# Date 2008-01-16 Time 05:03:52 PST -0800 (1200488632.42 s)
#phil __OFF__

Command line arguments: "../578.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14213
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 578

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.6339, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.77, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99063
Completeness in resolution range: 0.95907
Completeness with d_max=infinity: 0.956074

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9592
                             d_min =   1.9906

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9592 1.99063
Completeness in resolution range: 0.95907
Completeness with d_max=infinity: 0.956074

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9596 -  4.2588 [2155/2183]  1940   215  10.0%
  bin  2:  4.2588 -  3.3933 [2044/2063]  1839   205  10.0%
  bin  3:  3.3933 -  2.9682 [2049/2069]  1844   205  10.0%
  bin  4:  2.9682 -  2.6985 [2007/2032]  1808   199   9.9%
  bin  5:  2.6985 -  2.5061 [2009/2028]  1804   205  10.2%
  bin  6:  2.5061 -  2.3589 [1979/2026]  1789   190   9.6%
  bin  7:  2.3589 -  2.2412 [1994/2026]  1791   203  10.2%
  bin  8:  2.2412 -  2.1439 [1960/1996]  1759   201  10.3%
  bin  9:  2.1439 -  2.0616 [1963/1993]  1769   194   9.9%
  bin 10:  2.0616 -  1.9906 [1429/2009]  1287   142   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_578/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.11 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 18
        2.42 -     3.04: 2171
        3.04 -     3.66: 4654
        3.66 -     4.28: 8935
        4.28 -     4.90: 12305
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.170 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  2.199 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.219 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28078 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_578/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_578/model_refine_001.geo

CPU time processing inputs: 8.07


============================ 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 = 69.89875 47.63395 86.82195 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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3430   r_free= 0.3339   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.104227                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7497 0.99   1396  156 0.2905 0.3085      6.3677      6.3732|
|  2:  4.7497 -  3.7902 0.99   1334  149 0.2718 0.2615       6.517      6.5122|
|  3:  3.7902 -  3.3170 0.99   1323  150 0.3023 0.2761      6.4276       6.363|
|  4:  3.3170 -  3.0164 0.99   1306  135 0.3264 0.3065      6.3027      6.1712|
|  5:  3.0164 -  2.8018 0.99   1293  146 0.3560 0.3027      6.1796      6.1032|
|  6:  2.8018 -  2.6375 0.98   1291  143 0.3601 0.3699      6.0984      6.0217|
|  7:  2.6375 -  2.5061 0.99   1292  150 0.3613 0.3472      6.0623      5.9602|
|  8:  2.5061 -  2.3974 0.98   1297  136 0.3748 0.3894      6.0291      6.0562|
|  9:  2.3974 -  2.3055 0.98   1264  146 0.3775 0.3641       5.973      5.9507|
| 10:  2.3055 -  2.2262 0.97   1252  136 0.3981 0.3729      5.9882      5.8875|
| 11:  2.2262 -  2.1568 0.99   1284  147 0.3806 0.3658      5.9004      5.9037|
| 12:  2.1568 -  2.0953 0.98   1281  141 0.4010 0.4243      5.8661       5.954|
| 13:  2.0953 -  2.0403 0.97   1255  134 0.4174 0.3851      5.8052       5.747|
| 14:  2.0403 -  1.9906 0.61    762   90 0.3759 0.4465       5.723      5.7397|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7497  1396   156  0.77  28.22   0.86     0.78      49196.94|
|  2:  4.7497 -  3.7902  1334   149  0.83  23.41   0.96     0.89      51148.25|
|  3:  3.7902 -  3.3170  1323   150  0.80  26.28   0.97     0.93      47576.06|
|  4:  3.3170 -  3.0164  1306   135  0.78  28.83   0.97     0.92      39818.80|
|  5:  3.0164 -  2.8018  1293   146  0.71  34.26   0.97     0.87      34426.21|
|  6:  2.8018 -  2.6375  1291   143  0.70  36.11   0.98     0.85      31553.63|
|  7:  2.6375 -  2.5061  1292   150  0.68  37.32   0.99     0.84      29961.05|
|  8:  2.5061 -  2.3974  1297   136  0.68  37.82   0.98     0.87      28732.47|
|  9:  2.3974 -  2.3055  1264   146  0.66  38.82   1.00     0.88      26171.76|
| 10:  2.3055 -  2.2262  1252   136  0.66  38.89   1.00     0.89      24146.72|
| 11:  2.2262 -  2.1568  1284   147  0.66  39.34   1.00     0.90      23385.93|
| 12:  2.1568 -  2.0953  1281   141  0.62  42.41   1.02     0.88      24200.46|
| 13:  2.0953 -  2.0403  1255   134  0.57  46.71   0.99     0.80      23685.47|
| 14:  2.0403 -  1.9906   762    90  0.52  50.77   1.03     0.68      21593.28|
|alpha:            min =        0.68 max =            0.93 mean =         0.86|
|beta:             min =    21593.28 max =        51148.25 mean =     33102.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           90.00 mean =        35.80|
|phase err.(test): min =        0.00 max =           89.84 mean =        36.27|
|-----------------------------------------------------------------------------|

============================== 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 = 5.969278              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.485   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.697085              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.901   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      182 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1989 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2813 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4580 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4355 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5609 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6696 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.155 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    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: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3430   r_free= 0.3339   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.104227                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3284   r_free= 0.3186   ksol= 0.31   Bsol= 43.51   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,3.41,-1.12,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.080957                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.528954              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.373   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.397651              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.699   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3284      final r-factor (work) = 0.1993          |
| start r-factor (free) = 0.3186      final r-factor (free) = 0.2197          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9898 = 5.53 * 0.50 * 6.0872 + 1.00 * 0.1619                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1142 = 5.53 * 0.50 * 5.7995 + 1.00 * 0.0815                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1993      final r-factor (work) = 0.1833          |
| start r-factor (free) = 0.2197      final r-factor (free) = 0.2239          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3125 = 0.40 * 1.00 * 5.7995 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2440 = 0.40 * 1.00 * 5.5564 + 1.00 * 0.0345                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.18   16.44    None  None   None       |
|    all(noH): 2823   0      0.00    67.18   16.44    None  None   None       |
|    Sol.    : 438    0      7.39    64.12   37.43    None  None   None       |
|    Mac.    : 2385   0      0.00    67.18   12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.718:  382   |   5:    33.591 -  40.309:   95        |
|      1:     6.718 -  13.436: 1207   |   6:    40.309 -  47.027:  108        |
|      2:    13.436 -  20.155:  589   |   7:    47.027 -  53.745:   78        |
|      3:    20.155 -  26.873:  191   |   8:    53.745 -  60.464:   37        |
|      4:    26.873 -  33.591:  130   |   9:    60.464 -  67.182:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1833 r_free = 0.2239             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1830 r_free = 0.2242             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1830   r_free= 0.2242   ksol= 0.31   Bsol= 43.51   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,3.41,-1.12,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.563956                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1804   r_free= 0.2200   ksol= 0.33   Bsol= 59.33   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-0.11,-1.19,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.553067                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.256405              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.102  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.294564              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.234   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1804      final r-factor (work) = 0.1341          |
| start r-factor (free) = 0.2200      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1284 = 3.26 * 0.50 * 5.5564 + 1.00 * 0.0815                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8979 = 3.26 * 0.50 * 5.4258 + 1.00 * 0.0636                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1341      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6127 = 0.29 * 1.00 * 5.4258 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5518 = 0.29 * 1.00 * 5.2388 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.59    80.47   16.67    None  None   None       |
|    all(noH): 2823   0      1.59    80.47   16.67    None  None   None       |
|    Sol.    : 438    0      3.96    71.91   38.81    None  None   None       |
|    Mac.    : 2385   0      1.59    80.47   12.60    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:     1.591 -   9.478:  979   |   5:    41.029 -  48.917:  111        |
|      1:     9.478 -  17.366: 1089   |   6:    48.917 -  56.804:   78        |
|      2:    17.366 -  25.254:  260   |   7:    56.804 -  64.692:   48        |
|      3:    25.254 -  33.141:  128   |   8:    64.692 -  72.580:   16        |
|      4:    33.141 -  41.029:  113   |   9:    72.580 -  80.467:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1245 r_free = 0.1630             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1244 r_free = 0.1630             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1630   ksol= 0.33   Bsol= 59.33   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-0.11,-1.19,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.217412                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1244   r_free= 0.1622   ksol= 0.33   Bsol= 59.33   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-1.03,-0.88,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.214616                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.878717              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.332  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.239239              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.585  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6027 = 2.88 * 0.50 * 5.2378 + 1.00 * 0.0636                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5162 = 2.88 * 0.50 * 5.1729 + 1.00 * 0.0705                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1550          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2461 = 0.24 * 1.00 * 5.1729 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2394 = 0.24 * 1.00 * 5.1465 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.16    81.60   16.39    None  None   None       |
|    all(noH): 2823   0      1.16    81.60   16.39    None  None   None       |
|    Sol.    : 438    0      1.74    72.61   38.24    None  None   None       |
|    Mac.    : 2385   0      1.16    81.60   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:     1.164 -   9.208:  934   |   5:    41.384 -  49.429:  108        |
|      1:     9.208 -  17.252: 1142   |   6:    49.429 -  57.473:   83        |
|      2:    17.252 -  25.296:  269   |   7:    57.473 -  65.517:   38        |
|      3:    25.296 -  33.340:  126   |   8:    65.517 -  73.561:   13        |
|      4:    33.340 -  41.384:  108   |   9:    73.561 -  81.605:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1550             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1550             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1550   ksol= 0.33   Bsol= 59.33   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-1.03,-0.88,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141623                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1550   ksol= 0.32   Bsol= 55.40   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-1.22,-0.69,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.141248                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.041220              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.228  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.377413              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.774  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1550      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3230 = 2.04 * 0.50 * 5.1464 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3097 = 2.04 * 0.50 * 5.1437 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9494 = 0.38 * 1.00 * 5.1437 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9491 = 0.38 * 1.00 * 5.1414 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    84.03   16.25    None  None   None       |
|    all(noH): 2823   0      0.49    84.03   16.25    None  None   None       |
|    Sol.    : 438    0      2.26    74.85   38.20    None  None   None       |
|    Mac.    : 2385   0      0.49    84.03   12.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.491 -   8.845:  888   |   5:    42.261 -  50.615:  106        |
|      1:     8.845 -  17.199: 1191   |   6:    50.615 -  58.969:   77        |
|      2:    17.199 -  25.553:  272   |   7:    58.969 -  67.323:   34        |
|      3:    25.553 -  33.907:  130   |   8:    67.323 -  75.677:    8        |
|      4:    33.907 -  42.261:  114   |   9:    75.677 -  84.031:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1563             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1564             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1564   ksol= 0.32   Bsol= 55.40   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-1.22,-0.69,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145041                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1563   ksol= 0.32   Bsol= 55.40   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.16,-0.49,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.145095                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.380173              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.132  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.054241              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.295  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1794 = 2.38 * 0.50 * 5.1420 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1796 = 2.38 * 0.50 * 5.1374 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4247 = 1.05 * 1.00 * 5.1374 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4217 = 1.05 * 1.00 * 5.1334 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.68   16.27    None  None   None       |
|    all(noH): 2823   0      0.00    88.68   16.27    None  None   None       |
|    Sol.    : 438    0      3.93    79.54   38.99    None  None   None       |
|    Mac.    : 2385   0      0.00    88.68   12.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.868:  962   |   5:    44.338 -  53.205:  102        |
|      1:     8.868 -  17.735: 1160   |   6:    53.205 -  62.073:   76        |
|      2:    17.735 -  26.603:  245   |   7:    62.073 -  70.941:   27        |
|      3:    26.603 -  35.470:  123   |   8:    70.941 -  79.808:    5        |
|      4:    35.470 -  44.338:  119   |   9:    79.808 -  88.676:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1575             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1091 r_free = 0.1575             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1575   ksol= 0.32   Bsol= 55.40   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-1.16,-0.49,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.137656                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7497 0.99   1396  156 0.0967 0.1324      5.3783      5.5417|
|  2:  4.7497 -  3.7902 0.99   1334  149 0.0827 0.1060      5.4132      5.6112|
|  3:  3.7902 -  3.3170 0.99   1323  150 0.1020 0.1460      5.4471      5.8263|
|  4:  3.3170 -  3.0164 0.99   1306  135 0.1181 0.1527      5.4307      5.5863|
|  5:  3.0164 -  2.8018 0.99   1293  146 0.1303 0.1670      5.3227      5.5152|
|  6:  2.8018 -  2.6375 0.98   1291  143 0.1220 0.1999      5.2194      5.4863|
|  7:  2.6375 -  2.5061 0.99   1292  150 0.1203 0.1708      5.1532      5.3644|
|  8:  2.5061 -  2.3974 0.98   1297  136 0.1133 0.1656       5.075      5.3371|
|  9:  2.3974 -  2.3055 0.98   1264  146 0.1141 0.1856      5.0142      5.3416|
| 10:  2.3055 -  2.2262 0.97   1252  136 0.1124 0.1702        4.98      5.1679|
| 11:  2.2262 -  2.1568 0.99   1284  147 0.1118 0.1808      4.9266      5.2735|
| 12:  2.1568 -  2.0953 0.98   1281  141 0.1086 0.1660      4.8696      5.1576|
| 13:  2.0953 -  2.0403 0.97   1255  134 0.1068 0.1713      4.7706      5.0352|
| 14:  2.0403 -  1.9906 0.61    762   90 0.1022 0.1833      4.6773      4.9932|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7497  1396   156  0.94   9.28   0.97     0.94       7385.26|
|  2:  4.7497 -  3.7902  1334   149  0.95   7.85   1.00     0.99       8689.15|
|  3:  3.7902 -  3.3170  1323   150  0.94  10.91   1.02     1.01       9899.27|
|  4:  3.3170 -  3.0164  1306   135  0.92  13.29   1.00     0.99       9977.44|
|  5:  3.0164 -  2.8018  1293   146  0.90  15.95   0.99     0.96       8356.09|
|  6:  2.8018 -  2.6375  1291   143  0.90  16.44   0.97     0.94       7223.96|
|  7:  2.6375 -  2.5061  1292   150  0.91  15.40   0.98     0.95       6179.49|
|  8:  2.5061 -  2.3974  1297   136  0.91  15.22   0.98     0.95       5522.44|
|  9:  2.3974 -  2.3055  1264   146  0.91  15.55   0.99     0.95       4954.88|
| 10:  2.3055 -  2.2262  1252   136  0.90  16.27   0.98     0.94       4680.74|
| 11:  2.2262 -  2.1568  1284   147  0.90  15.87   0.98     0.94       4311.32|
| 12:  2.1568 -  2.0953  1281   141  0.91  15.36   0.99     0.97       3966.54|
| 13:  2.0953 -  2.0403  1255   134  0.90  15.97   0.98     0.97       3333.13|
| 14:  2.0403 -  1.9906   762    90  0.92  14.58   0.95     0.91       2607.64|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2607.64 max =         9977.44 mean =      6365.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.06|
|phase err.(test): min =        0.00 max =           89.55 mean =        13.59|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1573   ksol= 0.32   Bsol= 55.75   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-0.93,-0.23,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.137727                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1573   ksol= 0.32   Bsol= 55.75   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-0.93,-0.23,-0.00,-0.00,-0.00); trace/3= -1.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.137727                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9596 -  4.7497 0.99   1396  156 0.0967 0.1327      5.3788      5.5434|
|  2:  4.7497 -  3.7902 0.99   1334  149 0.0829 0.1061      5.4145      5.6117|
|  3:  3.7902 -  3.3170 0.99   1323  150 0.1021 0.1460      5.4475      5.8267|
|  4:  3.3170 -  3.0164 0.99   1306  135 0.1180 0.1526      5.4305      5.5862|
|  5:  3.0164 -  2.8018 0.99   1293  146 0.1303 0.1669      5.3223      5.5147|
|  6:  2.8018 -  2.6375 0.98   1291  143 0.1220 0.1998      5.2191      5.4857|
|  7:  2.6375 -  2.5061 0.99   1292  150 0.1204 0.1708      5.1531      5.3646|
|  8:  2.5061 -  2.3974 0.98   1297  136 0.1133 0.1655      5.0751      5.3369|
|  9:  2.3974 -  2.3055 0.98   1264  146 0.1141 0.1855      5.0143      5.3416|
| 10:  2.3055 -  2.2262 0.97   1252  136 0.1124 0.1703      4.9802      5.1683|
| 11:  2.2262 -  2.1568 0.99   1284  147 0.1118 0.1806      4.9265      5.2732|
| 12:  2.1568 -  2.0953 0.98   1281  141 0.1086 0.1659      4.8693      5.1575|
| 13:  2.0953 -  2.0403 0.97   1255  134 0.1068 0.1713      4.7704      5.0348|
| 14:  2.0403 -  1.9906 0.61    762   90 0.1022 0.1833      4.6773       4.993|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9596 -  4.7497  1396   156  0.94   9.30   0.97     0.95       7400.53|
|  2:  4.7497 -  3.7902  1334   149  0.95   7.86   1.01     0.99       8704.92|
|  3:  3.7902 -  3.3170  1323   150  0.94  10.92   1.02     1.02       9910.90|
|  4:  3.3170 -  3.0164  1306   135  0.92  13.29   1.01     0.99       9974.61|
|  5:  3.0164 -  2.8018  1293   146  0.90  15.95   1.00     0.97       8347.98|
|  6:  2.8018 -  2.6375  1291   143  0.90  16.43   0.98     0.95       7217.06|
|  7:  2.6375 -  2.5061  1292   150  0.91  15.40   0.99     0.96       6176.27|
|  8:  2.5061 -  2.3974  1297   136  0.91  15.23   0.99     0.96       5522.71|
|  9:  2.3974 -  2.3055  1264   146  0.91  15.56   1.00     0.96       4957.36|
| 10:  2.3055 -  2.2262  1252   136  0.90  16.27   0.99     0.95       4680.83|
| 11:  2.2262 -  2.1568  1284   147  0.90  15.87   0.99     0.95       4309.73|
| 12:  2.1568 -  2.0953  1281   141  0.91  15.36   1.00     0.99       3964.77|
| 13:  2.0953 -  2.0403  1255   134  0.90  15.97   0.99     0.98       3331.15|
| 14:  2.0403 -  1.9906   762    90  0.92  14.57   0.96     0.92       2605.69|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2605.69 max =         9974.61 mean =      6366.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.06|
|phase err.(test): min =        0.00 max =           89.56 mean =        13.60|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.68   16.27    None  None   None       |
|    all(noH): 2823   0      0.00    88.68   16.27    None  None   None       |
|    Sol.    : 438    0      3.94    79.54   38.99    None  None   None       |
|    Mac.    : 2385   0      0.00    88.68   12.10    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 -   8.871:  962   |   5:    44.341 -  53.208:  102        |
|      1:     8.871 -  17.738: 1160   |   6:    53.208 -  62.076:   76        |
|      2:    17.738 -  26.606:  245   |   7:    62.076 -  70.943:   27        |
|      3:    26.606 -  35.473:  123   |   8:    70.943 -  79.811:    5        |
|      4:    35.473 -  44.341:  119   |   9:    79.811 -  88.679:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.483 - 4.863
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 299
   mapped sites are within: 0.744 - 4.863

peak=    5.296 closest distance to " NH2 ARG A  56 " =    2.341
peak=    5.292 closest distance to " CB  GLN A 223 " =    1.411
peak=    5.257 closest distance to " CG  PRO A  54 " =    1.282
peak=    5.180 closest distance to " CB  ARG A 275 " =    0.943
peak=    4.945 closest distance to " O   HOH Z 232 " =    2.328
peak=    4.904 closest distance to " CB  GLN A 183 " =    1.309
peak=    4.880 closest distance to " CB  ARG A 190 " =    1.715
peak=    4.820 closest distance to " CB  SER A  63 " =    1.173
peak=    4.691 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.655 closest distance to " CG  PRO A 213 " =    1.190
peak=    4.626 closest distance to " O   HOH Z 126 " =    1.916
peak=    4.568 closest distance to " CB  GLU A 152 " =    1.140
peak=    4.524 closest distance to " C   PRO A 198 " =    1.465
peak=    4.444 closest distance to " CB  TYR A 169 " =    0.807
peak=    4.422 closest distance to " O   HOH Z 403 " =    1.708
peak=    4.396 closest distance to " CB  ARG A  79 " =    1.330
peak=    4.385 closest distance to " O   HOH Z 369 " =    2.253
peak=    4.382 closest distance to " O   HOH Z 234 " =    3.753
peak=    4.365 closest distance to " O   HOH Z 298 " =    1.839
peak=    4.352 closest distance to " CG  PRO A 198 " =    1.231
peak=    4.342 closest distance to " O   HOH Z 142 " =    1.559
peak=    4.309 closest distance to " CG  PRO A  90 " =    1.161
peak=    4.235 closest distance to " CB  PRO A  54 " =    0.904
peak=    4.222 closest distance to " CB  ASN A 148 " =    1.410
peak=    4.185 closest distance to " O   HOH Z 236 " =    2.059
peak=    4.184 closest distance to " O   SER A  87 " =    2.192
peak=    4.163 closest distance to " O   HOH Z 280 " =    2.986
peak=    4.137 closest distance to " O   HOH Z  15 " =    2.118
peak=    4.118 closest distance to " O   HOH Z 203 " =    1.760
peak=    4.115 closest distance to " CZ  PHE A 218 " =    1.123
peak=    4.112 closest distance to " CB  GLU A 128 " =    1.101
peak=    4.109 closest distance to " NE2 GLN A  11 " =    1.018
peak=    4.107 closest distance to " CA  ARG A  36 " =    1.116
peak=    4.103 closest distance to " O   HOH Z 272 " =    1.868
peak=    4.099 closest distance to " O   HOH Z 303 " =    2.171
peak=    4.089 closest distance to " O   HOH Z 209 " =    2.237
peak=    4.072 closest distance to " O   HOH Z  40 " =    2.019
peak=    4.062 closest distance to " CB  GLU A 277 " =    3.678
peak=    4.053 closest distance to " O   HOH Z 402 " =    1.460
peak=    4.041 closest distance to " CD  ARG A 269 " =    0.975
peak=    4.024 closest distance to " NZ  LYS A 117 " =    3.319
peak=    4.020 closest distance to " CA  ALA A  51 " =    0.922
peak=    4.019 closest distance to " O   HOH Z 128 " =    2.000
peak=    3.997 closest distance to " O   HOH Z 427 " =    2.998
peak=    3.994 closest distance to " O   HOH Z  43 " =    1.999
peak=    3.979 closest distance to " O   HOH Z 193 " =    1.814
peak=    3.977 closest distance to " CB  LEU A 228 " =    1.090
peak=    3.973 closest distance to " O   HOH Z 158 " =    3.091
peak=    3.968 closest distance to " O   HOH Z 346 " =    1.605
peak=    3.965 closest distance to " OD1 ASN A  69 " =    2.470
peak=    3.957 closest distance to " O   HOH Z 423 " =    1.984
peak=    3.948 closest distance to " CG1 ILE A  33 " =    1.182
peak=    3.940 closest distance to " O   HOH Z 250 " =    1.448
peak=    3.935 closest distance to " O   HOH Z 368 " =    2.129
peak=    3.930 closest distance to " O   HOH Z  97 " =    1.953
peak=    3.927 closest distance to " CB  ARG A  79 " =    0.916
peak=    3.914 closest distance to " CG2 ILE A 120 " =    1.065
peak=    3.900 closest distance to " CB  ASP A 140 " =    0.995
peak=    3.896 closest distance to " O   HOH Z 214 " =    2.220
peak=    3.891 closest distance to " CA  ALA A  21 " =    1.273
peak=    3.887 closest distance to " CD2 TRP A 179 " =    1.365
peak=    3.881 closest distance to " CB  TRP A 266 " =    0.987
peak=    3.868 closest distance to " CB  VAL A 202 " =    1.503
peak=    3.861 closest distance to " O   HOH Z  78 " =    1.657
peak=    3.851 closest distance to " CA  ARG A 195 " =    1.344
peak=    3.851 closest distance to " CG  PRO A 243 " =    1.095
peak=    3.848 closest distance to " O   HOH Z 147 " =    1.847
peak=    3.837 closest distance to " O   HOH Z  44 " =    1.913
peak=    3.833 closest distance to " O   HOH Z 180 " =    2.237
peak=    3.830 closest distance to " CD2 LEU A 297 " =    0.861
peak=    3.819 closest distance to " NH2 ARG A 156 " =    1.166
peak=    3.815 closest distance to " O   HOH Z 183 " =    1.512
peak=    3.811 closest distance to " O   HOH Z 291 " =    1.505
peak=    3.810 closest distance to " CG  ARG A  66 " =    2.471
peak=    3.810 closest distance to " O   HOH Z  63 " =    1.922
peak=    3.806 closest distance to " CB  VAL A 265 " =    1.226
peak=    3.797 closest distance to " OG ASER A 258 " =    3.158
peak=    3.786 closest distance to " NH2BARG A 145 " =    2.123
peak=    3.783 closest distance to " O   HOH Z 406 " =    1.529
peak=    3.776 closest distance to " O   HOH Z 279 " =    2.186
peak=    3.774 closest distance to " CG1BVAL A  72 " =    1.802
peak=    3.774 closest distance to " CE  LYS A  76 " =    0.849
peak=    3.771 closest distance to " C   ILE A 106 " =    1.902
peak=    3.765 closest distance to " ND2 ASN A 187 " =    1.479
peak=    3.764 closest distance to " O   HOH Z 189 " =    2.520
peak=    3.757 closest distance to " CD1 LEU A 300 " =    1.225
peak=    3.738 closest distance to " O   HOH Z 126 " =    1.601
peak=    3.730 closest distance to " CA  ASN A 176 " =    1.251
peak=    3.727 closest distance to " OG1 THR A 294 " =    2.416
peak=    3.720 closest distance to " CA  PRO A  54 " =    1.348
peak=    3.719 closest distance to " O   HOH Z 426 " =    1.616
peak=    3.713 closest distance to " O   HOH Z  21 " =    1.851
peak=    3.707 closest distance to " O   HOH Z 133 " =    2.721
peak=    3.705 closest distance to " OD2 ASP A 298 " =    3.852
peak=    3.704 closest distance to " CG2 VAL A 257 " =    0.869
peak=    3.702 closest distance to " O   HOH Z 421 " =    1.669
peak=    3.700 closest distance to " O   HOH Z 371 " =    3.321
peak=    3.700 closest distance to " CB  GLU A  46 " =    0.991
peak=    3.685 closest distance to " CA  ASN A 215 " =    1.085
peak=    3.672 closest distance to " O   HOH Z 265 " =    2.146
peak=    3.671 closest distance to " O   HOH Z 412 " =    3.790
peak=    3.649 closest distance to " O   HOH Z 185 " =    1.749
peak=    3.643 closest distance to " CB  TRP A 179 " =    1.318
peak=    3.636 closest distance to " CB  ASN A  39 " =    0.845
peak=    3.636 closest distance to " CD  LYS A 166 " =    1.333
peak=    3.635 closest distance to " O   HOH Z 197 " =    2.776
peak=    3.633 closest distance to " O   HOH Z 171 " =    1.809
peak=    3.632 closest distance to " CA  ALA A  84 " =    1.248
peak=    3.627 closest distance to " NE2 GLN A  77 " =    3.241
peak=    3.625 closest distance to " O   HOH Z  54 " =    1.685
peak=    3.623 closest distance to " O   HOH Z 359 " =    1.476
peak=    3.610 closest distance to " CB  SER A   3 " =    1.395
peak=    3.607 closest distance to " O   HOH Z  68 " =    1.893
peak=    3.597 closest distance to " CA  ALA A 160 " =    0.895
peak=    3.593 closest distance to " CD  ARG A 159 " =    0.804
peak=    3.592 closest distance to " O   HOH Z  59 " =    2.384
peak=    3.590 closest distance to " CA  LYS A 117 " =    1.261
peak=    3.583 closest distance to " CA  THR A 221 " =    0.957
peak=    3.577 closest distance to " O   HOH Z 108 " =    2.874
peak=    3.570 closest distance to " O   HOH Z  97 " =    2.345
peak=    3.566 closest distance to " O   HOH Z 389 " =    1.924
peak=    3.552 closest distance to " NH1AARG A 145 " =    1.262
peak=    3.544 closest distance to " ND1 HIS A  81 " =    1.633
peak=    3.537 closest distance to " CB  ALA A 248 " =    1.321
peak=    3.522 closest distance to " O   HOH Z 299 " =    4.430
peak=    3.510 closest distance to " O   HOH Z  80 " =    1.718
peak=    3.507 closest distance to " OG BSER A 164 " =    2.356
peak=    3.505 closest distance to " OE1 GLU A   2 " =    2.193
peak=    3.501 closest distance to " CB  THR A  31 " =    1.667
peak=    3.497 closest distance to " O   HOH Z 325 " =    2.296
peak=    3.492 closest distance to " CG2 THR A 221 " =    1.099
peak=    3.491 closest distance to " CB  ASN A 215 " =    1.190
peak=    3.490 closest distance to " CB  GLN A 103 " =    0.853
peak=    3.488 closest distance to " O   HOH Z 163 " =    1.555
peak=    3.486 closest distance to " O   HOH Z  19 " =    1.753
peak=    3.485 closest distance to " O   HOH Z 245 " =    1.337
peak=    3.484 closest distance to " CG  MET A 185 " =    1.137
peak=    3.482 closest distance to " O   ALA A 165 " =    1.467
peak=    3.480 closest distance to " O   HOH Z 148 " =    3.310
peak=    3.479 closest distance to " O   HOH Z 383 " =    2.163
peak=    3.475 closest distance to " O   HOH Z 285 " =    2.907
peak=    3.472 closest distance to " O   HOH Z 261 " =    1.707
peak=    3.467 closest distance to " O   HOH Z 416 " =    2.890
peak=    3.466 closest distance to " O   ASN A  74 " =    1.575
peak=    3.465 closest distance to " O   HOH Z 362 " =    3.598
peak=    3.463 closest distance to " CG  GLN A  58 " =    2.778
peak=    3.456 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.452 closest distance to " O   HOH Z 365 " =    2.874
peak=    3.450 closest distance to " O   HOH Z 357 " =    2.056
peak=    3.447 closest distance to " CB  ALA A 291 " =    1.318
peak=    3.446 closest distance to " CB  ARG A 139 " =    0.905
peak=    3.445 closest distance to " CE1 TYR A 186 " =    1.266
peak=    3.445 closest distance to " CB  ASN A 142 " =    1.144
peak=    3.443 closest distance to " CA  ALA A 248 " =    1.227
peak=    3.441 closest distance to " CG2 ILE A  20 " =    1.282
peak=    3.436 closest distance to " O   HOH Z 345 " =    1.653
peak=    3.431 closest distance to " CG AARG A 275 " =    1.141
peak=    3.430 closest distance to " O   HOH Z 102 " =    1.292
peak=    3.428 closest distance to " O   HOH Z 258 " =    2.176
peak=    3.426 closest distance to " ND2 ASN A 110 " =    1.570
peak=    3.423 closest distance to " O   HOH Z  66 " =    2.184
peak=    3.422 closest distance to " O   HOH Z 261 " =    1.944
peak=    3.419 closest distance to " N   ASN A  39 " =    1.355
peak=    3.416 closest distance to " O   HOH Z 403 " =    1.384
peak=    3.416 closest distance to " CA  MET A 105 " =    1.045
peak=    3.411 closest distance to " OD2 ASP A 286 " =    2.838
peak=    3.410 closest distance to " O   HOH Z 305 " =    3.719
peak=    3.407 closest distance to " CA  TYR A 116 " =    1.403
peak=    3.407 closest distance to " O   HOH Z 353 " =    2.757
peak=    3.401 closest distance to " O   HOH Z 391 " =    2.939
peak=    3.400 closest distance to " O   HOH Z 417 " =    3.006
peak=    3.392 closest distance to " CB  SER A 212 " =    1.071
peak=    3.387 closest distance to " CA  ALA A 295 " =    1.077
peak=    3.385 closest distance to " CB  SER A  26 " =    1.729
peak=    3.385 closest distance to " CB  MET A  47 " =    0.978
peak=    3.385 closest distance to " O   HOH Z 173 " =    2.115
peak=    3.385 closest distance to " O   HOH Z  35 " =    2.372
peak=    3.373 closest distance to " O   HOH Z 227 " =    1.640
peak=    3.372 closest distance to " O   HOH Z 193 " =    2.171
peak=    3.371 closest distance to " CB  SER A 141 " =    1.004
peak=    3.371 closest distance to " CB  SER A  62 " =    0.874
peak=    3.365 closest distance to " CG  GLU A  37 " =    0.880
peak=    3.365 closest distance to " CG2 VAL A 197 " =    1.107
peak=    3.365 closest distance to " CD1 ILE A 106 " =    0.911
peak=    3.360 closest distance to " O   HOH Z 422 " =    2.633
peak=    3.358 closest distance to " CB  ILE A 120 " =    1.251
peak=    3.354 closest distance to " CB  TYR A 169 " =    0.834
peak=    3.347 closest distance to " O   THR A 251 " =    1.081
peak=    3.342 closest distance to " O   HOH Z 425 " =    1.978
peak=    3.341 closest distance to " O   THR A 220 " =    1.216
peak=    3.335 closest distance to " O   HOH Z 134 " =    1.284
peak=    3.334 closest distance to " O   TRP A 274 " =    1.908
peak=    3.331 closest distance to " O   HOH Z  10 " =    1.784
peak=    3.329 closest distance to " O   HOH Z 374 " =    2.711
peak=    3.328 closest distance to " NH2AARG A 275 " =    3.583
peak=    3.327 closest distance to " CG1 VAL A 153 " =    0.959
peak=    3.321 closest distance to " O   HOH Z 380 " =    1.944
peak=    3.318 closest distance to " O   HOH Z 344 " =    3.162
peak=    3.317 closest distance to " O   HOH Z 132 " =    2.581
peak=    3.316 closest distance to " CA  ALA A 291 " =    0.792
peak=    3.310 closest distance to " O   ALA A 158 " =    1.153
peak=    3.304 closest distance to " O   HOH Z 417 " =    2.131
peak=    3.301 closest distance to " CB  ASP A 298 " =    1.222
peak=    3.295 closest distance to " O   HOH Z 345 " =    3.053
peak=    3.290 closest distance to " OG BSER A 134 " =    2.913
peak=    3.279 closest distance to " CA  ALA A 233 " =    1.532
peak=    3.277 closest distance to " CD BLYS A 290 " =    0.984
peak=    3.270 closest distance to " CD1AILE A 234 " =    0.909
peak=    3.268 closest distance to " CA  MET A  40 " =    1.113
peak=    3.267 closest distance to " O   HOH Z 128 " =    2.269
peak=    3.267 closest distance to " OG  SER A  22 " =    2.667
peak=    3.267 closest distance to " CA  ASP A 191 " =    0.891
peak=    3.266 closest distance to " NZ  LYS A  48 " =    1.302
peak=    3.265 closest distance to " O   HOH Z 234 " =    1.790
peak=    3.258 closest distance to " O   HOH Z  20 " =    1.427
peak=    3.258 closest distance to " O   HOH Z 427 " =    3.139
peak=    3.251 closest distance to " O   HOH Z 250 " =    1.554
peak=    3.239 closest distance to " O   HOH Z   1 " =    2.277
peak=    3.238 closest distance to " CG2BVAL A  41 " =    0.828
peak=    3.236 closest distance to " CG  LYS A  76 " =    1.034
peak=    3.234 closest distance to " CB  GLN A  88 " =    1.169
peak=    3.233 closest distance to " CZ  PHE A  38 " =    1.285
peak=    3.231 closest distance to " CB  GLN A 205 " =    1.070
peak=    3.228 closest distance to " O   HOH Z 393 " =    3.225
peak=    3.226 closest distance to " O   HOH Z 411 " =    1.699
peak=    3.223 closest distance to " CA  ASP A 140 " =    1.176
peak=    3.223 closest distance to " O   ASP A 124 " =    1.267
peak=    3.221 closest distance to " C   SER A  32 " =    1.066
peak=    3.220 closest distance to " CZ2 TRP A 179 " =    1.704
peak=    3.212 closest distance to " CB  ALA A 227 " =    1.069
peak=    3.210 closest distance to " O   HOH Z  62 " =    2.267
peak=    3.201 closest distance to " CB  ALA A   1 " =    4.863
peak=    3.197 closest distance to " CD1 ILE A 199 " =    1.067
peak=    3.196 closest distance to " C   TYR A 214 " =    1.461
peak=    3.189 closest distance to " CD  PRO A  54 " =    1.088
peak=    3.186 closest distance to " O   HOH Z 298 " =    2.469
peak=    3.186 closest distance to " O   HOH Z 294 " =    1.490
peak=    3.186 closest distance to " O   HOH Z  44 " =    3.427
peak=    3.186 closest distance to " CA  SER A  87 " =    1.068
peak=    3.185 closest distance to " NE2 GLN A  58 " =    3.062
peak=    3.182 closest distance to " CB  SER A 273 " =    0.856
peak=    3.181 closest distance to " OH  TYR A 116 " =    1.080
peak=    3.179 closest distance to " CA  VAL A 125 " =    1.152
peak=    3.178 closest distance to " CB  TYR A 116 " =    0.780
peak=    3.175 closest distance to " CB  THR A  52 " =    0.842
peak=    3.173 closest distance to " CA  THR A 264 " =    0.865
peak=    3.173 closest distance to " O   HOH Z  88 " =    3.326
peak=    3.172 closest distance to " CG  ARG A 219 " =    1.164
peak=    3.171 closest distance to " O   HOH Z 193 " =    1.598
peak=    3.169 closest distance to " O   HOH Z 109 " =    2.596
peak=    3.167 closest distance to " N   ASN A 127 " =    1.270
peak=    3.164 closest distance to " CG1 ILE A  49 " =    1.557
peak=    3.164 closest distance to " O   HOH Z  61 " =    1.495
peak=    3.163 closest distance to " O   HOH Z 313 " =    1.883
peak=    3.161 closest distance to " CG BARG A 275 " =    1.400
peak=    3.154 closest distance to " CB  PHE A 204 " =    0.937
peak=    3.153 closest distance to " CZ3 TRP A  85 " =    0.864
peak=    3.150 closest distance to " O  BHOH Z 338 " =    2.306
peak=    3.149 closest distance to " O   HOH Z 336 " =    1.615
peak=    3.142 closest distance to " O   HOH Z 350 " =    1.794
peak=    3.142 closest distance to " O   HOH Z 156 " =    2.522
peak=    3.139 closest distance to " O   HOH Z 359 " =    3.968
peak=    3.139 closest distance to " ND2 ASN A 249 " =    0.879
peak=    3.137 closest distance to " CA  ASP A 191 " =    1.117
peak=    3.137 closest distance to " CB  ALA A   9 " =    1.539
peak=    3.131 closest distance to " CG  GLN A  11 " =    1.536
peak=    3.129 closest distance to " O   HOH Z 423 " =    3.377
peak=    3.127 closest distance to " CB  HIS A 108 " =    0.790
peak=    3.126 closest distance to " CB  ALA A 114 " =    1.056
peak=    3.125 closest distance to " CA  ASN A 217 " =    1.216
peak=    3.120 closest distance to " O   HOH Z 336 " =    1.758
peak=    3.116 closest distance to " CG  MET A 185 " =    1.014
peak=    3.114 closest distance to " OG  SER A 245 " =    1.569
peak=    3.113 closest distance to " O   HOH Z  85 " =    2.238
peak=    3.111 closest distance to " OG1 THR A 279 " =    1.793
peak=    3.107 closest distance to " CB  ASN A 285 " =    0.952
peak=    3.104 closest distance to " CE  LYS A  48 " =    1.045
peak=    3.103 closest distance to " CD2 TYR A  30 " =    1.003
peak=    3.101 closest distance to " CD  LYS A 119 " =    1.368
peak=    3.097 closest distance to " CG2 THR A 220 " =    0.744
peak=    3.087 closest distance to " O   HOH Z 267 " =    1.983
peak=    3.087 closest distance to " O   HOH Z 293 " =    1.953
peak=    3.085 closest distance to " O   HOH Z 327 " =    1.608
peak=    3.084 closest distance to " O   HOH Z  88 " =    2.604
peak=    3.068 closest distance to " O   HOH Z 163 " =    1.842
peak=    3.063 closest distance to " O   ALA A 100 " =    1.579
peak=    3.063 closest distance to " CB  PRO A  90 " =    1.184
peak=    3.058 closest distance to " O   HOH Z 251 " =    1.528
peak=    3.042 closest distance to " CD  ARG A  66 " =    2.548
peak=    3.028 closest distance to " O   GLU A   2 " =    1.655
peak=    3.024 closest distance to " CA  THR A 221 " =    1.467
peak=    3.023 closest distance to " CA  ILE A 106 " =    0.800
peak=    3.014 closest distance to " O   HOH Z 392 " =    1.959

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.841 - 5.849
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.841 - 5.849

peak=   -4.844 closest distance to " O   HOH Z 266 " =    4.957
peak=   -4.611 closest distance to " CD  GLN A  58 " =    1.011
peak=   -4.584 closest distance to " CB  PRO A 243 " =    2.679
peak=   -4.460 closest distance to " C   HIS A 108 " =    1.142
peak=   -4.197 closest distance to " O   HOH Z 372 " =    2.411
peak=   -4.170 closest distance to " O   HOH Z 231 " =    2.325
peak=   -4.167 closest distance to " O   VAL A  67 " =    2.727
peak=   -4.159 closest distance to " CA  ASP A 298 " =    1.052
peak=   -4.158 closest distance to " CD  ARG A 156 " =    2.087
peak=   -4.125 closest distance to " SG  CYS A 254 " =    3.433
peak=   -4.078 closest distance to " O   HOH Z  10 " =    1.580
peak=   -4.076 closest distance to " OXT GLY A 302 " =    2.861
peak=   -4.064 closest distance to " CG  ASP A 132 " =    2.352
peak=   -4.056 closest distance to " OG  SER A  97 " =    2.251
peak=   -4.054 closest distance to " O   HOH Z 377 " =    2.095
peak=   -4.044 closest distance to " CD1 LEU A 101 " =    2.389
peak=   -4.013 closest distance to " CB  ALA A 161 " =    2.629
peak=   -4.002 closest distance to " O   HOH Z 196 " =    1.975
peak=   -3.992 closest distance to " OE1 GLN A 223 " =    2.068
peak=   -3.961 closest distance to " O   HOH Z 394 " =    1.553
peak=   -3.952 closest distance to " CZ3 TRP A 179 " =    1.218
peak=   -3.917 closest distance to " CD1 PHE A  59 " =    1.955
peak=   -3.913 closest distance to " O   HOH Z 198 " =    2.121
peak=   -3.884 closest distance to " OG BSER A 134 " =    1.335
peak=   -3.874 closest distance to " CG1 VAL A 250 " =    2.677
peak=   -3.868 closest distance to " O   HOH Z 292 " =    4.623
peak=   -3.867 closest distance to " O   HOH Z  13 " =    1.727
peak=   -3.847 closest distance to " CG2 ILE A 263 " =    2.322
peak=   -3.814 closest distance to " N   ALA A  43 " =    2.678
peak=   -3.814 closest distance to " O   HOH Z 353 " =    2.217
peak=   -3.808 closest distance to " CB  ALA A 291 " =    2.282
peak=   -3.799 closest distance to " O   HOH Z 283 " =    2.247
peak=   -3.797 closest distance to " CA  VAL A  67 " =    2.950
peak=   -3.796 closest distance to " CE2 PHE A  61 " =    2.548
peak=   -3.792 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.783 closest distance to " CE2 TYR A  30 " =    2.715
peak=   -3.782 closest distance to " ND2 ASN A  45 " =    1.768
peak=   -3.768 closest distance to " O   HOH Z 166 " =    1.756
peak=   -3.766 closest distance to " O   HOH Z  52 " =    1.516
peak=   -3.765 closest distance to " O   HOH Z 290 " =    1.179
peak=   -3.753 closest distance to " CB  PHE A 192 " =    2.071
peak=   -3.747 closest distance to " CB  PHE A 208 " =    2.286
peak=   -3.737 closest distance to " CG1 VAL A 112 " =    2.800
peak=   -3.705 closest distance to " CD1 LEU A  25 " =    2.502
peak=   -3.677 closest distance to " O   SER A 210 " =    1.927
peak=   -3.676 closest distance to " NE2 GLN A  88 " =    1.824
peak=   -3.675 closest distance to " N   THR A  52 " =    1.660
peak=   -3.675 closest distance to " O   PRO A 163 " =    2.123
peak=   -3.669 closest distance to " CD  ARG A 139 " =    1.601
peak=   -3.646 closest distance to " CE3 TRP A 150 " =    2.197
peak=   -3.642 closest distance to " CD  GLN A 223 " =    1.255
peak=   -3.639 closest distance to " O   HOH Z 114 " =    3.236
peak=   -3.638 closest distance to " CB  ASN A  39 " =    2.388
peak=   -3.628 closest distance to " NH2 ARG A 159 " =    2.367
peak=   -3.617 closest distance to " O   HOH Z 126 " =    1.971
peak=   -3.612 closest distance to " OD1 ASN A 148 " =    1.491
peak=   -3.611 closest distance to " O   HOH Z 211 " =    1.624
peak=   -3.594 closest distance to " ND2 ASN A 187 " =    1.558
peak=   -3.582 closest distance to " ND2 ASN A  45 " =    1.113
peak=   -3.575 closest distance to " CG1 VAL A 112 " =    2.809
peak=   -3.572 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -3.563 closest distance to " O   HOH Z 171 " =    2.084
peak=   -3.558 closest distance to " O   PHE A 218 " =    1.571
peak=   -3.553 closest distance to " CD2 TYR A 293 " =    2.055
peak=   -3.536 closest distance to " CB  ASP A 286 " =    1.898
peak=   -3.535 closest distance to " O   HOH Z 165 " =    1.889
peak=   -3.517 closest distance to " O   HOH Z 407 " =    3.074
peak=   -3.516 closest distance to " CB  ALA A 248 " =    2.256
peak=   -3.515 closest distance to " O   HOH Z 123 " =    2.357
peak=   -3.507 closest distance to " O   HOH Z   6 " =    2.255
peak=   -3.506 closest distance to " NH2 ARG A  79 " =    2.060
peak=   -3.504 closest distance to " OG BSER A 210 " =    2.190
peak=   -3.499 closest distance to " CA  GLY A 203 " =    2.454
peak=   -3.497 closest distance to " ND2 ASN A 249 " =    2.402
peak=   -3.486 closest distance to " CZ  TYR A 169 " =    1.838
peak=   -3.483 closest distance to " CG1 VAL A  67 " =    3.133
peak=   -3.481 closest distance to " O   HOH Z 177 " =    1.792
peak=   -3.474 closest distance to " O   HOH Z 252 " =    3.893
peak=   -3.469 closest distance to " CB  ALA A 291 " =    2.307
peak=   -3.467 closest distance to " N   GLN A  58 " =    1.474
peak=   -3.465 closest distance to " O   HOH Z 185 " =    2.457
peak=   -3.461 closest distance to " O   HOH Z  71 " =    1.873
peak=   -3.459 closest distance to " CD  ARG A 195 " =    5.135
peak=   -3.456 closest distance to " CE BMET A  47 " =    1.944
peak=   -3.455 closest distance to " CG2 ILE A  49 " =    2.711
peak=   -3.448 closest distance to " O   HOH Z 311 " =    3.758
peak=   -3.447 closest distance to " O   ALA A  10 " =    1.769
peak=   -3.447 closest distance to " OG BSER A 134 " =    1.867
peak=   -3.442 closest distance to " O   HOH Z 234 " =    4.185
peak=   -3.438 closest distance to " O   HOH Z 351 " =    1.477
peak=   -3.430 closest distance to " CB  ALA A  43 " =    2.568
peak=   -3.428 closest distance to " CG  GLU A 277 " =    1.118
peak=   -3.419 closest distance to " CD2 LEU A 300 " =    2.759
peak=   -3.418 closest distance to " CB  TRP A  85 " =    2.461
peak=   -3.413 closest distance to " C   SER A 206 " =    1.497
peak=   -3.412 closest distance to " CA  GLY A 133 " =    2.334
peak=   -3.410 closest distance to " O   HOH Z 389 " =    1.824
peak=   -3.400 closest distance to " O   HOH Z   6 " =    1.621
peak=   -3.395 closest distance to " N   ALA A 226 " =    2.052
peak=   -3.393 closest distance to " CB  PHE A  16 " =    2.609
peak=   -3.387 closest distance to " O   HOH Z 166 " =    1.617
peak=   -3.387 closest distance to " OD1 ASP A 171 " =    1.602
peak=   -3.386 closest distance to " CD2 TYR A 247 " =    2.418
peak=   -3.384 closest distance to " O   HOH Z 243 " =    1.908
peak=   -3.375 closest distance to " NH2AARG A 275 " =    5.246
peak=   -3.372 closest distance to " CG  ASP A 231 " =    0.866
peak=   -3.371 closest distance to " O   VAL A 189 " =    2.658
peak=   -3.370 closest distance to " N   ALA A 248 " =    1.702
peak=   -3.369 closest distance to " O   HOH Z 102 " =    1.553
peak=   -3.368 closest distance to " O   HOH Z  37 " =    1.824
peak=   -3.368 closest distance to " CD1 LEU A 228 " =    2.201
peak=   -3.359 closest distance to " O   SER A  62 " =    2.118
peak=   -3.355 closest distance to " SG ACYS A 201 " =    1.922
peak=   -3.353 closest distance to " CZ  PHE A 155 " =    1.241
peak=   -3.352 closest distance to " NE2 GLN A 103 " =    1.760
peak=   -3.352 closest distance to " O   HOH Z 256 " =    2.397
peak=   -3.348 closest distance to " OD1 ASN A  39 " =    2.239
peak=   -3.346 closest distance to " O   HOH Z 377 " =    1.790
peak=   -3.346 closest distance to " N   SER A 276 " =    1.413
peak=   -3.341 closest distance to " O   HOH Z 111 " =    1.690
peak=   -3.338 closest distance to " O   HOH Z  15 " =    1.453
peak=   -3.332 closest distance to " C   LEU A 143 " =    1.045
peak=   -3.321 closest distance to " O   ALA A  34 " =    2.307
peak=   -3.316 closest distance to " OD2 ASP A 191 " =    1.504
peak=   -3.311 closest distance to " CB  ALA A 248 " =    2.170
peak=   -3.308 closest distance to " NE2 GLN A 194 " =    1.857
peak=   -3.305 closest distance to " O   HOH Z  43 " =    1.617
peak=   -3.304 closest distance to " CE3 TRP A 274 " =    2.519
peak=   -3.293 closest distance to " CG2 VAL A 189 " =    2.228
peak=   -3.293 closest distance to " CD2 LEU A 237 " =    2.791
peak=   -3.291 closest distance to " CD2 PHE A 225 " =    1.227
peak=   -3.289 closest distance to " O   HOH Z 393 " =    1.418
peak=   -3.275 closest distance to " O   HOH Z 264 " =    1.776
peak=   -3.272 closest distance to " OD2 ASP A 171 " =    2.465
peak=   -3.271 closest distance to " O   ARG A  24 " =    2.103
peak=   -3.270 closest distance to " CZ  PHE A  59 " =    1.774
peak=   -3.270 closest distance to " CA  GLY A 241 " =    3.135
peak=   -3.266 closest distance to " N   MET A 105 " =    2.557
peak=   -3.264 closest distance to " O   HOH Z 377 " =    1.877
peak=   -3.263 closest distance to " O   HOH Z 414 " =    1.539
peak=   -3.256 closest distance to " NH2 ARG A  66 " =    5.849
peak=   -3.254 closest distance to " CD  GLU A 236 " =    1.072
peak=   -3.252 closest distance to " O   HOH Z 193 " =    1.827
peak=   -3.252 closest distance to " CB  ALA A  10 " =    2.248
peak=   -3.248 closest distance to " CZ2 TRP A 274 " =    1.104
peak=   -3.244 closest distance to " O   PRO A 198 " =    1.339
peak=   -3.239 closest distance to " ND2BASN A 224 " =    1.741
peak=   -3.238 closest distance to " NH2 ARG A  79 " =    1.588
peak=   -3.235 closest distance to " OG  SER A  62 " =    1.663
peak=   -3.235 closest distance to " CG  GLU A  53 " =    1.490
peak=   -3.223 closest distance to " CG  TRP A 266 " =    1.927
peak=   -3.221 closest distance to " OE2 GLU A   2 " =    1.775
peak=   -3.220 closest distance to " CA  GLY A 241 " =    2.355
peak=   -3.214 closest distance to " C   ALA A 158 " =    1.326
peak=   -3.204 closest distance to " CG  PHE A 283 " =    2.559
peak=   -3.201 closest distance to " NH1 ARG A 195 " =    2.608
peak=   -3.200 closest distance to " O   HOH Z 149 " =    2.053
peak=   -3.196 closest distance to " N   THR A 235 " =    1.353
peak=   -3.194 closest distance to " CG  GLN A  11 " =    1.768
peak=   -3.191 closest distance to " O   ALA A   1 " =    1.881
peak=   -3.189 closest distance to " O   HOH Z  60 " =    2.250
peak=   -3.189 closest distance to " O   MET A  40 " =    2.802
peak=   -3.189 closest distance to " O   HOH Z 134 " =    2.787
peak=   -3.189 closest distance to " O   HOH Z 128 " =    2.618
peak=   -3.186 closest distance to " CE  MET A 105 " =    2.268
peak=   -3.183 closest distance to " O   GLY A 196 " =    1.094
peak=   -3.182 closest distance to " O   HOH Z 357 " =    2.039
peak=   -3.182 closest distance to " O   HOH Z  38 " =    1.562
peak=   -3.180 closest distance to " O   HOH Z 353 " =    2.197
peak=   -3.173 closest distance to " OD1 ASN A 187 " =    1.747
peak=   -3.171 closest distance to " NE  ARG A  66 " =    4.202
peak=   -3.170 closest distance to " CG  LEU A  83 " =    1.975
peak=   -3.165 closest distance to " CG1 VAL A 125 " =    2.353
peak=   -3.163 closest distance to " CE  MET A  93 " =    1.274
peak=   -3.157 closest distance to " CD  GLN A 223 " =    0.841
peak=   -3.156 closest distance to " O   HOH Z 350 " =    2.202
peak=   -3.149 closest distance to " O   LEU A 101 " =    2.061
peak=   -3.149 closest distance to " CD1 ILE A 151 " =    2.331
peak=   -3.140 closest distance to " NE1 TRP A 266 " =    2.377
peak=   -3.136 closest distance to " CB  PRO A 163 " =    2.522
peak=   -3.133 closest distance to " CD  PRO A 213 " =    2.172
peak=   -3.132 closest distance to " CG1AVAL A  41 " =    2.866
peak=   -3.128 closest distance to " OE1 GLN A 183 " =    1.520
peak=   -3.128 closest distance to " O   HOH Z   9 " =    2.222
peak=   -3.123 closest distance to " OG ASER A 134 " =    1.287
peak=   -3.119 closest distance to " O   HOH Z 171 " =    2.240
peak=   -3.119 closest distance to " O   HOH Z  76 " =    2.074
peak=   -3.117 closest distance to " O   SER A 135 " =    1.548
peak=   -3.112 closest distance to " NH1BARG A 275 " =    2.332
peak=   -3.108 closest distance to " CG  PRO A 163 " =    2.576
peak=   -3.094 closest distance to " C   MET A 188 " =    1.598
peak=   -3.092 closest distance to " O   HOH Z 126 " =    1.781
peak=   -3.091 closest distance to " O   ASN A 301 " =    1.397
peak=   -3.091 closest distance to " O   PRO A 198 " =    1.907
peak=   -3.082 closest distance to " CZ  PHE A  38 " =    1.956
peak=   -3.080 closest distance to " OD1 ASP A 191 " =    1.537
peak=   -3.078 closest distance to " O   HOH Z 421 " =    3.630
peak=   -3.072 closest distance to " CG  MET A 105 " =    0.967
peak=   -3.057 closest distance to " O   HOH Z 174 " =    4.017
peak=   -3.026 closest distance to " O   HOH Z 236 " =    1.555
peak=   -3.018 closest distance to " CD2 TYR A 293 " =    2.148

================= 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    :  0.3430 0.3339   6.104227e+00   6.067112e+00
   1_bss:  0.3284 0.3186   6.080957e+00   6.038444e+00
   1_xyz:  0.1993 0.2197   5.612860e+00   5.703077e+00
   1_adp:  0.1833 0.2239   5.564776e+00   5.723662e+00
   1_occ:  0.1830 0.2242   5.563956e+00   5.723613e+00
   2_bss:  0.1804 0.2200   5.553067e+00   5.712177e+00
   2_xyz:  0.1341 0.1697   5.276713e+00   5.468737e+00
   2_adp:  0.1245 0.1630   5.217983e+00   5.427233e+00
   2_occ:  0.1244 0.1630   5.217412e+00   5.427031e+00
   3_bss:  0.1244 0.1622   5.214616e+00   5.422483e+00
   3_xyz:  0.1128 0.1566   5.151834e+00   5.386243e+00
   3_adp:  0.1118 0.1550   5.141812e+00   5.376959e+00
   3_occ:  0.1118 0.1550   5.141623e+00   5.377140e+00
   4_bss:  0.1117 0.1550   5.141248e+00   5.376958e+00
   4_xyz:  0.1121 0.1556   5.145274e+00   5.380540e+00
   4_adp:  0.1116 0.1563   5.145047e+00   5.384693e+00
   4_occ:  0.1115 0.1564   5.145041e+00   5.384920e+00
   5_bss:  0.1115 0.1563   5.145095e+00   5.384998e+00
   5_xyz:  0.1095 0.1565   5.136851e+00   5.384577e+00
   5_adp:  0.1091 0.1575   5.137679e+00   5.389456e+00
   5_occ:  0.1091 0.1575   5.137656e+00   5.389584e+00
   5_bss:  0.1090 0.1573   5.137727e+00   5.389656e+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:  0.307  43.512  -3.286   3.411  -1.117   0.000  -0.000  -0.000
   1_xyz:  0.307  43.512  -3.286   3.411  -1.117   0.000  -0.000  -0.000
   1_adp:  0.307  43.512  -3.286   3.411  -1.117   0.000  -0.000  -0.000
   1_occ:  0.307  43.512  -3.286   3.411  -1.117   0.000  -0.000  -0.000
   2_bss:  0.326  59.332  -3.092  -0.114  -1.185  -0.000  -0.000  -0.000
   2_xyz:  0.326  59.332  -3.092  -0.114  -1.185  -0.000  -0.000  -0.000
   2_adp:  0.326  59.332  -3.092  -0.114  -1.185  -0.000  -0.000  -0.000
   2_occ:  0.326  59.332  -3.092  -0.114  -1.185  -0.000  -0.000  -0.000
   3_bss:  0.326  59.332  -2.651  -1.031  -0.884  -0.000  -0.000  -0.000
   3_xyz:  0.326  59.332  -2.651  -1.031  -0.884  -0.000  -0.000  -0.000
   3_adp:  0.326  59.332  -2.651  -1.031  -0.884  -0.000  -0.000  -0.000
   3_occ:  0.326  59.332  -2.651  -1.031  -0.884  -0.000  -0.000  -0.000
   4_bss:  0.324  55.398  -2.394  -1.218  -0.685  -0.000  -0.000  -0.000
   4_xyz:  0.324  55.398  -2.394  -1.218  -0.685  -0.000  -0.000  -0.000
   4_adp:  0.324  55.398  -2.394  -1.218  -0.685  -0.000  -0.000  -0.000
   4_occ:  0.324  55.398  -2.394  -1.218  -0.685  -0.000  -0.000  -0.000
   5_bss:  0.324  55.398  -2.176  -1.157  -0.489  -0.000  -0.000  -0.000
   5_xyz:  0.324  55.398  -2.176  -1.157  -0.489  -0.000  -0.000  -0.000
   5_adp:  0.324  55.398  -2.176  -1.157  -0.489  -0.000  -0.000  -0.000
   5_occ:  0.324  55.398  -2.176  -1.157  -0.489  -0.000  -0.000  -0.000
   5_bss:  0.322  55.746  -1.881  -0.933  -0.230  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.845 0.6944  0.8611    33101.351
   1_bss:  34.719 0.7055  0.8636    29680.191
   1_xyz:  21.848 0.8442  0.9824    12644.322
   1_adp:  22.532 0.8366  0.9673    13169.460
   1_occ:  22.540 0.8365  0.9667    13162.251
   2_bss:  22.048 0.8416  0.9376    12778.028
   2_xyz:  16.033 0.8973  0.9724     7424.036
   2_adp:  15.031 0.9062  0.9689     6855.850
   2_occ:  15.026 0.9062  0.9689     6852.883
   3_bss:  14.931 0.9070  0.9683     6787.825
   3_xyz:  14.106 0.9140  0.9721     6331.944
   3_adp:  13.881 0.9160  0.9663     6247.741
   3_occ:  13.880 0.9161  0.9662     6247.825
   4_bss:  13.873 0.9161  0.9698     6245.672
   4_xyz:  13.883 0.9161  0.9693     6263.376
   4_adp:  13.947 0.9157  0.9618     6309.961
   4_occ:  13.947 0.9157  0.9617     6312.765
   5_bss:  13.948 0.9157  0.9673     6314.511
   5_xyz:  13.925 0.9159  0.9679     6322.638
   5_adp:  14.017 0.9152  0.9598     6362.407
   5_occ:  14.015 0.9152  0.9597     6363.761
   5_bss:  14.018 0.9152  0.9688     6365.227
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6186e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6186e-01
   1_xyz:   1.262  0.010  0.076 15.151  0.005  4.112   8.1525e-02
   1_adp:   1.262  0.010  0.076 15.151  0.005  4.112   8.1525e-02
   1_occ:   1.262  0.010  0.076 15.151  0.005  4.112   8.1525e-02
   2_bss:   1.262  0.010  0.076 15.151  0.005  4.112   8.1525e-02
   2_xyz:   1.036  0.008  0.075 14.700  0.004  4.126   6.3607e-02
   2_adp:   1.036  0.008  0.075 14.700  0.004  4.126   6.3607e-02
   2_occ:   1.036  0.008  0.075 14.700  0.004  4.126   6.3607e-02
   3_bss:   1.036  0.008  0.075 14.700  0.004  4.126   6.3607e-02
   3_xyz:   1.089  0.009  0.081 14.821  0.004  4.115   7.0541e-02
   3_adp:   1.089  0.009  0.081 14.821  0.004  4.115   7.0541e-02
   3_occ:   1.089  0.009  0.081 14.821  0.004  4.115   7.0541e-02
   4_bss:   1.089  0.009  0.081 14.821  0.004  4.115   7.0541e-02
   4_xyz:   0.997  0.008  0.077 14.519  0.004  4.116   6.0075e-02
   4_adp:   0.997  0.008  0.077 14.519  0.004  4.116   6.0075e-02
   4_occ:   0.997  0.008  0.077 14.519  0.004  4.116   6.0075e-02
   5_bss:   0.997  0.008  0.077 14.519  0.004  4.116   6.0075e-02
   5_xyz:   1.048  0.009  0.080 14.613  0.004  4.117   6.5690e-02
   5_adp:   1.048  0.009  0.080 14.613  0.004  4.117   6.5690e-02
   5_occ:   1.048  0.009  0.080 14.613  0.004  4.117   6.5690e-02
   5_bss:   1.048  0.009  0.080 14.613  0.004  4.117   6.5690e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4234e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4234e-01
   1_xyz:   8.492  0.048  0.311 86.742  0.026  2.201   7.6538e-02
   1_adp:   8.492  0.048  0.311 86.742  0.026  2.201   7.6538e-02
   1_occ:   8.492  0.048  0.311 86.742  0.026  2.201   7.6538e-02
   2_bss:   8.492  0.048  0.311 86.742  0.026  2.201   7.6538e-02
   2_xyz:   7.142  0.055  0.240 82.266  0.046  2.351   7.3009e-02
   2_adp:   7.142  0.055  0.240 82.266  0.046  2.351   7.3009e-02
   2_occ:   7.142  0.055  0.240 82.266  0.046  2.351   7.3009e-02
   3_bss:   7.142  0.055  0.240 82.266  0.046  2.351   7.3009e-02
   3_xyz:   8.117  0.049  0.258 82.883  0.041  2.345   5.1427e-02
   3_adp:   8.117  0.049  0.258 82.883  0.041  2.345   5.1427e-02
   3_occ:   8.117  0.049  0.258 82.883  0.041  2.345   5.1427e-02
   4_bss:   8.117  0.049  0.258 82.883  0.041  2.345   5.1427e-02
   4_xyz:   7.475  0.050  0.248 81.407  0.037  2.368   4.1446e-02
   4_adp:   7.475  0.050  0.248 81.407  0.037  2.368   4.1446e-02
   4_occ:   7.475  0.050  0.248 81.407  0.037  2.368   4.1446e-02
   5_bss:   7.475  0.050  0.248 81.407  0.037  2.368   4.1446e-02
   5_xyz:   7.840  0.051  0.262 82.315  0.037  2.328   4.5982e-02
   5_adp:   7.840  0.051  0.262 82.315  0.037  2.328   4.5982e-02
   5_occ:   7.840  0.051  0.262 82.315  0.037  2.328   4.5982e-02
   5_bss:   7.840  0.051  0.262 82.315  0.037  2.328   4.5982e-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:  67.18   0.00  16.44  67.18   0.00  12.59  64.12   7.39  37.43
   1_occ:  67.18   0.00  16.44  67.18   0.00  12.59  64.12   7.39  37.43
   2_bss:  67.18   0.00  16.44  67.18   0.00  12.59  64.12   7.39  37.43
   2_xyz:  67.18   0.00  16.44  67.18   0.00  12.59  64.12   7.39  37.43
   2_adp:  80.47   1.59  16.67  80.47   1.59  12.60  71.91   3.96  38.81
   2_occ:  80.47   1.59  16.67  80.47   1.59  12.60  71.91   3.96  38.81
   3_bss:  80.47   1.59  16.67  80.47   1.59  12.60  71.91   3.96  38.81
   3_xyz:  80.47   1.59  16.67  80.47   1.59  12.60  71.91   3.96  38.81
   3_adp:  81.60   1.16  16.39  81.60   1.16  12.38  72.61   1.74  38.24
   3_occ:  81.60   1.16  16.39  81.60   1.16  12.38  72.61   1.74  38.24
   4_bss:  81.60   1.16  16.39  81.60   1.16  12.38  72.61   1.74  38.24
   4_xyz:  81.60   1.16  16.39  81.60   1.16  12.38  72.61   1.74  38.24
   4_adp:  84.03   0.49  16.25  84.03   0.49  12.22  74.85   2.26  38.20
   4_occ:  84.03   0.49  16.25  84.03   0.49  12.22  74.85   2.26  38.20
   5_bss:  84.03   0.49  16.25  84.03   0.49  12.22  74.85   2.26  38.20
   5_xyz:  84.03   0.49  16.25  84.03   0.49  12.22  74.85   2.26  38.20
   5_adp:  88.68   0.00  16.27  88.68   0.00  12.09  79.54   3.93  38.99
   5_occ:  88.68   0.00  16.27  88.68   0.00  12.09  79.54   3.93  38.99
   5_bss:  88.68   0.00  16.27  88.68   0.00  12.10  79.54   3.94  38.99
------------------------------------------------------------------------
 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:    1.152    0.027    0.358
   1_adp:    1.152    0.027    0.358
   1_occ:    1.152    0.027    0.358
   2_bss:    1.152    0.027    0.358
   2_xyz:    0.978    0.023    0.437
   2_adp:    0.978    0.023    0.437
   2_occ:    0.978    0.023    0.437
   3_bss:    0.978    0.023    0.437
   3_xyz:    1.006    0.044    0.469
   3_adp:    1.006    0.044    0.469
   3_occ:    1.006    0.044    0.469
   4_bss:    1.006    0.044    0.469
   4_xyz:    0.984    0.035    0.481
   4_adp:    0.984    0.035    0.481
   4_occ:    0.984    0.035    0.481
   5_bss:    0.984    0.035    0.481
   5_xyz:    1.016    0.039    0.487
   5_adp:    1.016    0.039    0.487
   5_occ:    1.016    0.039    0.487
   5_bss:    1.016    0.039    0.487
------------------------------------------------------------------------

CPU time actual refinement: 279.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_578/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_578/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_578/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_578/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_578/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 279.32 
  Macro-tasks:
    bulk solvent and scale       = 33.39  
    individual site refinement   = 120.86 
    weights calculation          = 24.05  
    collect and process          = 5.46   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 183.85 
  Micro-tasks:
    mask                            = 0.98   
    f_calc                          = 88.00  
    alpha_beta                      = 6.87   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 97.89  
    fmodel                         = 5.48   
    r_factors                      = 0.15   
    phase_errors                   = 9.14   
    foms                           = 0.19   
    TOTAL for micro-tasks          = 209.69 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.860 micro seconds
Total CPU time: 4.85 minutes
from_scatterers_fft:    670 calls, 87.75 s
gradients_fft:          615 calls, 85.11 s

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

# Date 2008-01-16 Time 05:08:42 PST -0800 (1200488922.20 s)
Start R-work = 0.3430, R-free = 0.3339 (no bulk solvent and anisotropic scale)
Final R-work = 0.1293, R-free = 0.1731 (no bulk solvent and anisotropic scale)

Start R-work = 0.3284, R-free = 0.3186
Final R-work = 0.1090, R-free = 0.1573