest distance to " O   HOH Z 374 " =    2.594
peak=    3.962 closest distance to " O   HOH Z 303 " =    2.308
peak=    3.950 closest distance to " CB  ARG A 190 " =    1.766
peak=    3.930 closest distance to " O   HOH Z 163 " =    1.588
peak=    3.930 closest distance to " CA  ASN A 176 " =    1.633
peak=    3.928 closest distance to " O   HOH Z 214 " =    1.517
peak=    3.928 closest distance to " O   HOH Z 245 " =    1.451
peak=    3.927 closest distance to " CG AARG A 275 " =    0.991
peak=    3.918 closest distance to " CG  ARG A  66 " =    0.987
peak=    3.909 closest distance to " O   HOH Z 236 " =    1.370
peak=    3.904 closest distance to " CG2BVAL A  41 " =    0.934
peak=    3.898 closest distance to " O   HOH Z 227 " =    1.822
peak=    3.883 closest distance to " CG2 THR A 220 " =    0.801
peak=    3.881 closest distance to " O   HOH Z  48 " =    1.774
peak=    3.880 closest distance to " O   HOH Z 196 " =    1.408
peak=    3.872 closest distance to " O   HOH Z 423 " =    1.867
peak=    3.870 closest distance to " O   HOH Z 411 " =    3.435
peak=    3.862 closest distance to " O   HOH Z 132 " =    2.504
peak=    3.856 closest distance to " O   HOH Z 345 " =    2.532
peak=    3.843 closest distance to " CB  GLU A 152 " =    1.103
peak=    3.827 closest distance to " O   ALA A 165 " =    1.316
peak=    3.827 closest distance to " O   HOH Z 128 " =    1.913
peak=    3.822 closest distance to " O   HOH Z  66 " =    2.094
peak=    3.815 closest distance to " O   HOH Z 150 " =    1.717
peak=    3.814 closest distance to " O   HOH Z  68 " =    2.174
peak=    3.810 closest distance to " O   HOH Z 435 " =    1.831
peak=    3.808 closest distance to " O   HOH Z  54 " =    1.737
peak=    3.794 closest distance to " O   HOH Z 412 " =    3.682
peak=    3.793 closest distance to " O   HOH Z 345 " =    1.854
peak=    3.769 closest distance to " O   HOH Z 418 " =    1.834
peak=    3.765 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.765 closest distance to " CB  LEU A 228 " =    1.173
peak=    3.761 closest distance to " CB  VAL A 202 " =    1.465
peak=    3.759 closest distance to " CB  SER A  26 " =    1.750
peak=    3.755 closest distance to " O   HOH Z  39 " =    1.976
peak=    3.752 closest distance to " NZ  LYS A 117 " =    3.227
peak=    3.747 closest distance to " O   HOH Z 132 " =    2.050
peak=    3.745 closest distance to " N   ASN A  39 " =    1.269
peak=    3.742 closest distance to " CG AARG A 275 " =    1.136
peak=    3.738 closest distance to " O   HOH Z 408 " =    1.985
peak=    3.735 closest distance to " CG  PRO A 198 " =    1.358
peak=    3.731 closest distance to " CB  TRP A 179 " =    1.216
peak=    3.725 closest distance to " CG2 THR A 221 " =    1.078
peak=    3.724 closest distance to " O   HOH Z 250 " =    1.786
peak=    3.720 closest distance to " O   HOH Z 395 " =    1.544
peak=    3.718 closest distance to " CB  ASN A 285 " =    0.903
peak=    3.709 closest distance to " O   HOH Z 425 " =    1.471
peak=    3.702 closest distance to " O   HOH Z 298 " =    2.004
peak=    3.693 closest distance to " CB  SER A  62 " =    0.820
peak=    3.690 closest distance to " CA  ASP A 191 " =    0.935
peak=    3.689 closest distance to " O   HOH Z 132 " =    1.325
peak=    3.689 closest distance to " O   HOH Z 427 " =    3.137
peak=    3.671 closest distance to " CA  ALA A  51 " =    0.980
peak=    3.670 closest distance to " CB  SER A   3 " =    1.345
peak=    3.667 closest distance to " CG2 VAL A 197 " =    1.169
peak=    3.666 closest distance to " O   HOH Z 336 " =    1.734
peak=    3.661 closest distance to " NZ  LYS A 117 " =    1.838
peak=    3.645 closest distance to " O   HOH Z 339 " =    1.330
peak=    3.636 closest distance to " OE1 GLN A  11 " =    1.972
peak=    3.622 closest distance to " O   HOH Z 369 " =    2.075
peak=    3.619 closest distance to " O   HOH Z 128 " =    2.215
peak=    3.618 closest distance to " CB  ARG A 139 " =    1.108
peak=    3.614 closest distance to " O   HOH Z 346 " =    1.548
peak=    3.608 closest distance to " O   HOH Z 193 " =    1.778
peak=    3.608 closest distance to " O   HOH Z 208 " =    1.545
peak=    3.608 closest distance to " CD  ARG A 159 " =    0.836
peak=    3.591 closest distance to " O   HOH Z 402 " =    2.509
peak=    3.588 closest distance to " OD1 ASN A  60 " =    1.248
peak=    3.584 closest distance to " CB  ALA A 100 " =    1.297
peak=    3.583 closest distance to " O   HOH Z  11 " =    1.307
peak=    3.581 closest distance to " O   HOH Z 431 " =    1.313
peak=    3.574 closest distance to " O   HOH Z 403 " =    1.664
peak=    3.573 closest distance to " CB  GLU A 128 " =    1.108
peak=    3.572 closest distance to " CG1BVAL A  72 " =    1.701
peak=    3.567 closest distance to " O   HOH Z 359 " =    1.913
peak=    3.565 closest distance to " O   HOH Z 130 " =    2.380
peak=    3.563 closest distance to " O   HOH Z  78 " =    1.686
peak=    3.555 closest distance to " OE1 GLU A   2 " =    2.112
peak=    3.555 closest distance to " NE2 GLN A  77 " =    3.298
peak=    3.554 closest distance to " NH2AARG A 145 " =    2.259
peak=    3.550 closest distance to " CB  LEU A   5 " =    1.086
peak=    3.545 closest distance to " O   HOH Z 418 " =    2.994
peak=    3.543 closest distance to " NH1AARG A 275 " =    1.019
peak=    3.542 closest distance to " C   ILE A 106 " =    1.824
peak=    3.542 closest distance to " O   HOH Z 380 " =    1.831
peak=    3.541 closest distance to " O   HOH Z 147 " =    1.823
peak=    3.538 closest distance to " CD2 LEU A 297 " =    0.950
peak=    3.535 closest distance to " O   HOH Z  20 " =    1.588
peak=    3.533 closest distance to " CB  ALA A  71 " =    1.235
peak=    3.532 closest distance to " O   HOH Z 173 " =    2.140
peak=    3.527 closest distance to " O   HOH Z 371 " =    3.251
peak=    3.523 closest distance to " CE  LYS A 119 " =    1.145
peak=    3.522 closest distance to " O   HOH Z 315 " =    1.857
peak=    3.522 closest distance to " O   HOH Z 232 " =    2.441
peak=    3.518 closest distance to " ND1 HIS A  81 " =    1.449
peak=    3.510 closest distance to " O   HOH Z 257 " =    2.175
peak=    3.509 closest distance to " O   HOH Z 250 " =    1.452
peak=    3.505 closest distance to " O   HOH Z 128 " =    1.560
peak=    3.503 closest distance to " CG2 ILE A  20 " =    1.407
peak=    3.493 closest distance to " O   HOH Z 386 " =    2.293
peak=    3.492 closest distance to " O   HOH Z 394 " =    1.766
peak=    3.485 closest distance to " O   HOH Z 437 " =    1.863
peak=    3.482 closest distance to " O   ASN A  74 " =    1.894
peak=    3.481 closest distance to " O   HOH Z 261 " =    1.855
peak=    3.481 closest distance to " CA  ALA A  21 " =    1.255
peak=    3.475 closest distance to " O   HOH Z  46 " =    1.445
peak=    3.471 closest distance to " CD  ARG A 269 " =    1.048
peak=    3.467 closest distance to " O   HOH Z 438 " =    2.361
peak=    3.467 closest distance to " O   HOH Z  35 " =    1.994
peak=    3.463 closest distance to " CB  THR A  52 " =    1.076
peak=    3.457 closest distance to " O   HOH Z 365 " =    2.522
peak=    3.456 closest distance to " OD2 ASP A 286 " =    2.773
peak=    3.450 closest distance to " O   HOH Z 130 " =    2.401
peak=    3.448 closest distance to " CB  ARG A  79 " =    0.719
peak=    3.448 closest distance to " CG  PRO A 243 " =    1.310
peak=    3.446 closest distance to " CE BMET A  47 " =    1.524
peak=    3.446 closest distance to " O   HOH Z  88 " =    3.155
peak=    3.444 closest distance to " O   HOH Z 421 " =    1.963
peak=    3.438 closest distance to " O   HOH Z 234 " =    1.924
peak=    3.426 closest distance to " O   HOH Z 291 " =    1.478
peak=    3.425 closest distance to " O   HOH Z 162 " =    1.922
peak=    3.424 closest distance to " O   GLY A  91 " =    1.249
peak=    3.423 closest distance to " O   HOH Z 109 " =    2.044
peak=    3.422 closest distance to " O  BHOH Z 338 " =    1.063
peak=    3.417 closest distance to " O   HOH Z 271 " =    2.766
peak=    3.415 closest distance to " CB  TRP A 266 " =    1.045
peak=    3.415 closest distance to " NE1 TRP A 274 " =    0.860
peak=    3.414 closest distance to " CA  VAL A 125 " =    1.069
peak=    3.412 closest distance to " O   HOH Z 358 " =    2.108
peak=    3.411 closest distance to " CB  TYR A 169 " =    0.707
peak=    3.410 closest distance to " CE1 HIS A 108 " =    1.145
peak=    3.401 closest distance to " CA  LEU A  83 " =    1.362
peak=    3.395 closest distance to " CG  GLN A  58 " =    2.375
peak=    3.388 closest distance to " N   SER A 164 " =    0.969
peak=    3.386 closest distance to " O   ALA A 158 " =    1.194
peak=    3.386 closest distance to " O   HOH Z  18 " =    1.604
peak=    3.385 closest distance to " CA  ASP A 162 " =    0.992
peak=    3.374 closest distance to " CB  PHE A  16 " =    1.161
peak=    3.372 closest distance to " O   HOH Z 111 " =    1.565
peak=    3.370 closest distance to " O   ASP A 124 " =    1.591
peak=    3.370 closest distance to " O   HOH Z 185 " =    1.684
peak=    3.369 closest distance to " O   HOH Z 126 " =    1.791
peak=    3.369 closest distance to " CD  GLN A 194 " =    1.621
peak=    3.364 closest distance to " CD  ARG A 139 " =    1.339
peak=    3.360 closest distance to " O   HOH Z 368 " =    1.997
peak=    3.360 closest distance to " OG BSER A 212 " =    2.512
peak=    3.358 closest distance to " O   HOH Z 139 " =    4.531
peak=    3.356 closest distance to " O   HOH Z 255 " =    1.756
peak=    3.355 closest distance to " O   HOH Z 146 " =    1.399
peak=    3.353 closest distance to " CA  GLU A 152 " =    0.956
peak=    3.352 closest distance to " O   HOH Z 404 " =    1.559
peak=    3.352 closest distance to " O   THR A 251 " =    1.278
peak=    3.351 closest distance to " O   HOH Z  47 " =    1.280
peak=    3.348 closest distance to " CZ  PHE A  38 " =    1.291
peak=    3.339 closest distance to " O   HOH Z 279 " =    2.035
peak=    3.338 closest distance to " OG  SER A  62 " =    3.013
peak=    3.335 closest distance to " O   HOH Z 313 " =    1.921
peak=    3.331 closest distance to " CA  ILE A 106 " =    0.745
peak=    3.327 closest distance to " ND2 ASN A 301 " =    1.346
peak=    3.326 closest distance to " OG BSER A 164 " =    2.465
peak=    3.325 closest distance to " CB  PHE A 218 " =    1.915
peak=    3.324 closest distance to " NZ  LYS A 119 " =    1.645
peak=    3.324 closest distance to " O   HOH Z  95 " =    1.526
peak=    3.319 closest distance to " O   HOH Z 298 " =    5.163
peak=    3.317 closest distance to " CE1 TYR A 186 " =    1.182
peak=    3.317 closest distance to " OG BSER A 216 " =    0.834
peak=    3.317 closest distance to " O   HOH Z 423 " =    3.132
peak=    3.313 closest distance to " CB  ASN A 148 " =    1.485
peak=    3.312 closest distance to " OG  SER A 245 " =    1.521
peak=    3.305 closest distance to " O   THR A 264 " =    1.331
peak=    3.304 closest distance to " CB  GLU A 277 " =    1.020
peak=    3.302 closest distance to " CB  PRO A 198 " =    0.997
peak=    3.299 closest distance to " O   HOH Z 263 " =    2.217
peak=    3.293 closest distance to " CB  LEU A  83 " =    0.776
peak=    3.293 closest distance to " CG2 ILE A 120 " =    1.149
peak=    3.292 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.291 closest distance to " CA  SER A  12 " =    1.601
peak=    3.285 closest distance to " CD  PRO A  54 " =    0.851
peak=    3.285 closest distance to " O   HOH Z 365 " =    1.393
peak=    3.283 closest distance to " CG  GLN A  89 " =    1.501
peak=    3.279 closest distance to " CA  PRO A  90 " =    0.967
peak=    3.278 closest distance to " CB  ASN A  39 " =    0.781
peak=    3.269 closest distance to " O   HOH Z  64 " =    2.246
peak=    3.266 closest distance to " O   HOH Z 281 " =    4.333
peak=    3.266 closest distance to " CA  ARG A  66 " =    1.062
peak=    3.265 closest distance to " O   HOH Z 298 " =    2.316
peak=    3.262 closest distance to " O   HOH Z 284 " =    2.861
peak=    3.259 closest distance to " N   PHE A 130 " =    1.291
peak=    3.254 closest distance to " CG1BVAL A  72 " =    3.204
peak=    3.252 closest distance to " CB  ASN A 187 " =    1.241
peak=    3.252 closest distance to " CA  VAL A  41 " =    0.860
peak=    3.245 closest distance to " CD  LYS A 119 " =    1.868
peak=    3.244 closest distance to " CE BLYS A 290 " =    0.802
peak=    3.241 closest distance to " CD  PRO A 213 " =    1.167
peak=    3.238 closest distance to " OG1 THR A 294 " =    2.414
peak=    3.228 closest distance to " OD1 ASN A  69 " =    2.422
peak=    3.228 closest distance to " O   HOH Z  88 " =    3.218
peak=    3.226 closest distance to " O   HOH Z 355 " =    1.804
peak=    3.221 closest distance to " O   HOH Z 112 " =    3.061
peak=    3.215 closest distance to " O   HOH Z 191 " =    4.966
peak=    3.213 closest distance to " O   HOH Z 293 " =    1.909
peak=    3.206 closest distance to " O   HOH Z  48 " =    1.577
peak=    3.206 closest distance to " O   HOH Z 162 " =    1.436
peak=    3.202 closest distance to " CZ  PHE A 218 " =    1.155
peak=    3.199 closest distance to " O   SER A  26 " =    1.908
peak=    3.199 closest distance to " O   HOH Z 156 " =    2.534
peak=    3.198 closest distance to " O   HOH Z 316 " =    2.859
peak=    3.197 closest distance to " O   HOH Z 143 " =    1.423
peak=    3.196 closest distance to " N   ARG A 156 " =    1.407
peak=    3.194 closest distance to " CG  MET A 185 " =    1.061
peak=    3.192 closest distance to " NH1AARG A 275 " =    3.236
peak=    3.190 closest distance to " OD2 ASP A 286 " =    2.944
peak=    3.190 closest distance to " CA  GLY A  80 " =    0.726
peak=    3.188 closest distance to " O   HOH Z 152 " =    1.814
peak=    3.186 closest distance to " CA  ASP A 149 " =    1.121
peak=    3.185 closest distance to " O   HOH Z 353 " =    2.624
peak=    3.182 closest distance to " O   HOH Z  50 " =    1.740
peak=    3.160 closest distance to " CA  CYS A 260 " =    1.696
peak=    3.159 closest distance to " O   HOH Z 200 " =    1.631
peak=    3.158 closest distance to " CZ3 TRP A  85 " =    1.022
peak=    3.156 closest distance to " CB  ALA A 256 " =    1.052
peak=    3.156 closest distance to " O   HOH Z 261 " =    1.981
peak=    3.153 closest distance to " CD1 LEU A 222 " =    0.747
peak=    3.145 closest distance to " CA  ARG A 195 " =    1.057
peak=    3.144 closest distance to " O   HOH Z 248 " =    1.704
peak=    3.141 closest distance to " CB  SER A  97 " =    1.727
peak=    3.138 closest distance to " CB  PRO A  90 " =    1.145
peak=    3.138 closest distance to " O   HOH Z 214 " =    2.451
peak=    3.131 closest distance to " CG2 VAL A 126 " =    0.830
peak=    3.123 closest distance to " CG2 THR A  42 " =    0.900
peak=    3.122 closest distance to " NH2 ARG A 156 " =    1.147
peak=    3.113 closest distance to " CB  ALA A  51 " =    0.841
peak=    3.109 closest distance to " CA  THR A 221 " =    0.980
peak=    3.102 closest distance to " CA  SER A  87 " =    1.009
peak=    3.098 closest distance to " O   ILE A  33 " =    1.282
peak=    3.088 closest distance to " O   HOH Z 189 " =    2.573
peak=    3.086 closest distance to " O   HOH Z 339 " =    2.154
peak=    3.085 closest distance to " O   HOH Z  85 " =    1.942
peak=    3.076 closest distance to " N   GLU A  44 " =    2.158
peak=    3.071 closest distance to " OH  TYR A  30 " =    1.234
peak=    3.068 closest distance to " O   HOH Z 420 " =    1.934
peak=    3.064 closest distance to " O   HOH Z 195 " =    1.572
peak=    3.052 closest distance to " CA  ARG A  36 " =    1.017
peak=    3.046 closest distance to " CA  SER A  32 " =    1.569
peak=    3.040 closest distance to " O   HOH Z 145 " =    2.355
peak=    3.038 closest distance to " CB  LYS A 289 " =    1.009
peak=    3.018 closest distance to " CB  PHE A 283 " =    0.719
peak=    3.014 closest distance to " OE1 GLU A 152 " =    1.644
peak=    3.005 closest distance to " O   HOH Z  94 " =    1.654

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.590 - 5.987
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 203
   mapped sites are within: 0.706 - 5.987

peak=   -4.759 closest distance to " O   HOH Z 266 " =    4.644
peak=   -4.504 closest distance to " O   HOH Z 210 " =    0.814
peak=   -4.407 closest distance to " CD1 LEU A 167 " =    2.222
peak=   -4.400 closest distance to " O   HOH Z 290 " =    0.859
peak=   -4.359 closest distance to " C   HIS A 108 " =    1.073
peak=   -4.296 closest distance to " OXT GLY A 302 " =    2.719
peak=   -4.291 closest distance to " O   HOH Z   7 " =    1.051
peak=   -4.282 closest distance to " O   HOH Z 422 " =    1.379
peak=   -4.231 closest distance to " OG  SER A  97 " =    2.206
peak=   -4.229 closest distance to " CD  GLN A  58 " =    1.375
peak=   -4.226 closest distance to " O   PRO A 163 " =    2.058
peak=   -4.212 closest distance to " NE2 GLN A 223 " =    1.081
peak=   -4.134 closest distance to " CA  VAL A  67 " =    2.940
peak=   -4.092 closest distance to " CD2 TYR A  30 " =    2.720
peak=   -4.054 closest distance to " C   THR A 279 " =    1.221
peak=   -4.045 closest distance to " CD1 LEU A 101 " =    2.466
peak=   -4.025 closest distance to " CA  TYR A  68 " =    2.862
peak=   -3.938 closest distance to " O   HOH Z  71 " =    1.922
peak=   -3.911 closest distance to " CD  ARG A 156 " =    2.003
peak=   -3.908 closest distance to " O   HOH Z 196 " =    1.651
peak=   -3.902 closest distance to " O   HOH Z 377 " =    0.916
peak=   -3.885 closest distance to " O   HOH Z 155 " =    1.714
peak=   -3.879 closest distance to " O   HOH Z   6 " =    1.542
peak=   -3.864 closest distance to " O  BHOH Z 338 " =    1.377
peak=   -3.846 closest distance to " O   HOH Z 422 " =    1.140
peak=   -3.824 closest distance to " O   HOH Z 348 " =    2.358
peak=   -3.818 closest distance to " CD1 PHE A  59 " =    2.003
peak=   -3.805 closest distance to " O   HOH Z 407 " =    1.614
peak=   -3.800 closest distance to " O   HOH Z  56 " =    0.869
peak=   -3.780 closest distance to " CD1 TRP A 179 " =    1.103
peak=   -3.766 closest distance to " CG2 VAL A 189 " =    2.141
peak=   -3.743 closest distance to " NE2 GLN A 103 " =    1.427
peak=   -3.739 closest distance to " O   HOH Z 109 " =    3.467
peak=   -3.727 closest distance to " O   HOH Z 165 " =    2.008
peak=   -3.724 closest distance to " C   ASN A 285 " =    2.312
peak=   -3.718 closest distance to " O   TRP A  92 " =    1.981
peak=   -3.700 closest distance to " CD  ARG A 195 " =    5.027
peak=   -3.689 closest distance to " O   HOH Z 120 " =    0.774
peak=   -3.681 closest distance to " O   PRO A 198 " =    1.351
peak=   -3.670 closest distance to " O   ALA A  34 " =    2.372
peak=   -3.668 closest distance to " CG1 VAL A 112 " =    2.481
peak=   -3.661 closest distance to " O   HOH Z 423 " =    2.306
peak=   -3.651 closest distance to " O   HOH Z 135 " =    1.570
peak=   -3.647 closest distance to " O   HOH Z 377 " =    2.145
peak=   -3.641 closest distance to " CG  ARG A 269 " =    2.346
peak=   -3.638 closest distance to " O   HOH Z 234 " =    4.068
peak=   -3.636 closest distance to " O   ASN A 187 " =    1.567
peak=   -3.636 closest distance to " O   PHE A 218 " =    1.397
peak=   -3.628 closest distance to " O   HOH Z  52 " =    2.203
peak=   -3.624 closest distance to " CD  GLN A 223 " =    1.622
peak=   -3.580 closest distance to " CZ  TYR A 169 " =    1.903
peak=   -3.577 closest distance to " CB  SER A 210 " =    1.237
peak=   -3.572 closest distance to " O   HOH Z 120 " =    1.364
peak=   -3.562 closest distance to " CB  ALA A 248 " =    2.265
peak=   -3.558 closest distance to " O   HOH Z 396 " =    1.752
peak=   -3.556 closest distance to " CD  GLN A  88 " =    0.706
peak=   -3.555 closest distance to " O   HOH Z 428 " =    0.988
peak=   -3.546 closest distance to " CG2 ILE A  49 " =    2.607
peak=   -3.541 closest distance to " O   HOH Z 392 " =    1.026
peak=   -3.533 closest distance to " CD2 LEU A 300 " =    2.792
peak=   -3.528 closest distance to " CA  GLY A 203 " =    2.238
peak=   -3.525 closest distance to " SG  CYS A 254 " =    3.335
peak=   -3.523 closest distance to " O   VAL A 174 " =    2.059
peak=   -3.517 closest distance to " OG  SER A   3 " =    1.603
peak=   -3.515 closest distance to " ND2 ASN A  69 " =    1.628
peak=   -3.490 closest distance to " OG BSER A 210 " =    1.265
peak=   -3.489 closest distance to " O   HOH Z  15 " =    1.602
peak=   -3.483 closest distance to " CD2 LEU A 237 " =    2.550
peak=   -3.476 closest distance to " N   ALA A  43 " =    2.891
peak=   -3.469 closest distance to " C   SER A 206 " =    1.479
peak=   -3.468 closest distance to " CG2 THR A 182 " =    2.287
peak=   -3.465 closest distance to " O   ASP A 191 " =    2.079
peak=   -3.463 closest distance to " NH2 ARG A  79 " =    1.999
peak=   -3.461 closest distance to " O   HOH Z 351 " =    1.536
peak=   -3.461 closest distance to " OD1 ASP A 298 " =    1.760
peak=   -3.453 closest distance to " O   HOH Z  78 " =    1.522
peak=   -3.453 closest distance to " O   HOH Z 198 " =    1.067
peak=   -3.449 closest distance to " O   HOH Z 196 " =    2.025
peak=   -3.449 closest distance to " CG1BVAL A  72 " =    2.496
peak=   -3.443 closest distance to " CB  ALA A 291 " =    2.322
peak=   -3.441 closest distance to " O   ALA A   1 " =    2.042
peak=   -3.439 closest distance to " ND2 ASN A  60 " =    1.409
peak=   -3.438 closest distance to " O   HOH Z 197 " =    1.817
peak=   -3.435 closest distance to " OG BSER A 134 " =    1.422
peak=   -3.430 closest distance to " OE2 GLU A   2 " =    1.108
peak=   -3.430 closest distance to " CB  ALA A 161 " =    2.481
peak=   -3.428 closest distance to " CH2 TRP A 179 " =    1.249
peak=   -3.425 closest distance to " CD  GLN A  73 " =    0.732
peak=   -3.422 closest distance to " O   HOH Z 174 " =    2.280
peak=   -3.420 closest distance to " O   HOH Z 137 " =    1.267
peak=   -3.417 closest distance to " O   ASP A 298 " =    1.925
peak=   -3.408 closest distance to " O   HOH Z   5 " =    1.603
peak=   -3.407 closest distance to " CA  VAL A 197 " =    0.974
peak=   -3.400 closest distance to " CH2 TRP A 177 " =    1.923
peak=   -3.390 closest distance to " O   HOH Z 407 " =    1.107
peak=   -3.389 closest distance to " O   HOH Z 313 " =    1.321
peak=   -3.381 closest distance to " O   HOH Z 139 " =    3.363
peak=   -3.369 closest distance to " O   HOH Z 136 " =    1.967
peak=   -3.367 closest distance to " ND2 ASN A 187 " =    1.543
peak=   -3.367 closest distance to " CG  GLU A  53 " =    1.302
peak=   -3.359 closest distance to " CB  ASP A 162 " =    2.641
peak=   -3.358 closest distance to " C   ALA A 158 " =    1.221
peak=   -3.358 closest distance to " C   GLY A 133 " =    1.249
peak=   -3.351 closest distance to " CB  PRO A 163 " =    2.778
peak=   -3.350 closest distance to " O   TYR A  15 " =    1.708
peak=   -3.349 closest distance to " CA  ASP A 298 " =    1.090
peak=   -3.343 closest distance to " O   HOH Z  52 " =    0.949
peak=   -3.337 closest distance to " NH2 ARG A  66 " =    1.411
peak=   -3.332 closest distance to " OG  SER A  62 " =    1.366
peak=   -3.324 closest distance to " O   HOH Z 149 " =    1.702
peak=   -3.322 closest distance to " CG2 ILE A 263 " =    2.155
peak=   -3.314 closest distance to " CA  SER A 276 " =    1.495
peak=   -3.311 closest distance to " CG  LEU A  83 " =    1.916
peak=   -3.308 closest distance to " O   HOH Z 196 " =    1.803
peak=   -3.303 closest distance to " CB  ALA A 291 " =    2.343
peak=   -3.297 closest distance to " NE2 GLN A 194 " =    1.890
peak=   -3.295 closest distance to " O   HOH Z 200 " =    1.243
peak=   -3.290 closest distance to " O   HOH Z 283 " =    1.545
peak=   -3.290 closest distance to " O   HOH Z 412 " =    4.821
peak=   -3.290 closest distance to " O   HOH Z 397 " =    1.193
peak=   -3.289 closest distance to " OE1 GLN A 103 " =    1.180
peak=   -3.288 closest distance to " CD2 LEU A 300 " =    2.649
peak=   -3.287 closest distance to " O   HOH Z 418 " =    1.408
peak=   -3.284 closest distance to " CD1 PHE A 130 " =    2.345
peak=   -3.283 closest distance to " O   HOH Z 426 " =    1.626
peak=   -3.282 closest distance to " O   HOH Z  97 " =    1.171
peak=   -3.278 closest distance to " CB  PRO A 243 " =    2.699
peak=   -3.275 closest distance to " OE1 GLN A 223 " =    2.228
peak=   -3.275 closest distance to " OG BSER A 134 " =    1.823
peak=   -3.274 closest distance to " O   HOH Z 252 " =    4.079
peak=   -3.270 closest distance to " O   HOH Z 109 " =    5.987
peak=   -3.269 closest distance to " N   ALA A 248 " =    1.787
peak=   -3.269 closest distance to " CH2 TRP A 150 " =    1.047
peak=   -3.265 closest distance to " NH1 ARG A  66 " =    3.079
peak=   -3.261 closest distance to " CG1 VAL A 197 " =    2.067
peak=   -3.260 closest distance to " O   HOH Z 126 " =    1.486
peak=   -3.259 closest distance to " O   HOH Z 176 " =    1.655
peak=   -3.256 closest distance to " O   GLY A  75 " =    1.820
peak=   -3.254 closest distance to " CA  GLY A 133 " =    2.095
peak=   -3.251 closest distance to " NH1 ARG A 195 " =    2.298
peak=   -3.249 closest distance to " CD2 PHE A  59 " =    2.304
peak=   -3.249 closest distance to " O   HOH Z 120 " =    0.923
peak=   -3.235 closest distance to " O   HOH Z 145 " =    2.258
peak=   -3.233 closest distance to " CG  ASP A 231 " =    0.775
peak=   -3.231 closest distance to " O   HOH Z  22 " =    2.492
peak=   -3.229 closest distance to " O   HOH Z 393 " =    1.103
peak=   -3.223 closest distance to " CD2 LEU A 237 " =    2.176
peak=   -3.216 closest distance to " O   ALA A 161 " =    1.713
peak=   -3.216 closest distance to " C   ASN A 148 " =    1.754
peak=   -3.215 closest distance to " CD1 ILE A 109 " =    2.437
peak=   -3.214 closest distance to " CD  ARG A 139 " =    1.686
peak=   -3.213 closest distance to " O   SER A 273 " =    1.336
peak=   -3.211 closest distance to " CB  PRO A 163 " =    2.597
peak=   -3.210 closest distance to " O   HOH Z 353 " =    2.111
peak=   -3.210 closest distance to " O   HOH Z 312 " =    1.353
peak=   -3.209 closest distance to " NE1 TRP A 123 " =    1.435
peak=   -3.209 closest distance to " CG  ARG A 219 " =    2.346
peak=   -3.206 closest distance to " ND2 ASN A  45 " =    1.882
peak=   -3.203 closest distance to " OG1 THR A   4 " =    1.771
peak=   -3.200 closest distance to " OD1 ASN A 148 " =    1.561
peak=   -3.199 closest distance to " NH1 ARG A  66 " =    5.576
peak=   -3.196 closest distance to " ND2 ASN A  45 " =    1.154
peak=   -3.193 closest distance to " O   HOH Z 424 " =    3.144
peak=   -3.186 closest distance to " O   HOH Z 372 " =    2.435
peak=   -3.181 closest distance to " NH1 ARG A 195 " =    2.541
peak=   -3.175 closest distance to " C   ALA A 242 " =    2.087
peak=   -3.171 closest distance to " O   HOH Z 171 " =    2.262
peak=   -3.171 closest distance to " O   HOH Z 166 " =    1.450
peak=   -3.168 closest distance to " O   THR A  52 " =    1.908
peak=   -3.167 closest distance to " CD2 LEU A 167 " =    1.785
peak=   -3.166 closest distance to " O   GLY A 241 " =    2.195
peak=   -3.164 closest distance to " O   GLY A 196 " =    0.945
peak=   -3.161 closest distance to " O   HOH Z 265 " =    2.284
peak=   -3.161 closest distance to " O   SER A  95 " =    1.704
peak=   -3.160 closest distance to " CD1 TYR A 247 " =    2.334
peak=   -3.160 closest distance to " O   ALA A  10 " =    1.775
peak=   -3.154 closest distance to " CG  ASN A 110 " =    1.020
peak=   -3.147 closest distance to " O   HOH Z  93 " =    1.524
peak=   -3.144 closest distance to " OG  SER A  26 " =    0.889
peak=   -3.137 closest distance to " N   ALA A 242 " =    1.912
peak=   -3.131 closest distance to " CG  ASP A 162 " =    1.569
peak=   -3.128 closest distance to " CD1 ILE A 106 " =    2.131
peak=   -3.127 closest distance to " C   GLN A 144 " =    0.881
peak=   -3.125 closest distance to " CE2 TRP A 274 " =    1.292
peak=   -3.119 closest distance to " CE3 TRP A 274 " =    2.441
peak=   -3.119 closest distance to " CB  ASP A 132 " =    2.339
peak=   -3.115 closest distance to " O   HOH Z 151 " =    1.149
peak=   -3.109 closest distance to " O   HOH Z 185 " =    2.401
peak=   -3.106 closest distance to " O   HOH Z  48 " =    1.298
peak=   -3.105 closest distance to " OD1 ASN A 301 " =    1.995
peak=   -3.100 closest distance to " CD2 PHE A  61 " =    2.068
peak=   -3.100 closest distance to " CG2 THR A 178 " =    2.386
peak=   -3.099 closest distance to " ND2 ASN A  39 " =    1.149
peak=   -3.091 closest distance to " O   HOH Z  38 " =    1.682
peak=   -3.085 closest distance to " C   GLY A  91 " =    1.414
peak=   -3.081 closest distance to " O   HOH Z 191 " =    5.973
peak=   -3.066 closest distance to " O   HOH Z 236 " =    1.272
peak=   -3.064 closest distance to " O   HOH Z 368 " =    1.975
peak=   -3.058 closest distance to " OG1 THR A  82 " =    1.250

================= 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    :  0.4577 0.4459   6.271166e+00   6.250295e+00
   1_bss:  0.4489 0.4340   6.261403e+00   6.237983e+00
   1_xyz:  0.3664 0.3900   6.140500e+00   6.172863e+00
   1_adp:  0.3357 0.3963   6.088988e+00   6.179697e+00
   1_occ:  0.3352 0.3970   6.088186e+00   6.179575e+00
   2_bss:  0.3349 0.3951   6.089204e+00   6.179694e+00
   2_xyz:  0.2850 0.3470   5.959180e+00   6.089433e+00
   2_adp:  0.2743 0.3407   5.940906e+00   6.081148e+00
   2_occ:  0.2741 0.3407   5.940301e+00   6.081312e+00
   3_bss:  0.2742 0.3402   5.941579e+00   6.081215e+00
   3_xyz:  0.2132 0.2690   5.702394e+00   5.876943e+00
   3_adp:  0.1909 0.2476   5.613508e+00   5.806764e+00
   3_occ:  0.1907 0.2478   5.613382e+00   5.807004e+00
   4_bss:  0.1902 0.2468   5.611010e+00   5.803270e+00
   4_xyz:  0.1532 0.2006   5.408871e+00   5.617747e+00
   4_adp:  0.1429 0.1876   5.343293e+00   5.550642e+00
   4_occ:  0.1427 0.1875   5.342534e+00   5.550516e+00
   5_bss:  0.1428 0.1875   5.344271e+00   5.550975e+00
   5_xyz:  0.1230 0.1705   5.225640e+00   5.457450e+00
   5_adp:  0.1202 0.1656   5.201740e+00   5.432275e+00
   5_occ:  0.1201 0.1654   5.200774e+00   5.431768e+00
   5_bss:  0.1204 0.1646   5.201330e+00   5.430440e+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:  0.296  20.000  -2.070   4.888  -1.125   0.000  -0.000  -0.000
   1_xyz:  0.296  20.000  -2.070   4.888  -1.125   0.000  -0.000  -0.000
   1_adp:  0.296  20.000  -2.070   4.888  -1.125   0.000  -0.000  -0.000
   1_occ:  0.296  20.000  -2.070   4.888  -1.125   0.000  -0.000  -0.000
   2_bss:  0.295  34.247  -1.610   3.502  -0.261   0.000  -0.000  -0.000
   2_xyz:  0.295  34.247  -1.610   3.502  -0.261   0.000  -0.000  -0.000
   2_adp:  0.295  34.247  -1.610   3.502  -0.261   0.000  -0.000  -0.000
   2_occ:  0.295  34.247  -1.610   3.502  -0.261   0.000  -0.000  -0.000
   3_bss:  0.306  41.164  -1.299   2.548  -0.064   0.000  -0.000  -0.000
   3_xyz:  0.306  41.164  -1.299   2.548  -0.064   0.000  -0.000  -0.000
   3_adp:  0.306  41.164  -1.299   2.548  -0.064   0.000  -0.000  -0.000
   3_occ:  0.306  41.164  -1.299   2.548  -0.064   0.000  -0.000  -0.000
   4_bss:  0.322  57.282  -1.935   0.589  -0.647   0.000  -0.000  -0.000
   4_xyz:  0.322  57.282  -1.935   0.589  -0.647   0.000  -0.000  -0.000
   4_adp:  0.322  57.282  -1.935   0.589  -0.647   0.000  -0.000  -0.000
   4_occ:  0.322  57.282  -1.935   0.589  -0.647   0.000  -0.000  -0.000
   5_bss:  0.330  57.282  -2.336  -0.295  -0.832  -0.000  -0.000  -0.000
   5_xyz:  0.330  57.282  -2.336  -0.295  -0.832  -0.000  -0.000  -0.000
   5_adp:  0.330  57.282  -2.336  -0.295  -0.832  -0.000  -0.000  -0.000
   5_occ:  0.330  57.282  -2.336  -0.295  -0.832  -0.000  -0.000  -0.000
   5_bss:  0.328  57.285  -2.438  -0.744  -0.904  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.929 0.4982  0.6665    62263.471
   1_bss:  50.815 0.5110  0.6956    58740.134
   1_xyz:  44.878 0.5836  0.7753    46078.810
   1_adp:  44.884 0.5834  0.7790    46544.197
   1_occ:  44.847 0.5838  0.7778    46362.471
   2_bss:  44.598 0.5869  0.7853    46045.910
   2_xyz:  38.523 0.6587  0.8716    34286.660
   2_adp:  37.639 0.6697  0.8666    33373.020
   2_occ:  37.616 0.6700  0.8662    33325.400
   3_bss:  37.539 0.6710  0.8640    33293.073
   3_xyz:  27.759 0.7812  0.9756    19001.919
   3_adp:  24.950 0.8119  0.9859    16149.935
   3_occ:  24.946 0.8120  0.9862    16174.092
   4_bss:  24.717 0.8142  0.9532    15904.749
   4_xyz:  19.414 0.8666  0.9853    10210.254
   4_adp:  17.643 0.8837  0.9873     8926.836
   4_occ:  17.630 0.8838  0.9874     8924.942
   5_bss:  17.628 0.8838  0.9706     8935.557
   5_xyz:  15.637 0.9013  0.9805     7421.916
   5_adp:  15.061 0.9064  0.9777     7169.542
   5_occ:  15.043 0.9066  0.9778     7159.518
   5_bss:  15.017 0.9068  0.9710     7130.266
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8314e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8314e-01
   1_xyz:   1.416  0.010  0.085 15.566  0.005  4.107   1.0548e-01
   1_adp:   1.416  0.010  0.085 15.566  0.005  4.107   1.0548e-01
   1_occ:   1.416  0.010  0.085 15.566  0.005  4.107   1.0548e-01
   2_bss:   1.416  0.010  0.085 15.566  0.005  4.107   1.0548e-01
   2_xyz:   1.294  0.009  0.082 15.105  0.006  4.119   9.0959e-02
   2_adp:   1.294  0.009  0.082 15.105  0.006  4.119   9.0959e-02
   2_occ:   1.294  0.009  0.082 15.105  0.006  4.119   9.0959e-02
   3_bss:   1.294  0.009  0.082 15.105  0.006  4.119   9.0959e-02
   3_xyz:   1.316  0.010  0.081 15.122  0.006  4.112   9.5283e-02
   3_adp:   1.316  0.010  0.081 15.122  0.006  4.112   9.5283e-02
   3_occ:   1.316  0.010  0.081 15.122  0.006  4.112   9.5283e-02
   4_bss:   1.316  0.010  0.081 15.122  0.006  4.112   9.5283e-02
   4_xyz:   1.062  0.007  0.072 14.848  0.004  4.109   6.6046e-02
   4_adp:   1.062  0.007  0.072 14.848  0.004  4.109   6.6046e-02
   4_occ:   1.062  0.007  0.072 14.848  0.004  4.109   6.6046e-02
   5_bss:   1.062  0.007  0.072 14.848  0.004  4.109   6.6046e-02
   5_xyz:   1.140  0.009  0.079 15.150  0.005  4.110   7.5153e-02
   5_adp:   1.140  0.009  0.079 15.150  0.005  4.110   7.5153e-02
   5_occ:   1.140  0.009  0.079 15.150  0.005  4.110   7.5153e-02
   5_bss:   1.140  0.009  0.079 15.150  0.005  4.110   7.5153e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.484   2.4157e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.484   2.4157e-01
   1_xyz:   8.225  0.051  0.443 86.872  0.046  1.904   9.0018e-02
   1_adp:   8.225  0.051  0.443 86.872  0.046  1.904   9.0018e-02
   1_occ:   8.225  0.051  0.443 86.872  0.046  1.904   9.0018e-02
   2_bss:   8.225  0.051  0.443 86.872  0.046  1.904   9.0018e-02
   2_xyz:   8.375  0.065  0.291 82.456  0.036  2.142   1.1643e-01
   2_adp:   8.375  0.065  0.291 82.456  0.036  2.142   1.1643e-01
   2_occ:   8.375  0.065  0.291 82.456  0.036  2.142   1.1643e-01
   3_bss:   8.375  0.065  0.291 82.456  0.036  2.142   1.1643e-01
   3_xyz:   7.226  0.059  0.319 83.006  0.051  2.183   9.9445e-02
   3_adp:   7.226  0.059  0.319 83.006  0.051  2.183   9.9445e-02
   3_occ:   7.226  0.059  0.319 83.006  0.051  2.183   9.9445e-02
   4_bss:   7.226  0.059  0.319 83.006  0.051  2.183   9.9445e-02
   4_xyz:   7.510  0.056  0.237 79.670  0.030  2.261   6.0536e-02
   4_adp:   7.510  0.056  0.237 79.670  0.030  2.261   6.0536e-02
   4_occ:   7.510  0.056  0.237 79.670  0.030  2.261   6.0536e-02
   5_bss:   7.510  0.056  0.237 79.670  0.030  2.261   6.0536e-02
   5_xyz:   8.240  0.051  0.281 82.359  0.033  2.315   9.0060e-02
   5_adp:   8.240  0.051  0.281 82.359  0.033  2.315   9.0060e-02
   5_occ:   8.240  0.051  0.281 82.359  0.033  2.315   9.0060e-02
   5_bss:   8.240  0.051  0.281 82.359  0.033  2.315   9.0060e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  92.41   0.00  19.05  80.05   0.00  15.93  92.41   0.00  36.00
   1_occ:  92.41   0.00  19.05  80.05   0.00  15.93  92.41   0.00  36.00
   2_bss:  92.41   0.00  19.05  80.05   0.00  15.93  92.41   0.00  36.00
   2_xyz:  92.41   0.00  19.05  80.05   0.00  15.93  92.41   0.00  36.00
   2_adp:  94.82   0.00  18.29  94.82   0.00  15.17  92.36   2.39  35.25
   2_occ:  94.82   0.00  18.29  94.82   0.00  15.17  92.36   2.39  35.25
   3_bss:  94.82   0.00  18.29  94.82   0.00  15.17  92.36   2.39  35.25
   3_xyz:  94.82   0.00  18.29  94.82   0.00  15.17  92.36   2.39  35.25
   3_adp:  96.63   0.00  17.84  90.12   0.00  13.68  96.63   4.04  40.50
   3_occ:  96.63   0.00  17.84  90.12   0.00  13.68  96.63   4.04  40.50
   4_bss:  96.63   0.00  17.84  90.12   0.00  13.68  96.63   4.04  40.50
   4_xyz:  96.63   0.00  17.84  90.12   0.00  13.68  96.63   4.04  40.50
   4_adp:  97.42   1.01  17.20  97.42   1.01  12.81  92.72   3.81  41.06
   4_occ:  97.42   1.01  17.20  97.42   1.01  12.81  92.72   3.81  41.06
   5_bss:  97.42   1.01  17.20  97.42   1.01  12.81  92.72   3.81  41.06
   5_xyz:  97.42   1.01  17.20  97.42   1.01  12.81  92.72   3.81  41.06
   5_adp:  95.11   0.00  16.53  95.11   0.00  12.38  92.44   4.92  39.16
   5_occ:  95.11   0.00  16.53  95.11   0.00  12.38  92.44   4.92  39.16
   5_bss:  95.11   0.00  16.53  95.11   0.00  12.38  92.44   4.92  39.16
------------------------------------------------------------------------
 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:    1.740    0.019    0.288
   1_adp:    1.740    0.019    0.288
   1_occ:    1.740    0.019    0.288
   2_bss:    1.740    0.019    0.288
   2_xyz:    1.524    0.028    0.459
   2_adp:    1.524    0.028    0.459
   2_occ:    1.524    0.028    0.459
   3_bss:    1.524    0.028    0.459
   3_xyz:    1.541    0.049    0.687
   3_adp:    1.541    0.049    0.687
   3_occ:    1.541    0.049    0.687
   4_bss:    1.541    0.049    0.687
   4_xyz:    1.516    0.030    0.766
   4_adp:    1.516    0.030    0.766
   4_occ:    1.516    0.030    0.766
   5_bss:    1.516    0.030    0.766
   5_xyz:    1.668    0.061    0.826
   5_adp:    1.668    0.061    0.826
   5_occ:    1.668    0.061    0.826
   5_bss:    1.668    0.061    0.826
------------------------------------------------------------------------

CPU time actual refinement: 349.63


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_355/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_355/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_355/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_355/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_355/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.47 
  Macro-tasks:
    bulk solvent and scale       = 43.03  
    individual site refinement   = 147.15 
    weights calculation          = 29.37  
    collect and process          = 6.39   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 226.04 
  Micro-tasks:
    mask                            = 3.00   
    f_calc                          = 111.59 
    alpha_beta                      = 8.23   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.59 
    fmodel                         = 7.23   
    r_factors                      = 0.22   
    phase_errors                   = 10.50  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 263.73 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.882 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    662 calls, 111.24 s
gradients_fft:          607 calls, 107.77 s

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

# Date 2008-01-16 Time 04:38:09 PST -0800 (1200487089.22 s)
Start R-work = 0.4577, R-free = 0.4459 (no bulk solvent and anisotropic scale)
Final R-work = 0.1415, R-free = 0.1840 (no bulk solvent and anisotropic scale)

Start R-work = 0.4489, R-free = 0.4340
Final R-work = 0.1204, R-free = 0.1646