# Date 2008-01-16 Time 05:15:32 PST -0800 (1200489332.93 s)
#phil __OFF__

Command line arguments: "../658.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11871
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 658

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.35, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.99219
Completeness in resolution range: 0.959869
Completeness with d_max=infinity: 0.956915

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   1.9922

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.99219
Completeness in resolution range: 0.959869
Completeness with d_max=infinity: 0.956915

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0740 -  4.2627 [2148/2172]  1929   219  10.2%
  bin  2:  4.2627 -  3.3962 [2053/2073]  1849   204   9.9%
  bin  3:  3.3962 -  2.9706 [2031/2050]  1833   198   9.7%
  bin  4:  2.9706 -  2.7007 [2014/2044]  1811   203  10.1%
  bin  5:  2.7007 -  2.5081 [1996/2015]  1794   202  10.1%
  bin  6:  2.5081 -  2.3608 [2007/2032]  1803   204  10.2%
  bin  7:  2.3608 -  2.2430 [1972/2000]  1776   196   9.9%
  bin  8:  2.2430 -  2.1456 [1968/2004]  1772   196  10.0%
  bin  9:  2.1456 -  2.0632 [1958/2000]  1767   191   9.8%
  bin 10:  2.0632 -  1.9922 [1442/2018]  1296   146  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_658/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.66 -     2.31: 10
        2.31 -     2.95: 1647
        2.95 -     3.60: 4485
        3.60 -     4.25: 9094
        4.25 -     4.90: 12844
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.656 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.768 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.802 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.903 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28075 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_658/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_658/model_refine_001.geo

CPU time processing inputs: 9.74


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3413   r_free= 0.3361   ksol= 0.00   Bsol= 0.00   scale= 0.954    |
|                                                                             |
| 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: 6.097738                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7544 0.99   1393  154 0.2927 0.2738      6.3936      6.2799|
|  2:  4.7544 -  3.7935 0.99   1339  152 0.2633 0.2895      6.4839      6.5469|
|  3:  3.7935 -  3.3198 0.99   1303  142 0.2998 0.2731      6.4287      6.3766|
|  4:  3.3198 -  3.0189 0.99   1310  145 0.3175 0.3361      6.3049      6.3322|
|  5:  3.0189 -  2.8040 0.99   1297  147 0.3566 0.3052      6.1731      6.0969|
|  6:  2.8040 -  2.6396 0.99   1300  143 0.3461 0.3930      6.0573      6.0438|
|  7:  2.6396 -  2.5081 0.99   1274  143 0.3594 0.3517      6.0489      5.9907|
|  8:  2.5081 -  2.3993 0.98   1279  137 0.3842 0.3594      6.0523      6.0375|
|  9:  2.3993 -  2.3073 0.98   1275  147 0.3692 0.3791      5.9565      5.9754|
| 10:  2.3073 -  2.2279 1.00   1297  139 0.4092 0.3685      6.0026      5.9046|
| 11:  2.2279 -  2.1585 0.97   1258  140 0.4049 0.3981      5.9224      5.9421|
| 12:  2.1585 -  2.0970 0.98   1250  144 0.3983 0.3562      5.8572      5.8565|
| 13:  2.0970 -  2.0419 0.99   1276  135 0.3962 0.4282       5.754      5.7717|
| 14:  2.0419 -  1.9922 0.60    779   91 0.3650 0.3834       5.721      5.6167|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0740 -  4.7544  1393   154  0.81  24.14   0.85     0.83      38232.60|
|  2:  4.7544 -  3.7935  1339   152  0.84  22.70   0.96     0.91      49864.64|
|  3:  3.7935 -  3.3198  1303   142  0.79  27.21   0.97     0.93      50620.17|
|  4:  3.3198 -  3.0189  1310   145  0.75  30.84   0.97     0.89      44716.74|
|  5:  3.0189 -  2.8040  1297   147  0.70  35.48   0.99     0.85      35599.24|
|  6:  2.8040 -  2.6396  1300   143  0.68  37.32   0.97     0.83      32526.45|
|  7:  2.6396 -  2.5081  1274   143  0.67  37.88   0.99     0.84      29981.25|
|  8:  2.5081 -  2.3993  1279   137  0.67  38.14   0.96     0.85      27757.51|
|  9:  2.3993 -  2.3073  1275   147  0.68  37.41   1.01     0.87      25767.34|
| 10:  2.3073 -  2.2279  1297   139  0.65  39.99   1.01     0.86      24510.41|
| 11:  2.2279 -  2.1585  1258   140  0.64  40.84   0.99     0.89      25081.38|
| 12:  2.1585 -  2.0970  1250   144  0.63  41.60   1.02     0.88      23236.98|
| 13:  2.0970 -  2.0419  1276   135  0.61  43.68   0.99     0.86      20738.79|
| 14:  2.0419 -  1.9922   779    91  0.64  41.17   1.06     0.80      17131.29|
|alpha:            min =        0.80 max =            0.93 mean =         0.86|
|beta:             min =    17131.29 max =        50620.17 mean =     32431.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           89.96 mean =        35.29|
|phase err.(test): min =        0.00 max =           89.85 mean =        35.17|
|-----------------------------------------------------------------------------|

============================== 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 = 4.990268              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.158   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.698691              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.134   (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 |  1.656 -  1.981:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.981 -  2.305:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.305 -  2.629:       47 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.629 -  2.954:     1600 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.954 -  3.278:     1894 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.278 -  3.603:     2591 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.603 -  3.927:     4707 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.927 -  4.251:     4387 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.251 -  4.576:     5881 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.576 -  4.900:     6963 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.656 |       0.222 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3413   r_free= 0.3361   ksol= 0.00   Bsol= 0.00   scale= 0.954    |
|                                                                             |
| 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: 6.097738                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3237   r_free= 0.3223   ksol= 0.32   Bsol= 50.00   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,-2.44,4.54,-0.00,0.00,0.00); trace/3= -0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.069872                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.246887              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.008   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.383986              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.884   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3237      final r-factor (work) = 0.1978          |
| start r-factor (free) = 0.3223      final r-factor (free) = 0.2266          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0532 = 4.25 * 0.50 * 6.0688 + 1.00 * 0.1664                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3590 = 4.25 * 0.50 * 5.7859 + 1.00 * 0.0730                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1978      final r-factor (work) = 0.1883          |
| start r-factor (free) = 0.2266      final r-factor (free) = 0.2269          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2294 = 0.38 * 1.00 * 5.7859 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3149 = 0.38 * 1.00 * 5.5675 + 1.00 * 0.1770                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.21   16.13    None  None   None       |
|    all(noH): 2823   0      0.00    82.21   16.13    None  None   None       |
|    Sol.    : 438    0      4.17    62.82   37.09    None  None   None       |
|    Mac.    : 2385   0      0.00    82.21   12.28    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 -   8.221:  503   |   5:    41.106 -  49.327:   98        |
|      1:     8.221 -  16.442: 1556   |   6:    49.327 -  57.548:   74        |
|      2:    16.442 -  24.663:  305   |   7:    57.548 -  65.769:   17        |
|      3:    24.663 -  32.884:  147   |   8:    65.769 -  73.990:    0        |
|      4:    32.884 -  41.106:  122   |   9:    73.990 -  82.211:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1883 r_free = 0.2269             target_work(ml) = 5.568         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1878 r_free = 0.2265             target_work(ml) = 5.567         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1878   r_free= 0.2265   ksol= 0.32   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.29,-2.44,4.54,-0.00,0.00,0.00); trace/3= -0.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.566748                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1835   r_free= 0.2220   ksol= 0.33   Bsol= 62.17   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-2.60,0.32,-0.00,0.00,0.00); trace/3= -1.77                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.550629                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.057983              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.743   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.244300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.583   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1835      final r-factor (work) = 0.1379          |
| start r-factor (free) = 0.2220      final r-factor (free) = 0.1671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8050 = 2.06 * 0.50 * 5.5705 + 1.00 * 0.0730                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6272 = 2.06 * 0.50 * 5.4138 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1379      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1671      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7872 = 1.24 * 1.00 * 5.4138 + 1.00 * 0.0508                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5233 = 1.24 * 1.00 * 5.2341 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.53   17.40    None  None   None       |
|    all(noH): 2823   0      0.00    81.53   17.40    None  None   None       |
|    Sol.    : 438    0      2.65    81.53   41.91    None  None   None       |
|    Mac.    : 2385   0      0.00    77.14   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.153:  624   |   5:    40.763 -  48.916:   94        |
|      1:     8.153 -  16.305: 1355   |   6:    48.916 -  57.068:   75        |
|      2:    16.305 -  24.458:  325   |   7:    57.068 -  65.221:   76        |
|      3:    24.458 -  32.611:  130   |   8:    65.221 -  73.374:   37        |
|      4:    32.611 -  40.763:   96   |   9:    73.374 -  81.526:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1275 r_free = 0.1709             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1273 r_free = 0.1707             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1273   r_free= 0.1707   ksol= 0.33   Bsol= 62.17   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,-2.60,0.32,-0.00,0.00,0.00); trace/3= -1.77                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.240791                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1273   r_free= 0.1703   ksol= 0.33   Bsol= 67.30   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.36,-0.14,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.239179                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.731704              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.233  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.279618              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.481  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1273      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1703      final r-factor (free) = 0.1613          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2042 = 2.73 * 0.50 * 5.2332 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1609 = 2.73 * 0.50 * 5.1951 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1613      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4631 = 0.28 * 1.00 * 5.1951 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4527 = 0.28 * 1.00 * 5.1636 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.54   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    80.54   16.85    None  None   None       |
|    Sol.    : 438    0      0.00    80.54   39.75    None  None   None       |
|    Mac.    : 2385   0      0.81    80.23   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.054:  595   |   5:    40.269 -  48.323:   88        |
|      1:     8.054 -  16.108: 1380   |   6:    48.323 -  56.376:   77        |
|      2:    16.108 -  24.161:  339   |   7:    56.376 -  64.430:   54        |
|      3:    24.161 -  32.215:  129   |   8:    64.430 -  72.484:   28        |
|      4:    32.215 -  40.269:  124   |   9:    72.484 -  80.538:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1142 r_free = 0.1578             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1140 r_free = 0.1576             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1576   ksol= 0.33   Bsol= 67.30   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.36,-0.14,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153138                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1575   ksol= 0.33   Bsol= 59.84   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.12,-0.15,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.153056                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.121815              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.329  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.113309              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.123  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5433 = 2.12 * 0.50 * 5.1636 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5327 = 2.12 * 0.50 * 5.1531 + 1.00 * 0.0658                               |
|-----------------------------------------------------------------------------|
| number of iterations = 1       |    number of function evaluations = 1      |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5928 = 0.11 * 1.00 * 5.1531 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5920 = 0.11 * 1.00 * 5.1639 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.69    73.28   16.08    None  None   None       |
|    all(noH): 2823   0      1.69    73.28   16.08    None  None   None       |
|    Sol.    : 438    0      3.70    73.28   36.46    None  None   None       |
|    Mac.    : 2385   0      1.69    72.36   12.34    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:     1.688 -   8.847:  801   |   5:    37.485 -  44.644:  102        |
|      1:     8.847 -  16.006: 1191   |   6:    44.644 -  51.803:   90        |
|      2:    16.006 -  23.166:  321   |   7:    51.803 -  58.963:   40        |
|      3:    23.166 -  30.325:  131   |   8:    58.963 -  66.122:   11        |
|      4:    30.325 -  37.485:  127   |   9:    66.122 -  73.282:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1161 r_free = 0.1570             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1160 r_free = 0.1569             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1569   ksol= 0.33   Bsol= 59.84   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.12,-0.15,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161675                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1569   ksol= 0.33   Bsol= 59.84   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.07,-0.14,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161745                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.133623              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.898  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.105877              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 165.420  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5747 = 2.13 * 0.50 * 5.1639 + 1.00 * 0.0658                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5597 = 2.13 * 0.50 * 5.1531 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5524 = 0.11 * 1.00 * 5.1531 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5523 = 0.11 * 1.00 * 5.1567 + 1.00 * 0.0063                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    71.75   15.86    None  None   None       |
|    all(noH): 2823   0      2.09    71.75   15.86    None  None   None       |
|    Sol.    : 438    0      3.72    71.75   35.64    None  None   None       |
|    Mac.    : 2385   0      2.09    71.02   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:     2.092 -   9.057:  863   |   5:    36.921 -  43.886:   97        |
|      1:     9.057 -  16.023: 1149   |   6:    43.886 -  50.852:   95        |
|      2:    16.023 -  22.989:  312   |   7:    50.852 -  57.818:   37        |
|      3:    22.989 -  29.955:  125   |   8:    57.818 -  64.784:   11        |
|      4:    29.955 -  36.921:  125   |   9:    64.784 -  71.750:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1569             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1569             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1569   ksol= 0.33   Bsol= 59.84   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.07,-0.14,-0.00,-0.00,-0.00); trace/3= -1.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157239                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7544 0.99   1393  154 0.1052 0.1338      5.4338      5.5692|
|  2:  4.7544 -  3.7935 0.99   1339  152 0.0913 0.1161       5.486      5.6769|
|  3:  3.7935 -  3.3198 0.99   1303  142 0.1100 0.1479      5.5068      5.8226|
|  4:  3.3198 -  3.0189 0.99   1310  145 0.1230 0.1648      5.4533      5.5953|
|  5:  3.0189 -  2.8040 0.99   1297  147 0.1355 0.1593      5.3355      5.5339|
|  6:  2.8040 -  2.6396 0.99   1300  143 0.1223 0.2014      5.2201      5.5212|
|  7:  2.6396 -  2.5081 0.99   1274  143 0.1315 0.1664      5.1973      5.3511|
|  8:  2.5081 -  2.3993 0.98   1279  137 0.1181 0.1627      5.0851      5.3347|
|  9:  2.3993 -  2.3073 0.98   1275  147 0.1169 0.1818      5.0398      5.3034|
| 10:  2.3073 -  2.2279 1.00   1297  139 0.1177 0.1710      4.9598      5.1748|
| 11:  2.2279 -  2.1585 0.97   1258  140 0.1149 0.1674      4.9369      5.2043|
| 12:  2.1585 -  2.0970 0.98   1250  144 0.1143 0.1688      4.8813      5.2355|
| 13:  2.0970 -  2.0419 0.99   1276  135 0.1103 0.1648      4.7685      5.0031|
| 14:  2.0419 -  1.9922 0.60    779   91 0.0948 0.1562      4.6226      4.8514|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0740 -  4.7544  1393   154  0.94   9.38   0.98     0.94       7560.86|
|  2:  4.7544 -  3.7935  1339   152  0.95   8.18   1.00     0.99       9622.18|
|  3:  3.7935 -  3.3198  1303   142  0.93  11.46   1.01     1.00      10645.44|
|  4:  3.3198 -  3.0189  1310   145  0.92  13.42   0.99     0.97      10010.95|
|  5:  3.0189 -  2.8040  1297   147  0.90  15.45   0.99     0.96       8111.46|
|  6:  2.8040 -  2.6396  1300   143  0.90  16.07   0.98     0.95       7089.78|
|  7:  2.6396 -  2.5081  1274   143  0.90  15.88   0.99     0.95       6433.12|
|  8:  2.5081 -  2.3993  1279   137  0.91  15.12   0.98     0.96       5368.87|
|  9:  2.3993 -  2.3073  1275   147  0.91  14.87   1.00     0.97       4991.61|
| 10:  2.3073 -  2.2279  1297   139  0.90  15.93   1.00     0.97       4310.45|
| 11:  2.2279 -  2.1585  1258   140  0.90  15.79   0.99     0.95       4256.56|
| 12:  2.1585 -  2.0970  1250   144  0.91  15.58   1.00     1.00       3903.41|
| 13:  2.0970 -  2.0419  1276   135  0.91  15.47   0.99     0.98       3180.70|
| 14:  2.0419 -  1.9922   779    91  0.93  12.82   0.97     0.94       2320.97|
|alpha:            min =        0.94 max =            1.00 mean =         0.97|
|beta:             min =     2320.97 max =        10645.44 mean =      6424.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.68 mean =        13.94|
|phase err.(test): min =        0.00 max =           89.89 mean =        13.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1570   ksol= 0.32   Bsol= 51.87   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-1.99,-0.09,-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: 5.157435                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1570   ksol= 0.32   Bsol= 51.87   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-1.99,-0.09,-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: 5.157435                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7544 0.99   1393  154 0.1046 0.1331      5.4282      5.5642|
|  2:  4.7544 -  3.7935 0.99   1339  152 0.0909 0.1159       5.482      5.6738|
|  3:  3.7935 -  3.3198 0.99   1303  142 0.1097 0.1481      5.5051      5.8232|
|  4:  3.3198 -  3.0189 0.99   1310  145 0.1232 0.1650      5.4549      5.5971|
|  5:  3.0189 -  2.8040 0.99   1297  147 0.1358 0.1595      5.3379      5.5363|
|  6:  2.8040 -  2.6396 0.99   1300  143 0.1227 0.2023      5.2226      5.5243|
|  7:  2.6396 -  2.5081 0.99   1274  143 0.1317 0.1671      5.1996      5.3538|
|  8:  2.5081 -  2.3993 0.98   1279  137 0.1184 0.1630      5.0867      5.3361|
|  9:  2.3993 -  2.3073 0.98   1275  147 0.1170 0.1817      5.0407      5.3032|
| 10:  2.3073 -  2.2279 1.00   1297  139 0.1179 0.1714      4.9607      5.1767|
| 11:  2.2279 -  2.1585 0.97   1258  140 0.1150 0.1674      4.9377      5.2046|
| 12:  2.1585 -  2.0970 0.98   1250  144 0.1143 0.1689      4.8817      5.2359|
| 13:  2.0970 -  2.0419 0.99   1276  135 0.1103 0.1651      4.7691      5.0041|
| 14:  2.0419 -  1.9922 0.60    779   91 0.0949 0.1562      4.6235      4.8518|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0740 -  4.7544  1393   154  0.94   9.32   0.97     0.94       7466.20|
|  2:  4.7544 -  3.7935  1339   152  0.95   8.14   1.01     0.99       9558.58|
|  3:  3.7935 -  3.3198  1303   142  0.93  11.44   1.01     1.00      10631.02|
|  4:  3.3198 -  3.0189  1310   145  0.92  13.43   0.99     0.97      10040.37|
|  5:  3.0189 -  2.8040  1297   147  0.90  15.49   0.99     0.96       8151.86|
|  6:  2.8040 -  2.6396  1300   143  0.90  16.14   0.98     0.95       7126.14|
|  7:  2.6396 -  2.5081  1274   143  0.90  15.93   0.98     0.95       6468.62|
|  8:  2.5081 -  2.3993  1279   137  0.91  15.14   0.98     0.96       5385.35|
|  9:  2.3993 -  2.3073  1275   147  0.91  14.89   1.00     0.97       5002.78|
| 10:  2.3073 -  2.2279  1297   139  0.90  15.94   1.00     0.97       4314.80|
| 11:  2.2279 -  2.1585  1258   140  0.90  15.81   0.99     0.95       4264.20|
| 12:  2.1585 -  2.0970  1250   144  0.91  15.60   1.00     1.00       3908.18|
| 13:  2.0970 -  2.0419  1276   135  0.91  15.49   0.99     0.98       3184.75|
| 14:  2.0419 -  1.9922   779    91  0.93  12.82   0.97     0.94       2324.16|
|alpha:            min =        0.94 max =            1.00 mean =         0.97|
|beta:             min =     2324.16 max =        10631.02 mean =      6424.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.95|
|phase err.(test): min =        0.00 max =           89.02 mean =        13.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.033)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.02    71.67   15.78    None  None   None       |
|    all(noH): 2823   0      2.02    71.67   15.78    None  None   None       |
|    Sol.    : 438    0      3.64    71.67   35.57    None  None   None       |
|    Mac.    : 2385   0      2.02    70.95   12.15    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:     2.016 -   8.982:  863   |   5:    36.845 -  43.811:   97        |
|      1:     8.982 -  15.948: 1149   |   6:    43.811 -  50.777:   95        |
|      2:    15.948 -  22.913:  312   |   7:    50.777 -  57.742:   37        |
|      3:    22.913 -  29.879:  125   |   8:    57.742 -  64.708:   11        |
|      4:    29.879 -  36.845:  125   |   9:    64.708 -  71.674:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 274         
Filter by distance & map next to the model:
   mapped sites are within: 0.561 - 4.836
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 274
   mapped sites are within: 0.710 - 4.836

peak=    5.658 closest distance to " NH2 ARG A  56 " =    2.153
peak=    5.401 closest distance to " CG  PRO A  54 " =    1.434
peak=    4.984 closest distance to " CB  GLN A 223 " =    1.438
peak=    4.952 closest distance to " CB  ARG A 275 " =    0.917
peak=    4.824 closest distance to " O   HOH Z 144 " =    1.854
peak=    4.755 closest distance to " O   HOH Z 126 " =    1.667
peak=    4.655 closest distance to " CB  PRO A  54 " =    0.997
peak=    4.649 closest distance to " NE2 GLN A  11 " =    1.141
peak=    4.627 closest distance to " CB  GLN A 183 " =    1.149
peak=    4.621 closest distance to " ND2 ASN A 187 " =    1.571
peak=    4.581 closest distance to " CZ  PHE A 218 " =    1.090
peak=    4.550 closest distance to " O   HOH Z 232 " =    2.350
peak=    4.525 closest distance to " CB  ARG A  79 " =    1.385
peak=    4.506 closest distance to " CB  GLU A 152 " =    1.184
peak=    4.472 closest distance to " O   HOH Z 369 " =    2.125
peak=    4.463 closest distance to " O   HOH Z 298 " =    1.977
peak=    4.462 closest distance to " CG  PRO A 213 " =    1.233
peak=    4.431 closest distance to " CB  ARG A 190 " =    1.508
peak=    4.385 closest distance to " CB  SER A  63 " =    1.202
peak=    4.369 closest distance to " CB  ASN A 187 " =    1.193
peak=    4.363 closest distance to " O   HOH Z  78 " =    1.839
peak=    4.331 closest distance to " O   HOH Z 236 " =    2.280
peak=    4.318 closest distance to " CG  PRO A 198 " =    1.309
peak=    4.316 closest distance to " O   HOH Z 303 " =    2.099
peak=    4.300 closest distance to " O   HOH Z 126 " =    2.015
peak=    4.296 closest distance to " CD  ARG A 159 " =    0.726
peak=    4.286 closest distance to " O   HOH Z 189 " =    2.812
peak=    4.273 closest distance to " CB  LEU A 228 " =    1.050
peak=    4.270 closest distance to " CG2 VAL A 257 " =    0.885
peak=    4.217 closest distance to " CB  ASN A 148 " =    1.493
peak=    4.212 closest distance to " CB  VAL A 265 " =    1.302
peak=    4.208 closest distance to " CB  ASN A  39 " =    0.886
peak=    4.197 closest distance to " O   HOH Z  15 " =    2.110
peak=    4.164 closest distance to " O   HOH Z 406 " =    1.718
peak=    4.143 closest distance to " O   HOH Z 346 " =    1.685
peak=    4.116 closest distance to " O   HOH Z 234 " =    3.872
peak=    4.063 closest distance to " CG  PRO A 243 " =    1.079
peak=    4.062 closest distance to " CD2 TRP A 179 " =    1.272
peak=    4.051 closest distance to " CE  LYS A  76 " =    0.912
peak=    4.045 closest distance to " CB  ASN A 142 " =    0.959
peak=    4.018 closest distance to " O   HOH Z  21 " =    1.782
peak=    4.008 closest distance to " CA  TYR A  30 " =    0.970
peak=    3.997 closest distance to " NH1AARG A 145 " =    1.308
peak=    3.983 closest distance to " CA  THR A 264 " =    0.909
peak=    3.981 closest distance to " O   HOH Z  40 " =    1.756
peak=    3.942 closest distance to " C   PRO A 198 " =    1.454
peak=    3.932 closest distance to " O   HOH Z 158 " =    3.172
peak=    3.928 closest distance to " O   HOH Z  78 " =    2.123
peak=    3.927 closest distance to " O   HOH Z  53 " =    2.547
peak=    3.909 closest distance to " CB  TRP A 266 " =    0.996
peak=    3.893 closest distance to " CA  SER A  87 " =    0.945
peak=    3.892 closest distance to " CB  GLU A  46 " =    0.958
peak=    3.885 closest distance to " O   HOH Z  61 " =    1.713
peak=    3.880 closest distance to " O   HOH Z 368 " =    2.056
peak=    3.880 closest distance to " CA  ARG A 195 " =    1.214
peak=    3.873 closest distance to " O   SER A  87 " =    2.331
peak=    3.861 closest distance to " O   HOH Z 248 " =    1.577
peak=    3.857 closest distance to " O   HOH Z 392 " =    3.019
peak=    3.854 closest distance to " O   HOH Z 419 " =    2.147
peak=    3.853 closest distance to " O   HOH Z  10 " =    1.793
peak=    3.852 closest distance to " OG ASER A 258 " =    3.122
peak=    3.847 closest distance to " O   HOH Z 250 " =    1.510
peak=    3.842 closest distance to " O   HOH Z 368 " =    3.527
peak=    3.835 closest distance to " O   HOH Z 214 " =    2.176
peak=    3.828 closest distance to " CB  ASP A 124 " =    0.765
peak=    3.826 closest distance to " O   HOH Z 148 " =    3.472
peak=    3.817 closest distance to " CB  GLU A 128 " =    0.825
peak=    3.817 closest distance to " O   HOH Z 403 " =    1.505
peak=    3.812 closest distance to " CB  GLU A 277 " =    3.616
peak=    3.811 closest distance to " CA  ALA A  51 " =    0.963
peak=    3.805 closest distance to " CB  PRO A  90 " =    1.105
peak=    3.792 closest distance to " CB  SER A 210 " =    0.716
peak=    3.768 closest distance to " CA  ASN A 215 " =    1.066
peak=    3.767 closest distance to " N   PHE A 130 " =    1.242
peak=    3.767 closest distance to " CB  ASN A 110 " =    0.922
peak=    3.765 closest distance to " CZ3 TRP A 266 " =    1.155
peak=    3.762 closest distance to " CG2AVAL A  72 " =    1.564
peak=    3.762 closest distance to " ND2 ASN A 249 " =    0.877
peak=    3.746 closest distance to " CB  SER A 212 " =    1.291
peak=    3.728 closest distance to " O   HOH Z  97 " =    2.453
peak=    3.723 closest distance to " N   ASN A  39 " =    1.233
peak=    3.722 closest distance to " O   HOH Z 285 " =    2.176
peak=    3.719 closest distance to " O  BHOH Z 338 " =    2.366
peak=    3.718 closest distance to " CB  VAL A 202 " =    1.520
peak=    3.709 closest distance to " CB  SER A   3 " =    1.354
peak=    3.695 closest distance to " O   ASN A  74 " =    1.404
peak=    3.691 closest distance to " CG  LEU A 167 " =    1.306
peak=    3.680 closest distance to " O   HOH Z 427 " =    2.927
peak=    3.678 closest distance to " OD1 ASN A  69 " =    2.595
peak=    3.671 closest distance to " O   HOH Z 234 " =    1.916
peak=    3.670 closest distance to " O   HOH Z 294 " =    1.541
peak=    3.669 closest distance to " O   HOH Z 313 " =    1.976
peak=    3.664 closest distance to " O   HOH Z 423 " =    1.833
peak=    3.659 closest distance to " CD  LYS A 166 " =    1.214
peak=    3.654 closest distance to " CB  ALA A 114 " =    1.111
peak=    3.653 closest distance to " CG  MET A 185 " =    1.120
peak=    3.650 closest distance to " CA  ARG A  36 " =    0.989
peak=    3.647 closest distance to " CG2 ILE A 120 " =    1.259
peak=    3.644 closest distance to " NZ  LYS A 117 " =    3.232
peak=    3.643 closest distance to " CG1 VAL A 153 " =    1.005
peak=    3.636 closest distance to " O   HOH Z 265 " =    2.287
peak=    3.635 closest distance to " O   HOH Z 273 " =    2.751
peak=    3.633 closest distance to " N   ARG A 156 " =    1.394
peak=    3.632 closest distance to " CZ  PHE A  38 " =    1.263
peak=    3.626 closest distance to " CZ2 TRP A 179 " =    1.827
peak=    3.622 closest distance to " O   HOH Z 394 " =    4.079
peak=    3.609 closest distance to " O   HOH Z 353 " =    2.597
peak=    3.601 closest distance to " O   HOH Z 209 " =    2.315
peak=    3.600 closest distance to " O   HOH Z 180 " =    2.102
peak=    3.596 closest distance to " O   HOH Z 402 " =    1.438
peak=    3.589 closest distance to " CB  MET A  40 " =    0.800
peak=    3.588 closest distance to " O   HOH Z 272 " =    1.826
peak=    3.582 closest distance to " O   HOH Z   1 " =    1.987
peak=    3.580 closest distance to " CB  GLN A  88 " =    1.171
peak=    3.575 closest distance to " CA  ILE A 234 " =    0.905
peak=    3.551 closest distance to " CB  LEU A  83 " =    0.712
peak=    3.540 closest distance to " CG2 THR A 221 " =    0.952
peak=    3.533 closest distance to " O   HOH Z  43 " =    1.978
peak=    3.533 closest distance to " CB  PHE A 204 " =    0.710
peak=    3.527 closest distance to " CA  ASP A 162 " =    0.912
peak=    3.521 closest distance to " CB  ILE A 120 " =    1.147
peak=    3.517 closest distance to " O   HOH Z 251 " =    1.693
peak=    3.517 closest distance to " CD  ARG A  66 " =    2.292
peak=    3.507 closest distance to " CA  ASN A 217 " =    1.258
peak=    3.491 closest distance to " CB  ALA A 291 " =    1.192
peak=    3.488 closest distance to " O   HOH Z 291 " =    1.555
peak=    3.477 closest distance to " CB  ASP A 140 " =    0.962
peak=    3.476 closest distance to " NE2 HIS A 207 " =    1.179
peak=    3.475 closest distance to " O   HOH Z 371 " =    1.758
peak=    3.470 closest distance to " CE1 PHE A 218 " =    1.011
peak=    3.467 closest distance to " CD  ARG A 269 " =    0.946
peak=    3.466 closest distance to " NE2 GLN A  73 " =    3.990
peak=    3.465 closest distance to " CA  TYR A 116 " =    1.406
peak=    3.461 closest distance to " O   HOH Z 147 " =    1.865
peak=    3.456 closest distance to " CB  MET A  47 " =    1.097
peak=    3.437 closest distance to " CD1 LEU A 300 " =    1.194
peak=    3.432 closest distance to " O   HOH Z 421 " =    2.059
peak=    3.432 closest distance to " O   PHE A 192 " =    1.393
peak=    3.428 closest distance to " O   HOH Z 128 " =    2.163
peak=    3.425 closest distance to " O   HOH Z 126 " =    1.630
peak=    3.425 closest distance to " O   HOH Z 172 " =    3.158
peak=    3.425 closest distance to " O   HOH Z 389 " =    1.814
peak=    3.421 closest distance to " O   HOH Z 365 " =    2.881
peak=    3.418 closest distance to " O   TYR A 116 " =    1.401
peak=    3.415 closest distance to " O   HOH Z 411 " =    3.911
peak=    3.414 closest distance to " O   HOH Z 171 " =    4.022
peak=    3.400 closest distance to " CA  ALA A 233 " =    1.334
peak=    3.397 closest distance to " O   HOH Z 380 " =    1.822
peak=    3.380 closest distance to " CG  LYS A 119 " =    1.142
peak=    3.374 closest distance to " O   HOH Z 193 " =    1.986
peak=    3.372 closest distance to " CG  GLN A  11 " =    1.675
peak=    3.370 closest distance to " O   HOH Z 329 " =    4.134
peak=    3.363 closest distance to " O   HOH Z 133 " =    2.778
peak=    3.359 closest distance to " CB  TRP A 179 " =    1.447
peak=    3.358 closest distance to " CD2 LEU A 297 " =    0.882
peak=    3.357 closest distance to " CB  ALA A 242 " =    0.840
peak=    3.356 closest distance to " CB  TYR A 116 " =    0.796
peak=    3.355 closest distance to " O   HOH Z 261 " =    1.752
peak=    3.354 closest distance to " CB  ALA A  34 " =    0.916
peak=    3.351 closest distance to " O   HOH Z  62 " =    1.998
peak=    3.342 closest distance to " N   ASP A 162 " =    1.205
peak=    3.338 closest distance to " OG BSER A 164 " =    2.439
peak=    3.336 closest distance to " CB  LEU A 300 " =    0.947
peak=    3.334 closest distance to " O   HOH Z 337 " =    3.679
peak=    3.333 closest distance to " CG2 ILE A  20 " =    1.273
peak=    3.331 closest distance to " O   HOH Z 141 " =    1.692
peak=    3.326 closest distance to " CA  ALA A 154 " =    1.021
peak=    3.318 closest distance to " O   HOH Z 371 " =    2.787
peak=    3.318 closest distance to " O   HOH Z 359 " =    1.545
peak=    3.317 closest distance to " CD1 LEU A  96 " =    0.724
peak=    3.308 closest distance to " O   HOH Z 116 " =    3.062
peak=    3.305 closest distance to " O   HOH Z 433 " =    1.788
peak=    3.303 closest distance to " CG1 ILE A  49 " =    1.570
peak=    3.300 closest distance to " CE1 TYR A 186 " =    1.425
peak=    3.299 closest distance to " O   HOH Z 305 " =    3.557
peak=    3.297 closest distance to " O   HOH Z 185 " =    1.903
peak=    3.292 closest distance to " CB  ARG A 138 " =    1.036
peak=    3.290 closest distance to " CB  THR A  31 " =    1.537
peak=    3.287 closest distance to " CG1 VAL A 189 " =    1.973
peak=    3.283 closest distance to " OE2 GLU A   2 " =    1.708
peak=    3.283 closest distance to " O   HOH Z 280 " =    3.058
peak=    3.281 closest distance to " CA  THR A 221 " =    1.024
peak=    3.279 closest distance to " CG AARG A 275 " =    1.141
peak=    3.278 closest distance to " CA  GLN A  94 " =    0.764
peak=    3.276 closest distance to " O   LEU A 228 " =    1.809
peak=    3.270 closest distance to " O   HOH Z   1 " =    1.714
peak=    3.263 closest distance to " CD1 ILE A 263 " =    1.250
peak=    3.262 closest distance to " CB  HIS A 108 " =    0.736
peak=    3.259 closest distance to " CB  ALA A 160 " =    1.283
peak=    3.258 closest distance to " CG  PHE A 204 " =    0.924
peak=    3.254 closest distance to " O   HOH Z 213 " =    2.041
peak=    3.250 closest distance to " O   HOH Z 193 " =    1.767
peak=    3.246 closest distance to " O   HOH Z 233 " =    1.737
peak=    3.246 closest distance to " O   HOH Z 417 " =    3.563
peak=    3.245 closest distance to " O   HOH Z  40 " =    1.788
peak=    3.241 closest distance to " O   HOH Z 175 " =    2.174
peak=    3.240 closest distance to " O   HOH Z  88 " =    1.846
peak=    3.240 closest distance to " O   HOH Z  88 " =    3.175
peak=    3.238 closest distance to " CG  ARG A 138 " =    1.180
peak=    3.237 closest distance to " CB  PRO A 243 " =    1.413
peak=    3.235 closest distance to " CA  VAL A 125 " =    1.072
peak=    3.230 closest distance to " O   HOH Z  48 " =    1.568
peak=    3.230 closest distance to " O   HOH Z 422 " =    2.743
peak=    3.224 closest distance to " CB  SER A 216 " =    0.748
peak=    3.222 closest distance to " O   SER A 164 " =    1.333
peak=    3.214 closest distance to " CE1 TYR A 116 " =    1.276
peak=    3.214 closest distance to " O   HOH Z 163 " =    1.912
peak=    3.209 closest distance to " O   HOH Z 423 " =    1.453
peak=    3.208 closest distance to " OE2 GLU A  53 " =    1.666
peak=    3.207 closest distance to " O   HOH Z  47 " =    1.854
peak=    3.206 closest distance to " O   HOH Z 234 " =    2.287
peak=    3.202 closest distance to " O   HOH Z   9 " =    3.541
peak=    3.198 closest distance to " O   HOH Z 130 " =    2.134
peak=    3.191 closest distance to " OG  SER A  22 " =    2.690
peak=    3.184 closest distance to " CG2 THR A 220 " =    0.850
peak=    3.183 closest distance to " O   HOH Z 188 " =    1.960
peak=    3.182 closest distance to " CB  ASN A 173 " =    0.987
peak=    3.178 closest distance to " NH2 ARG A 156 " =    1.101
peak=    3.174 closest distance to " CB  GLN A 103 " =    0.832
peak=    3.171 closest distance to " O   HOH Z 248 " =    1.740
peak=    3.171 closest distance to " CA  ARG A 159 " =    1.237
peak=    3.168 closest distance to " CD2 LEU A   5 " =    1.218
peak=    3.168 closest distance to " CB  ASP A 298 " =    1.137
peak=    3.165 closest distance to " OG  SER A  28 " =    1.574
peak=    3.165 closest distance to " OG ASER A  99 " =    1.384
peak=    3.161 closest distance to " CA  GLU A  46 " =    0.937
peak=    3.161 closest distance to " N   SER A 135 " =    1.299
peak=    3.160 closest distance to " OG1 THR A 264 " =    0.748
peak=    3.159 closest distance to " O   HOH Z 261 " =    1.868
peak=    3.158 closest distance to " N   ASN A 127 " =    1.248
peak=    3.158 closest distance to " N   GLY A  98 " =    1.058
peak=    3.156 closest distance to " O   HOH Z  66 " =    2.274
peak=    3.156 closest distance to " O   HOH Z 390 " =    2.630
peak=    3.156 closest distance to " CA  ALA A 158 " =    1.221
peak=    3.152 closest distance to " CD1 ILE A 106 " =    0.847
peak=    3.152 closest distance to " O   HOH Z 345 " =    1.817
peak=    3.152 closest distance to " ND1 HIS A  86 " =    1.589
peak=    3.150 closest distance to " O   HOH Z 152 " =    1.993
peak=    3.149 closest distance to " O   ASN A 209 " =    1.180
peak=    3.148 closest distance to " O   THR A 251 " =    1.064
peak=    3.142 closest distance to " O   HOH Z 128 " =    2.138
peak=    3.140 closest distance to " O   HOH Z 287 " =    2.169
peak=    3.138 closest distance to " CB  SER A 141 " =    0.943
peak=    3.137 closest distance to " CB  ARG A 139 " =    1.056
peak=    3.137 closest distance to " NH1BARG A 145 " =    1.178
peak=    3.127 closest distance to " O   HOH Z 384 " =    3.141
peak=    3.125 closest distance to " CG  LYS A  76 " =    0.879
peak=    3.123 closest distance to " OG BSER A 134 " =    2.902
peak=    3.119 closest distance to " O   GLY A  75 " =    1.445
peak=    3.116 closest distance to " O   HOH Z 426 " =    1.971
peak=    3.114 closest distance to " O   HOH Z 183 " =    1.405
peak=    3.113 closest distance to " CD1 ILE A 199 " =    0.885
peak=    3.113 closest distance to " CB  THR A 182 " =    1.233
peak=    3.111 closest distance to " O   HOH Z  78 " =    2.105
peak=    3.102 closest distance to " O   HOH Z 120 " =    3.523
peak=    3.102 closest distance to " O   HOH Z 344 " =    3.241
peak=    3.093 closest distance to " CG BARG A 102 " =    1.803
peak=    3.090 closest distance to " CG2 ILE A 234 " =    0.890
peak=    3.089 closest distance to " O   HOH Z 358 " =    3.719
peak=    3.088 closest distance to " CA  ILE A 106 " =    0.774
peak=    3.085 closest distance to " O   HOH Z 421 " =    2.968
peak=    3.084 closest distance to " CD1 LEU A 261 " =    1.195
peak=    3.083 closest distance to " CA  MET A 105 " =    0.902
peak=    3.073 closest distance to " O   HOH Z  85 " =    2.036
peak=    3.072 closest distance to " CD1 LEU A 281 " =    1.049
peak=    3.058 closest distance to " CB  ASN A 215 " =    1.126
peak=    3.045 closest distance to " CG  ARG A 159 " =    0.851
peak=    3.043 closest distance to " CB  ALA A  43 " =    0.808
peak=    3.031 closest distance to " CB  ALA A   1 " =    4.836

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.442 - 5.712
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 198
   mapped sites are within: 0.711 - 5.712

peak=   -4.668 closest distance to " CD  GLN A  58 " =    0.863
peak=   -4.658 closest distance to " CD  ARG A  14 " =    3.491
peak=   -4.649 closest distance to " CG1 VAL A 112 " =    2.666
peak=   -4.360 closest distance to " O   HOH Z 231 " =    2.189
peak=   -4.347 closest distance to " O   HOH Z 290 " =    1.047
peak=   -4.342 closest distance to " CD  ARG A 156 " =    2.086
peak=   -4.290 closest distance to " O   PRO A 198 " =    1.222
peak=   -4.210 closest distance to " CD2 PHE A 192 " =    2.044
peak=   -4.208 closest distance to " N   ALA A  43 " =    2.550
peak=   -4.176 closest distance to " CZ3 TRP A 179 " =    1.152
peak=   -4.162 closest distance to " O   VAL A  67 " =    2.646
peak=   -4.126 closest distance to " CB  PRO A 243 " =    2.677
peak=   -4.083 closest distance to " CG1 VAL A 112 " =    2.912
peak=   -4.070 closest distance to " C   HIS A 108 " =    1.125
peak=   -4.036 closest distance to " OG BSER A 134 " =    1.281
peak=   -3.996 closest distance to " CD2 TYR A 293 " =    2.046
peak=   -3.958 closest distance to " CB  ALA A  43 " =    2.509
peak=   -3.943 closest distance to " CA  VAL A  67 " =    2.964
peak=   -3.917 closest distance to " O   HOH Z 211 " =    1.345
peak=   -3.916 closest distance to " OG  SER A  97 " =    2.343
peak=   -3.905 closest distance to " O   HOH Z 266 " =    5.619
peak=   -3.863 closest distance to " CE BMET A  47 " =    1.448
peak=   -3.862 closest distance to " O   HOH Z 394 " =    1.480
peak=   -3.839 closest distance to " CG  GLN A 223 " =    1.951
peak=   -3.831 closest distance to " ND2 ASN A  45 " =    1.985
peak=   -3.828 closest distance to " CE2 PHE A  61 " =    2.712
peak=   -3.815 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -3.808 closest distance to " OD1 ASP A 171 " =    1.686
peak=   -3.801 closest distance to " CD1 LEU A 255 " =    2.944
peak=   -3.792 closest distance to " O   HOH Z 185 " =    2.392
peak=   -3.784 closest distance to " O   HOH Z 351 " =    1.514
peak=   -3.778 closest distance to " CE  MET A 105 " =    2.528
peak=   -3.764 closest distance to " ND2 ASN A 249 " =    2.201
peak=   -3.757 closest distance to " CB  PRO A 280 " =    2.175
peak=   -3.745 closest distance to " CG2 ILE A 263 " =    2.303
peak=   -3.744 closest distance to " O   HOH Z 389 " =    2.149
peak=   -3.743 closest distance to " O   HOH Z  73 " =    2.324
peak=   -3.737 closest distance to " O   VAL A 189 " =    2.609
peak=   -3.727 closest distance to " CA  GLY A 241 " =    3.372
peak=   -3.712 closest distance to " CB  ALA A 161 " =    2.579
peak=   -3.691 closest distance to " CB  ASN A  39 " =    2.259
peak=   -3.668 closest distance to " NH2AARG A 275 " =    5.382
peak=   -3.665 closest distance to " O   PRO A 163 " =    1.967
peak=   -3.662 closest distance to " O   HOH Z 407 " =    3.174
peak=   -3.656 closest distance to " O   HOH Z 372 " =    2.432
peak=   -3.644 closest distance to " NE2 GLN A 278 " =    1.640
peak=   -3.618 closest distance to " CD1 LEU A 101 " =    2.369
peak=   -3.617 closest distance to " O   HOH Z 357 " =    2.054
peak=   -3.616 closest distance to " CD  PRO A 243 " =    2.163
peak=   -3.596 closest distance to " C   MET A 188 " =    1.372
peak=   -3.596 closest distance to " N   SER A 212 " =    1.946
peak=   -3.586 closest distance to " CD  GLN A  88 " =    0.764
peak=   -3.586 closest distance to " O   HOH Z 196 " =    2.098
peak=   -3.574 closest distance to " CD  GLN A 223 " =    0.833
peak=   -3.565 closest distance to " O   HOH Z 198 " =    1.777
peak=   -3.564 closest distance to " O   HOH Z  38 " =    1.499
peak=   -3.554 closest distance to " CG  GLU A 277 " =    1.226
peak=   -3.543 closest distance to " OD1 ASN A 148 " =    1.472
peak=   -3.539 closest distance to " CA  GLY A 241 " =    2.372
peak=   -3.531 closest distance to " CB  ALA A 291 " =    2.153
peak=   -3.509 closest distance to " O   HOH Z 175 " =    3.956
peak=   -3.505 closest distance to " CG  ARG A 269 " =    2.364
peak=   -3.490 closest distance to " O   HOH Z 216 " =    1.285
peak=   -3.483 closest distance to " OXT GLY A 302 " =    2.901
peak=   -3.476 closest distance to " NH2 ARG A  79 " =    1.620
peak=   -3.470 closest distance to " CG  ARG A  66 " =    2.295
peak=   -3.455 closest distance to " O   HOH Z 134 " =    3.332
peak=   -3.454 closest distance to " NE2 GLN A 194 " =    1.888
peak=   -3.450 closest distance to " CG1 VAL A 197 " =    2.278
peak=   -3.449 closest distance to " O   HOH Z 313 " =    1.844
peak=   -3.438 closest distance to " O   ALA A  10 " =    1.661
peak=   -3.434 closest distance to " CZ3 TRP A 274 " =    0.999
peak=   -3.427 closest distance to " N   THR A  52 " =    1.718
peak=   -3.426 closest distance to " ND2 ASN A  45 " =    1.366
peak=   -3.426 closest distance to " CA  ASP A 298 " =    1.143
peak=   -3.423 closest distance to " O   HOH Z 377 " =    0.711
peak=   -3.422 closest distance to " CG  PHE A 283 " =    2.635
peak=   -3.416 closest distance to " O   TYR A 247 " =    2.819
peak=   -3.410 closest distance to " CZ  PHE A 155 " =    1.142
peak=   -3.400 closest distance to " O   HOH Z 421 " =    3.071
peak=   -3.395 closest distance to " OH  TYR A 247 " =    2.091
peak=   -3.394 closest distance to " CD  GLU A 152 " =    0.801
peak=   -3.391 closest distance to " CD2 PHE A  61 " =    2.124
peak=   -3.383 closest distance to " CG2 ILE A  49 " =    2.832
peak=   -3.382 closest distance to " ND2 ASN A  60 " =    1.351
peak=   -3.372 closest distance to " O   HOH Z  15 " =    1.522
peak=   -3.368 closest distance to " CB  ALA A 291 " =    2.235
peak=   -3.367 closest distance to " O   HOH Z 114 " =    3.087
peak=   -3.366 closest distance to " CB  ASP A 286 " =    2.041
peak=   -3.365 closest distance to " O   HOH Z 174 " =    2.638
peak=   -3.362 closest distance to " N   ALA A 248 " =    1.692
peak=   -3.361 closest distance to " CD1 PHE A  59 " =    2.047
peak=   -3.356 closest distance to " O   HOH Z 166 " =    2.084
peak=   -3.355 closest distance to " N   THR A 157 " =    1.534
peak=   -3.355 closest distance to " SG BCYS A 201 " =    2.045
peak=   -3.352 closest distance to " C   ASP A 231 " =    2.589
peak=   -3.348 closest distance to " CB  ALA A 248 " =    2.432
peak=   -3.344 closest distance to " C   ASN A 285 " =    2.395
peak=   -3.341 closest distance to " CB  ALA A 129 " =    2.488
peak=   -3.338 closest distance to " CB  PRO A 163 " =    2.506
peak=   -3.334 closest distance to " O   ILE A 106 " =    2.065
peak=   -3.332 closest distance to " CD1 ILE A 199 " =    2.565
peak=   -3.328 closest distance to " O   ARG A 145 " =    1.626
peak=   -3.318 closest distance to " O   HOH Z 429 " =    1.989
peak=   -3.315 closest distance to " CE  LYS A  76 " =    2.740
peak=   -3.314 closest distance to " NH2 ARG A 159 " =    2.365
peak=   -3.309 closest distance to " O   HOH Z  60 " =    2.266
peak=   -3.309 closest distance to " O   HOH Z 359 " =    3.116
peak=   -3.307 closest distance to " O   HOH Z  11 " =    1.696
peak=   -3.301 closest distance to " CA  GLY A 133 " =    2.069
peak=   -3.300 closest distance to " CD1 LEU A   5 " =    2.575
peak=   -3.296 closest distance to " CG  ASN A  69 " =    1.272
peak=   -3.296 closest distance to " CG  ASP A 231 " =    0.711
peak=   -3.292 closest distance to " OH  TYR A 172 " =    1.863
peak=   -3.288 closest distance to " N   GLN A  58 " =    1.647
peak=   -3.287 closest distance to " O   HOH Z  37 " =    1.752
peak=   -3.285 closest distance to " CG2 VAL A 189 " =    2.017
peak=   -3.285 closest distance to " CZ  PHE A  38 " =    2.068
peak=   -3.283 closest distance to " OE1 GLU A  44 " =    0.992
peak=   -3.282 closest distance to " CG  GLN A  11 " =    1.682
peak=   -3.278 closest distance to " CD  ARG A  79 " =    1.184
peak=   -3.274 closest distance to " CE3 TRP A 150 " =    2.162
peak=   -3.272 closest distance to " O   HOH Z  22 " =    2.472
peak=   -3.270 closest distance to " OD2 ASP A  27 " =    1.573
peak=   -3.269 closest distance to " O   HOH Z  10 " =    1.420
peak=   -3.268 closest distance to " C   ALA A 158 " =    1.568
peak=   -3.263 closest distance to " CG2 THR A 178 " =    2.423
peak=   -3.262 closest distance to " CA  GLY A 241 " =    2.871
peak=   -3.260 closest distance to " CE1 TYR A 172 " =    1.925
peak=   -3.245 closest distance to " O   ALA A 161 " =    1.740
peak=   -3.243 closest distance to " CA  GLY A 203 " =    2.427
peak=   -3.241 closest distance to " O   HOH Z 131 " =    4.117
peak=   -3.240 closest distance to " CA  GLY A 287 " =    1.493
peak=   -3.240 closest distance to " CG  LEU A  83 " =    1.917
peak=   -3.238 closest distance to " O   HOH Z  51 " =    1.589
peak=   -3.238 closest distance to " CD  GLU A 236 " =    1.020
peak=   -3.234 closest distance to " O   SER A  22 " =    2.533
peak=   -3.234 closest distance to " CA  SER A 135 " =    1.283
peak=   -3.234 closest distance to " CE2 PHE A 218 " =    2.583
peak=   -3.230 closest distance to " CB  ALA A   9 " =    2.406
peak=   -3.230 closest distance to " O   HOH Z 100 " =    1.076
peak=   -3.225 closest distance to " O   HOH Z 140 " =    1.531
peak=   -3.224 closest distance to " CG  HIS A  86 " =    1.146
peak=   -3.222 closest distance to " CG1 VAL A 125 " =    1.826
peak=   -3.220 closest distance to " OG BSER A 134 " =    1.786
peak=   -3.217 closest distance to " CG1 VAL A 250 " =    2.788
peak=   -3.216 closest distance to " O   HOH Z 317 " =    1.386
peak=   -3.215 closest distance to " NH2BARG A 275 " =    1.903
peak=   -3.209 closest distance to " C   LEU A 143 " =    1.039
peak=   -3.199 closest distance to " CG  TRP A 266 " =    1.852
peak=   -3.198 closest distance to " CZ  TYR A 169 " =    1.650
peak=   -3.192 closest distance to " O   HOH Z 128 " =    2.634
peak=   -3.191 closest distance to " O   HOH Z  51 " =    1.156
peak=   -3.186 closest distance to " CB  ASP A 132 " =    2.261
peak=   -3.185 closest distance to " CB  ALA A 100 " =    2.262
peak=   -3.185 closest distance to " O   HOH Z 171 " =    1.597
peak=   -3.184 closest distance to " CB  ASP A 171 " =    2.477
peak=   -3.180 closest distance to " ND2BASN A 224 " =    1.757
peak=   -3.180 closest distance to " CB  TRP A  85 " =    2.531
peak=   -3.178 closest distance to " O   HOH Z 102 " =    1.522
peak=   -3.172 closest distance to " CD  ARG A 139 " =    1.618
peak=   -3.167 closest distance to " O   HOH Z 191 " =    5.618
peak=   -3.161 closest distance to " ND2 ASN A 187 " =    1.149
peak=   -3.156 closest distance to " O   HOH Z 114 " =    1.504
peak=   -3.155 closest distance to " O   HOH Z  63 " =    1.861
peak=   -3.153 closest distance to " O   HOH Z 426 " =    1.541
peak=   -3.150 closest distance to " CD1 ILE A 239 " =    2.266
peak=   -3.144 closest distance to " O   TRP A  70 " =    1.456
peak=   -3.139 closest distance to " CG  MET A 105 " =    0.978
peak=   -3.139 closest distance to " O   PRO A 198 " =    1.279
peak=   -3.133 closest distance to " O   HOH Z  60 " =    0.788
peak=   -3.131 closest distance to " CB  ASP A 132 " =    2.425
peak=   -3.128 closest distance to " OD2 ASP A 191 " =    1.407
peak=   -3.122 closest distance to " C   ASP A  65 " =    1.682
peak=   -3.115 closest distance to " O   HOH Z 390 " =    2.372
peak=   -3.111 closest distance to " OG  SER A 206 " =    1.774
peak=   -3.109 closest distance to " O   HOH Z 111 " =    1.681
peak=   -3.108 closest distance to " N   ASP A 171 " =    2.305
peak=   -3.108 closest distance to " CG1BVAL A  41 " =    2.784
peak=   -3.108 closest distance to " O   ALA A   1 " =    1.655
peak=   -3.105 closest distance to " CG  PRO A 163 " =    2.669
peak=   -3.104 closest distance to " CZ  PHE A 192 " =    2.860
peak=   -3.103 closest distance to " O   HOH Z 200 " =    4.544
peak=   -3.101 closest distance to " O   PHE A 218 " =    1.440
peak=   -3.094 closest distance to " CD  PRO A 213 " =    2.124
peak=   -3.093 closest distance to " CA  TRP A 274 " =    1.240
peak=   -3.093 closest distance to " CE3 TRP A 274 " =    2.487
peak=   -3.088 closest distance to " O   HOH Z 281 " =    2.788
peak=   -3.083 closest distance to " CD2 HIS A 207 " =    2.406
peak=   -3.082 closest distance to " N   SER A 271 " =    1.402
peak=   -3.081 closest distance to " O   ASP A 270 " =    2.019
peak=   -3.067 closest distance to " O   HOH Z 323 " =    1.345
peak=   -3.026 closest distance to " O   HOH Z 283 " =    5.712
peak=   -3.009 closest distance to " O   HOH Z 417 " =    2.837

================= 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    :  0.3413 0.3361   6.097738e+00   6.071898e+00
   1_bss:  0.3237 0.3223   6.069872e+00   6.042248e+00
   1_xyz:  0.1978 0.2266   5.602619e+00   5.699328e+00
   1_adp:  0.1883 0.2269   5.568005e+00   5.703427e+00
   1_occ:  0.1878 0.2265   5.566748e+00   5.704064e+00
   2_bss:  0.1835 0.2220   5.550629e+00   5.689047e+00
   2_xyz:  0.1379 0.1671   5.282418e+00   5.441203e+00
   2_adp:  0.1275 0.1709   5.241438e+00   5.453256e+00
   2_occ:  0.1273 0.1707   5.240791e+00   5.452590e+00
   3_bss:  0.1273 0.1703   5.239179e+00   5.449994e+00
   3_xyz:  0.1152 0.1613   5.166435e+00   5.402547e+00
   3_adp:  0.1142 0.1578   5.153808e+00   5.385745e+00
   3_occ:  0.1140 0.1576   5.153138e+00   5.385812e+00
   4_bss:  0.1138 0.1575   5.153056e+00   5.386185e+00
   4_xyz:  0.1138 0.1575   5.153056e+00   5.386185e+00
   4_adp:  0.1161 0.1570   5.161754e+00   5.383984e+00
   4_occ:  0.1160 0.1569   5.161675e+00   5.384131e+00
   5_bss:  0.1160 0.1569   5.161745e+00   5.384197e+00
   5_xyz:  0.1139 0.1569   5.154631e+00   5.387549e+00
   5_adp:  0.1144 0.1569   5.157355e+00   5.388348e+00
   5_occ:  0.1143 0.1569   5.157239e+00   5.388489e+00
   5_bss:  0.1143 0.1570   5.157435e+00   5.389000e+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:  0.318  50.000  -3.292  -2.438   4.542  -0.000   0.000   0.000
   1_xyz:  0.318  50.000  -3.292  -2.438   4.542  -0.000   0.000   0.000
   1_adp:  0.318  50.000  -3.292  -2.438   4.542  -0.000   0.000   0.000
   1_occ:  0.318  50.000  -3.292  -2.438   4.542  -0.000   0.000   0.000
   2_bss:  0.331  62.173  -3.034  -2.599   0.318  -0.000   0.000   0.000
   2_xyz:  0.331  62.173  -3.034  -2.599   0.318  -0.000   0.000   0.000
   2_adp:  0.331  62.173  -3.034  -2.599   0.318  -0.000   0.000   0.000
   2_occ:  0.331  62.173  -3.034  -2.599   0.318  -0.000   0.000   0.000
   3_bss:  0.333  67.299  -2.699  -2.365  -0.139  -0.000  -0.000  -0.000
   3_xyz:  0.333  67.299  -2.699  -2.365  -0.139  -0.000  -0.000  -0.000
   3_adp:  0.333  67.299  -2.699  -2.365  -0.139  -0.000  -0.000  -0.000
   3_occ:  0.333  67.299  -2.699  -2.365  -0.139  -0.000  -0.000  -0.000
   4_bss:  0.326  59.835  -2.370  -2.117  -0.148  -0.000  -0.000  -0.000
   4_xyz:  0.326  59.835  -2.370  -2.117  -0.148  -0.000  -0.000  -0.000
   4_adp:  0.326  59.835  -2.370  -2.117  -0.148  -0.000  -0.000  -0.000
   4_occ:  0.326  59.835  -2.370  -2.117  -0.148  -0.000  -0.000  -0.000
   5_bss:  0.331  59.835  -2.319  -2.069  -0.139  -0.000  -0.000  -0.000
   5_xyz:  0.331  59.835  -2.319  -2.069  -0.139  -0.000  -0.000  -0.000
   5_adp:  0.331  59.835  -2.319  -2.069  -0.139  -0.000  -0.000  -0.000
   5_occ:  0.331  59.835  -2.319  -2.069  -0.139  -0.000  -0.000  -0.000
   5_bss:  0.319  51.874  -2.211  -1.985  -0.089  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.280 0.7013  0.8647    32431.105
   1_bss:  33.872 0.7158  0.8708    29130.194
   1_xyz:  21.385 0.8492  0.9897    12636.463
   1_adp:  21.505 0.8478  0.9840    12694.490
   1_occ:  21.538 0.8473  0.9836    12692.143
   2_bss:  20.851 0.8546  0.9467    12283.049
   2_xyz:  15.192 0.9054  0.9713     7186.319
   2_adp:  15.428 0.9032  0.9643     7301.556
   2_occ:  15.412 0.9034  0.9642     7288.491
   3_bss:  15.342 0.9039  0.9660     7240.851
   3_xyz:  14.313 0.9125  0.9715     6569.669
   3_adp:  13.945 0.9156  0.9667     6345.745
   3_occ:  13.949 0.9155  0.9665     6344.126
   4_bss:  13.955 0.9155  0.9731     6347.216
   4_xyz:  13.955 0.9155  0.9731     6347.216
   4_adp:  13.872 0.9163  0.9699     6360.764
   4_occ:  13.876 0.9162  0.9698     6360.927
   5_bss:  13.877 0.9162  0.9711     6362.689
   5_xyz:  13.893 0.9162  0.9714     6405.971
   5_adp:  13.886 0.9164  0.9676     6424.551
   5_occ:  13.889 0.9164  0.9675     6424.043
   5_bss:  13.900 0.9163  0.9675     6424.712
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6645e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6645e-01
   1_xyz:   1.110  0.009  0.077 15.528  0.004  4.113   7.2977e-02
   1_adp:   1.110  0.009  0.077 15.528  0.004  4.113   7.2977e-02
   1_occ:   1.110  0.009  0.077 15.528  0.004  4.113   7.2977e-02
   2_bss:   1.110  0.009  0.077 15.528  0.004  4.113   7.2977e-02
   2_xyz:   0.969  0.007  0.073 15.012  0.004  4.125   5.6452e-02
   2_adp:   0.969  0.007  0.073 15.012  0.004  4.125   5.6452e-02
   2_occ:   0.969  0.007  0.073 15.012  0.004  4.125   5.6452e-02
   3_bss:   0.969  0.007  0.073 15.012  0.004  4.125   5.6452e-02
   3_xyz:   1.040  0.009  0.079 15.004  0.004  4.130   6.5267e-02
   3_adp:   1.040  0.009  0.079 15.004  0.004  4.130   6.5267e-02
   3_occ:   1.040  0.009  0.079 15.004  0.004  4.130   6.5267e-02
   4_bss:   1.040  0.009  0.079 15.004  0.004  4.130   6.5267e-02
   4_xyz:   1.040  0.009  0.079 15.004  0.004  4.113   6.5808e-02
   4_adp:   1.040  0.009  0.079 15.004  0.004  4.113   6.5808e-02
   4_occ:   1.040  0.009  0.079 15.004  0.004  4.113   6.5808e-02
   5_bss:   1.040  0.009  0.079 15.004  0.004  4.113   6.5808e-02
   5_xyz:   1.004  0.008  0.078 14.845  0.004  4.115   6.2355e-02
   5_adp:   1.004  0.008  0.078 14.845  0.004  4.115   6.2355e-02
   5_occ:   1.004  0.008  0.078 14.845  0.004  4.115   6.2355e-02
   5_bss:   1.004  0.008  0.078 14.845  0.004  4.115   6.2355e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.656   2.4255e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.656   2.4255e-01
   1_xyz:   7.927  0.043  0.299 83.463  0.037  2.156   7.6331e-02
   1_adp:   7.927  0.043  0.299 83.463  0.037  2.156   7.6331e-02
   1_occ:   7.927  0.043  0.299 83.463  0.037  2.156   7.6331e-02
   2_bss:   7.927  0.043  0.299 83.463  0.037  2.156   7.6331e-02
   2_xyz:   6.756  0.034  0.224 82.581  0.033  2.334   5.0888e-02
   2_adp:   6.756  0.034  0.224 82.581  0.033  2.334   5.0888e-02
   2_occ:   6.756  0.034  0.224 82.581  0.033  2.334   5.0888e-02
   3_bss:   6.756  0.034  0.224 82.581  0.033  2.334   5.0888e-02
   3_xyz:   6.779  0.047  0.276 83.066  0.037  2.364   4.8740e-02
   3_adp:   6.779  0.047  0.276 83.066  0.037  2.364   4.8740e-02
   3_occ:   6.779  0.047  0.276 83.066  0.037  2.364   4.8740e-02
   4_bss:   6.779  0.047  0.276 83.066  0.037  2.364   4.8740e-02
   4_xyz:   6.779  0.047  0.276 83.066  0.037  2.364   4.9144e-02
   4_adp:   6.779  0.047  0.276 83.066  0.037  2.364   4.9144e-02
   4_occ:   6.779  0.047  0.276 83.066  0.037  2.364   4.9144e-02
   5_bss:   6.779  0.047  0.276 83.066  0.037  2.364   4.9144e-02
   5_xyz:   6.621  0.046  0.256 83.325  0.035  2.297   4.3500e-02
   5_adp:   6.621  0.046  0.256 83.325  0.035  2.297   4.3500e-02
   5_occ:   6.621  0.046  0.256 83.325  0.035  2.297   4.3500e-02
   5_bss:   6.621  0.046  0.256 83.325  0.035  2.297   4.3500e-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:  82.21   0.00  16.13  82.21   0.00  12.28  62.82   4.17  37.09
   1_occ:  82.21   0.00  16.13  82.21   0.00  12.28  62.82   4.17  37.09
   2_bss:  82.21   0.00  16.13  82.21   0.00  12.28  62.82   4.17  37.09
   2_xyz:  82.21   0.00  16.13  82.21   0.00  12.28  62.82   4.17  37.09
   2_adp:  81.53   0.00  17.40  77.14   0.00  12.90  81.53   2.65  41.91
   2_occ:  81.53   0.00  17.40  77.14   0.00  12.90  81.53   2.65  41.91
   3_bss:  81.53   0.00  17.40  77.14   0.00  12.90  81.53   2.65  41.91
   3_xyz:  81.53   0.00  17.40  77.14   0.00  12.90  81.53   2.65  41.91
   3_adp:  80.54   0.00  16.85  80.23   0.81  12.64  80.54   0.00  39.75
   3_occ:  80.54   0.00  16.85  80.23   0.81  12.64  80.54   0.00  39.75
   4_bss:  80.54   0.00  16.85  80.23   0.81  12.64  80.54   0.00  39.75
   4_xyz:  80.54   0.00  16.85  80.23   0.81  12.64  80.54   0.00  39.75
   4_adp:  73.28   1.69  16.08  72.36   1.69  12.34  73.28   3.70  36.46
   4_occ:  73.28   1.69  16.08  72.36   1.69  12.34  73.28   3.70  36.46
   5_bss:  73.28   1.69  16.08  72.36   1.69  12.34  73.28   3.70  36.46
   5_xyz:  73.28   1.69  16.08  72.36   1.69  12.34  73.28   3.70  36.46
   5_adp:  71.75   2.09  15.86  71.02   2.09  12.22  71.75   3.72  35.64
   5_occ:  71.75   2.09  15.86  71.02   2.09  12.22  71.75   3.72  35.64
   5_bss:  71.67   2.02  15.78  70.95   2.02  12.15  71.67   3.64  35.57
------------------------------------------------------------------------
 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:    1.460    0.016    0.333
   1_adp:    1.460    0.016    0.333
   1_occ:    1.460    0.016    0.333
   2_bss:    1.460    0.016    0.333
   2_xyz:    1.037    0.026    0.386
   2_adp:    1.037    0.026    0.386
   2_occ:    1.037    0.026    0.386
   3_bss:    1.037    0.026    0.386
   3_xyz:    1.051    0.032    0.416
   3_adp:    1.051    0.032    0.416
   3_occ:    1.051    0.032    0.416
   4_bss:    1.051    0.032    0.416
   4_xyz:    1.051    0.032    0.416
   4_adp:    1.051    0.032    0.416
   4_occ:    1.051    0.032    0.416
   5_bss:    1.051    0.032    0.416
   5_xyz:    1.351    0.031    0.431
   5_adp:    1.351    0.031    0.431
   5_occ:    1.351    0.031    0.431
   5_bss:    1.351    0.031    0.431
------------------------------------------------------------------------

CPU time actual refinement: 320.29


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_658/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_658/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_658/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_658/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_658/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.14 
  Macro-tasks:
    bulk solvent and scale       = 35.74  
    individual site refinement   = 127.47 
    weights calculation          = 29.51  
    collect and process          = 6.65   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 199.50 
  Micro-tasks:
    mask                            = 1.26   
    f_calc                          = 102.58 
    alpha_beta                      = 8.32   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 110.38 
    fmodel                         = 6.50   
    r_factors                      = 0.23   
    phase_errors                   = 10.83  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 241.58 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.628 micro seconds
Total CPU time: 5.57 minutes
from_scatterers_fft:    635 calls, 102.29 s
gradients_fft:          580 calls,  97.64 s

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

# Date 2008-01-16 Time 05:21:06 PST -0800 (1200489666.62 s)
Start R-work = 0.3413, R-free = 0.3361 (no bulk solvent and anisotropic scale)
Final R-work = 0.1372, R-free = 0.1762 (no bulk solvent and anisotropic scale)

Start R-work = 0.3237, R-free = 0.3223
Final R-work = 0.1143, R-free = 0.1570