# Date 2008-01-16 Time 06:06:58 PST -0800 (1200492418.30 s)
#phil __OFF__

Command line arguments: "../1016.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27747
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1016

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.6953, 85.9581, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.6953, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99038
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964453

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9904

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.6953, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99038
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964453

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2593 [2122/2147]  1912   210   9.9%
  bin  2:  4.2593 -  3.3932 [2045/2065]  1840   205  10.0%
  bin  3:  3.3932 -  2.9680 [2018/2037]  1813   205  10.2%
  bin  4:  2.9680 -  2.6983 [1996/2026]  1800   196   9.8%
  bin  5:  2.6983 -  2.5058 [1987/2006]  1793   194   9.8%
  bin  6:  2.5058 -  2.3587 [1989/2014]  1785   204  10.3%
  bin  7:  2.3587 -  2.2409 [1939/1967]  1743   196  10.1%
  bin  8:  2.2409 -  2.1437 [1976/2012]  1777   199  10.1%
  bin  9:  2.1437 -  2.0613 [1954/1996]  1759   195  10.0%
  bin 10:  2.0613 -  1.9904 [1563/1979]  1408   155   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1016/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 12
        2.42 -     3.04: 2193
        3.04 -     3.66: 4667
        3.66 -     4.28: 9048
        4.28 -     4.90: 12292
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.141 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.141 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.189 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28207 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_1016/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1016/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.69535 85.95805 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 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2950   r_free= 0.2973   ksol= 0.00   Bsol= 0.00   scale= 0.981    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.958452                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7507 0.99   1385  155 0.2762 0.2635      6.3152      6.2594|
|  2:  4.7507 -  3.7903 0.99   1329  146 0.2298 0.2348      6.3392      6.3208|
|  3:  3.7903 -  3.3169 0.99   1300  142 0.2456 0.2282      6.2126       6.293|
|  4:  3.3169 -  3.0163 0.99   1296  153 0.2604 0.2898      6.1204      6.1475|
|  5:  3.0163 -  2.8015 0.99   1289  138 0.2974 0.3027      6.0237      6.0988|
|  6:  2.8015 -  2.6373 0.99   1281  141 0.2982 0.3176      5.9404      5.9287|
|  7:  2.6373 -  2.5058 0.99   1278  135 0.3232 0.3022      5.9465      5.9611|
|  8:  2.5058 -  2.3972 0.98   1266  151 0.3277 0.3023      5.8908      5.8448|
|  9:  2.3972 -  2.3052 0.98   1243  138 0.3107 0.3188      5.8137      5.7965|
| 10:  2.3052 -  2.2259 1.00   1293  140 0.3320 0.3574       5.828      5.8592|
| 11:  2.2259 -  2.1565 0.97   1254  139 0.3442 0.3569      5.8052      5.8685|
| 12:  2.1565 -  2.0951 0.98   1251  140 0.3465 0.3521       5.747      5.8055|
| 13:  2.0951 -  2.0400 1.00   1263  137 0.3503 0.3545      5.6666      5.6058|
| 14:  2.0400 -  1.9904 0.71    902  104 0.3413 0.3478      5.5963      5.5355|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7507  1385   155  0.81  24.51   0.86     0.82      37884.26|
|  2:  4.7507 -  3.7903  1329   146  0.86  19.76   0.98     0.92      38355.75|
|  3:  3.7903 -  3.3169  1300   142  0.83  23.65   1.01     0.97      37469.78|
|  4:  3.3169 -  3.0163  1296   153  0.80  26.06   1.00     0.95      33749.43|
|  5:  3.0163 -  2.8015  1289   138  0.75  31.06   0.99     0.92      29536.09|
|  6:  2.8015 -  2.6373  1281   141  0.75  31.31   1.02     0.92      25044.00|
|  7:  2.6373 -  2.5058  1278   135  0.76  30.66   1.01     0.93      22069.95|
|  8:  2.5058 -  2.3972  1266   151  0.76  30.58   1.02     0.96      19561.09|
|  9:  2.3972 -  2.3052  1243   138  0.76  31.01   1.04     0.96      18748.68|
| 10:  2.3052 -  2.2259  1293   140  0.73  33.03   1.06     0.96      18778.18|
| 11:  2.2259 -  2.1565  1254   139  0.71  34.87   1.08     0.95      18810.43|
| 12:  2.1565 -  2.0951  1251   140  0.72  34.60   1.05     0.95      17191.05|
| 13:  2.0951 -  2.0400  1263   137  0.70  35.57   1.05     0.96      14440.25|
| 14:  2.0400 -  1.9904   902   104  0.74  32.54   1.06     0.94      10940.08|
|alpha:            min =        0.82 max =            0.97 mean =         0.94|
|beta:             min =    10940.08 max =        38355.75 mean =     24946.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.97 mean =        29.80|
|phase err.(test): min =        0.00 max =           89.91 mean =        29.73|
|-----------------------------------------------------------------------------|

============================== 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 = 4.341348              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.544   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.569557              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.467   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      200 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1993 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1832 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2835 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4658 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4390 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5588 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6704 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.147 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    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 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2950   r_free= 0.2973   ksol= 0.00   Bsol= 0.00   scale= 0.981    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.958452                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2807   r_free= 0.2829   ksol= 0.33   Bsol= 50.00   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,-2.32,-1.52,-0.00,-0.00,-0.00); trace/3= -1.21                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.932689                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.882105              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.904   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.292041              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.200   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2807      final r-factor (work) = 0.1569          |
| start r-factor (free) = 0.2829      final r-factor (free) = 0.1773          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7056 = 3.88 * 0.50 * 5.9477 + 1.00 * 0.1607                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0061 = 3.88 * 0.50 * 5.6388 + 1.00 * 0.0608                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1569      final r-factor (work) = 0.1455          |
| start r-factor (free) = 0.1773      final r-factor (free) = 0.1818          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6530 = 0.29 * 1.00 * 5.6388 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5823 = 0.29 * 1.00 * 5.3328 + 1.00 * 0.0249                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.96   16.57    None  None   None       |
|    all(noH): 2823   0      0.00    62.96   16.57    None  None   None       |
|    Sol.    : 438    0      5.57    62.96   37.42    None  None   None       |
|    Mac.    : 2385   0      0.00    55.27   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.296:  188   |   5:    31.481 -  37.777:   99        |
|      1:     6.296 -  12.593: 1269   |   6:    37.777 -  44.074:  101        |
|      2:    12.593 -  18.889:  695   |   7:    44.074 -  50.370:   76        |
|      3:    18.889 -  25.185:  209   |   8:    50.370 -  56.666:   56        |
|      4:    25.185 -  31.481:  105   |   9:    56.666 -  62.962:   25        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1455 r_free = 0.1818             target_work(ml) = 5.343         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1451 r_free = 0.1818             target_work(ml) = 5.340         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1451   r_free= 0.1818   ksol= 0.33   Bsol= 50.00   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,-2.32,-1.52,-0.00,-0.00,-0.00); trace/3= -1.21                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.340188                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1439   r_free= 0.1799   ksol= 0.33   Bsol= 54.53   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.95,-1.93,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.336496                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.531281              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.131  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200912              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.698   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1439      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1799      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8271 = 2.53 * 0.50 * 5.3461 + 1.00 * 0.0608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7055 = 2.53 * 0.50 * 5.2513 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0804 = 0.20 * 1.00 * 5.2513 + 1.00 * 0.0253                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0451 = 0.20 * 1.00 * 5.1659 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    69.25   16.83    None  None   None       |
|    all(noH): 2823   0      1.63    69.25   16.83    None  None   None       |
|    Sol.    : 438    0      5.57    69.25   37.77    None  None   None       |
|    Mac.    : 2385   0      1.63    68.08   12.98    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:     1.630 -   8.392:  539   |   5:    35.440 -  42.202:  109        |
|      1:     8.392 -  15.154: 1323   |   6:    42.202 -  48.964:   84        |
|      2:    15.154 -  21.916:  397   |   7:    48.964 -  55.725:   83        |
|      3:    21.916 -  28.678:  137   |   8:    55.725 -  62.487:   36        |
|      4:    28.678 -  35.440:  106   |   9:    62.487 -  69.249:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1561             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1153 r_free = 0.1561             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1561   ksol= 0.33   Bsol= 54.53   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.95,-1.93,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.152612                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1559   ksol= 0.33   Bsol= 54.53   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.75,-1.71,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.151806                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.848719              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.579  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.238718              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.019  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1559      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8337 = 1.85 * 0.50 * 5.1654 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8075 = 1.85 * 0.50 * 5.1398 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2342 = 0.24 * 1.00 * 5.1398 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2329 = 0.24 * 1.00 * 5.1333 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.44    71.17   16.77    None  None   None       |
|    all(noH): 2823   0      1.44    71.17   16.77    None  None   None       |
|    Sol.    : 438    0      5.30    71.17   37.73    None  None   None       |
|    Mac.    : 2385   0      1.44    70.40   12.92    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:     1.444 -   8.417:  574   |   5:    36.307 -  43.280:  115        |
|      1:     8.417 -  15.390: 1309   |   6:    43.280 -  50.252:   83        |
|      2:    15.390 -  22.362:  386   |   7:    50.252 -  57.225:   74        |
|      3:    22.362 -  29.335:  140   |   8:    57.225 -  64.198:   26        |
|      4:    29.335 -  36.307:  107   |   9:    64.198 -  71.170:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1109 r_free = 0.1551             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1551             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1551   ksol= 0.33   Bsol= 54.53   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.75,-1.71,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.133619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1548   ksol= 0.33   Bsol= 54.53   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.66,-1.62,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133686                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.404587              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.539  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.876368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.054  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2283 = 2.40 * 0.50 * 5.1334 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2222 = 2.40 * 0.50 * 5.1208 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1082      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4951 = 0.88 * 1.00 * 5.1208 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4905 = 0.88 * 1.00 * 5.1138 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.60    83.00   17.04    None  None   None       |
|    all(noH): 2823   0      0.60    83.00   17.04    None  None   None       |
|    Sol.    : 438    0      6.58    75.73   39.37    None  None   None       |
|    Mac.    : 2385   0      0.60    83.00   12.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.597 -   8.838:  743   |   5:    41.799 -  50.040:  101        |
|      1:     8.838 -  17.078: 1272   |   6:    50.040 -  58.280:   81        |
|      2:    17.078 -  25.319:  318   |   7:    58.280 -  66.521:   44        |
|      3:    25.319 -  33.559:  132   |   8:    66.521 -  74.761:   16        |
|      4:    33.559 -  41.799:  110   |   9:    74.761 -  83.001:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1563             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1071 r_free = 0.1563             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1563   ksol= 0.33   Bsol= 54.53   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.66,-1.62,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117331                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1070   r_free= 0.1562   ksol= 0.33   Bsol= 54.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.43,-1.38,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117094                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.334410              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.531  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.165241              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.854  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4780 = 1.33 * 0.50 * 5.1147 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4742 = 1.33 * 0.50 * 5.1313 + 1.00 * 0.0505                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8569 = 0.17 * 1.00 * 5.1313 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8574 = 0.17 * 1.00 * 5.1441 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.20    80.96   16.49    None  None   None       |
|    all(noH): 2823   0      1.20    80.96   16.49    None  None   None       |
|    Sol.    : 438    0      6.50    74.54   37.17    None  None   None       |
|    Mac.    : 2385   0      1.20    80.96   12.69    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:     1.203 -   9.178:  842   |   5:    41.079 -  49.054:   97        |
|      1:     9.178 -  17.154: 1213   |   6:    49.054 -  57.030:   76        |
|      2:    17.154 -  25.129:  292   |   7:    57.030 -  65.005:   25        |
|      3:    25.129 -  33.104:  132   |   8:    65.005 -  72.980:   10        |
|      4:    33.104 -  41.079:  131   |   9:    72.980 -  80.955:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1568             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1115 r_free = 0.1568             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1568   ksol= 0.33   Bsol= 54.53   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.43,-1.38,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141503                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7507 0.99   1385  155 0.1008 0.1297      5.3963      5.5315|
|  2:  4.7507 -  3.7903 0.99   1329  146 0.0876 0.1085      5.4528      5.6211|
|  3:  3.7903 -  3.3169 0.99   1300  142 0.1045 0.1510      5.4684      5.8683|
|  4:  3.3169 -  3.0163 0.99   1296  153 0.1203 0.1534      5.4595      5.5762|
|  5:  3.0163 -  2.8015 0.99   1289  138 0.1335 0.1822      5.3378       5.594|
|  6:  2.8015 -  2.6373 0.99   1281  141 0.1198 0.1756      5.2108      5.4214|
|  7:  2.6373 -  2.5058 0.99   1278  135 0.1269 0.1575      5.1736      5.3607|
|  8:  2.5058 -  2.3972 0.98   1266  151 0.1144 0.1748      5.0371      5.3471|
|  9:  2.3972 -  2.3052 0.98   1243  138 0.1146 0.1775      5.0252      5.2801|
| 10:  2.3052 -  2.2259 1.00   1293  140 0.1119 0.1794      4.9451       5.276|
| 11:  2.2259 -  2.1565 0.97   1254  139 0.1142 0.1742      4.9549      5.2587|
| 12:  2.1565 -  2.0951 0.98   1251  140 0.1098 0.1649      4.8767      5.1363|
| 13:  2.0951 -  2.0400 1.00   1263  137 0.1136 0.1754      4.7866      5.1055|
| 14:  2.0400 -  1.9904 0.71    902  104 0.1070 0.1608      4.6513       4.863|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7507  1385   155  0.94   9.30   0.97     0.95       7201.74|
|  2:  4.7507 -  3.7903  1329   146  0.95   7.94   1.01     1.00       9072.58|
|  3:  3.7903 -  3.3169  1300   142  0.94  11.02   1.01     1.01      10171.01|
|  4:  3.3169 -  3.0163  1296   153  0.92  13.65   1.00     0.98      10421.60|
|  5:  3.0163 -  2.8015  1289   138  0.90  15.96   0.99     0.96       8434.27|
|  6:  2.8015 -  2.6373  1281   141  0.90  15.64   0.98     0.96       7069.85|
|  7:  2.6373 -  2.5058  1278   135  0.91  15.43   0.99     0.97       6205.48|
|  8:  2.5058 -  2.3972  1266   151  0.91  14.49   0.98     0.96       4878.06|
|  9:  2.3972 -  2.3052  1243   138  0.91  14.78   1.00     0.97       4825.26|
| 10:  2.3052 -  2.2259  1293   140  0.91  14.93   0.99     0.95       4126.44|
| 11:  2.2259 -  2.1565  1254   139  0.90  16.27   0.99     0.95       4398.31|
| 12:  2.1565 -  2.0951  1251   140  0.92  14.59   1.00     1.00       3943.24|
| 13:  2.0951 -  2.0400  1263   137  0.90  15.99   0.99     0.98       3299.19|
| 14:  2.0400 -  1.9904   902   104  0.92  13.93   0.97     0.94       2384.70|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2384.70 max =        10421.60 mean =      6290.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.22 mean =        13.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1568   ksol= 0.33   Bsol= 54.49   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.32,-1.26,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141560                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1115   r_free= 0.1568   ksol= 0.33   Bsol= 54.49   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-2.32,-1.26,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141560                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7507 0.99   1385  155 0.1008 0.1297      5.3966      5.5317|
|  2:  4.7507 -  3.7903 0.99   1329  146 0.0876 0.1085      5.4528      5.6209|
|  3:  3.7903 -  3.3169 0.99   1300  142 0.1045 0.1510      5.4682       5.868|
|  4:  3.3169 -  3.0163 0.99   1296  153 0.1202 0.1534      5.4594      5.5762|
|  5:  3.0163 -  2.8015 0.99   1289  138 0.1336 0.1823      5.3379      5.5942|
|  6:  2.8015 -  2.6373 0.99   1281  141 0.1198 0.1755      5.2109      5.4212|
|  7:  2.6373 -  2.5058 0.99   1278  135 0.1269 0.1574      5.1734      5.3601|
|  8:  2.5058 -  2.3972 0.98   1266  151 0.1144 0.1749       5.037      5.3474|
|  9:  2.3972 -  2.3052 0.98   1243  138 0.1146 0.1775      5.0253      5.2802|
| 10:  2.3052 -  2.2259 1.00   1293  140 0.1119 0.1794      4.9452      5.2758|
| 11:  2.2259 -  2.1565 0.97   1254  139 0.1142 0.1744      4.9551      5.2591|
| 12:  2.1565 -  2.0951 0.98   1251  140 0.1098 0.1650      4.8769      5.1365|
| 13:  2.0951 -  2.0400 1.00   1263  137 0.1137 0.1755      4.7866      5.1059|
| 14:  2.0400 -  1.9904 0.71    902  104 0.1070 0.1609      4.6513       4.863|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7507  1385   155  0.94   9.30   0.97     0.95       7206.76|
|  2:  4.7507 -  3.7903  1329   146  0.95   7.94   1.01     1.00       9072.24|
|  3:  3.7903 -  3.3169  1300   142  0.94  11.02   1.02     1.01      10165.39|
|  4:  3.3169 -  3.0163  1296   153  0.92  13.65   1.00     0.98      10422.40|
|  5:  3.0163 -  2.8015  1289   138  0.90  15.96   0.99     0.96       8434.06|
|  6:  2.8015 -  2.6373  1281   141  0.90  15.64   0.98     0.96       7068.81|
|  7:  2.6373 -  2.5058  1278   135  0.91  15.42   0.99     0.97       6203.49|
|  8:  2.5058 -  2.3972  1266   151  0.91  14.49   0.99     0.96       4877.90|
|  9:  2.3972 -  2.3052  1243   138  0.91  14.78   1.00     0.97       4824.51|
| 10:  2.3052 -  2.2259  1293   140  0.91  14.93   0.99     0.96       4127.14|
| 11:  2.2259 -  2.1565  1254   139  0.90  16.27   0.99     0.95       4399.36|
| 12:  2.1565 -  2.0951  1251   140  0.92  14.59   1.01     1.00       3945.73|
| 13:  2.0951 -  2.0400  1263   137  0.90  16.00   0.99     0.99       3300.12|
| 14:  2.0400 -  1.9904   902   104  0.92  13.93   0.97     0.94       2385.24|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2385.24 max =        10422.40 mean =      6290.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.22 mean =        13.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.987)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.16    80.91   16.44    None  None   None       |
|    all(noH): 2823   0      1.16    80.91   16.44    None  None   None       |
|    Sol.    : 438    0      6.46    74.50   37.13    None  None   None       |
|    Mac.    : 2385   0      1.16    80.91   12.65    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:     1.161 -   9.136:  842   |   5:    41.037 -  49.012:   97        |
|      1:     9.136 -  17.111: 1213   |   6:    49.012 -  56.987:   76        |
|      2:    17.111 -  25.087:  292   |   7:    56.987 -  64.963:   25        |
|      3:    25.087 -  33.062:  132   |   8:    64.963 -  72.938:   10        |
|      4:    33.062 -  41.037:  131   |   9:    72.938 -  80.913:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.536 - 4.626
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 287 from: 291
   mapped sites are within: 0.705 - 4.626

peak=    5.646 closest distance to " CG  PRO A  54 " =    1.349
peak=    5.509 closest distance to " CB  GLN A 223 " =    1.441
peak=    5.452 closest distance to " NH2 ARG A  56 " =    2.196
peak=    5.288 closest distance to " O   HOH Z 126 " =    1.923
peak=    5.214 closest distance to " CG  PRO A 213 " =    1.243
peak=    5.027 closest distance to " CB  PRO A  54 " =    0.962
peak=    5.012 closest distance to " CB  SER A  63 " =    1.243
peak=    4.923 closest distance to " CB  ARG A 275 " =    0.899
peak=    4.862 closest distance to " NE2 GLN A  11 " =    1.148
peak=    4.852 closest distance to " CG  PRO A  90 " =    1.132
peak=    4.787 closest distance to " C   PRO A 198 " =    1.522
peak=    4.778 closest distance to " O   HOH Z 232 " =    2.298
peak=    4.658 closest distance to " CB  GLN A 183 " =    1.173
peak=    4.644 closest distance to " CB  ASN A 148 " =    1.395
peak=    4.643 closest distance to " O   HOH Z 298 " =    1.950
peak=    4.606 closest distance to " CB  ASN A 187 " =    1.339
peak=    4.581 closest distance to " O   HOH Z  78 " =    1.709
peak=    4.578 closest distance to " CG  PRO A 198 " =    1.290
peak=    4.563 closest distance to " CB  LEU A 228 " =    1.071
peak=    4.521 closest distance to " O   HOH Z  15 " =    2.256
peak=    4.518 closest distance to " CB  GLU A 128 " =    1.024
peak=    4.508 closest distance to " O   HOH Z 236 " =    2.045
peak=    4.441 closest distance to " O   HOH Z 369 " =    2.097
peak=    4.402 closest distance to " CA  TYR A  30 " =    0.952
peak=    4.388 closest distance to " CG  PRO A 243 " =    1.084
peak=    4.375 closest distance to " CB  GLU A 152 " =    1.208
peak=    4.347 closest distance to " ND2 ASN A 187 " =    1.486
peak=    4.294 closest distance to " O   HOH Z 142 " =    1.735
peak=    4.229 closest distance to " CB  TYR A 169 " =    0.705
peak=    4.198 closest distance to " CG2 VAL A 257 " =    0.993
peak=    4.155 closest distance to " OD1 ASN A  69 " =    2.562
peak=    4.151 closest distance to " CD1 LEU A 300 " =    1.207
peak=    4.136 closest distance to " O   HOH Z 234 " =    3.822
peak=    4.135 closest distance to " CZ  PHE A 218 " =    1.035
peak=    4.133 closest distance to " O   HOH Z 303 " =    2.095
peak=    4.112 closest distance to " O   HOH Z 272 " =    1.885
peak=    4.112 closest distance to " O   HOH Z 250 " =    1.488
peak=    4.094 closest distance to " CA  THR A 264 " =    0.872
peak=    4.087 closest distance to " CB  TRP A 266 " =    0.920
peak=    4.086 closest distance to " CB  ARG A  79 " =    1.351
peak=    4.050 closest distance to " O   HOH Z  78 " =    2.105
peak=    4.041 closest distance to " O   HOH Z 209 " =    2.285
peak=    4.021 closest distance to " O   HOH Z 261 " =    2.104
peak=    4.006 closest distance to " CB  SER A   3 " =    1.382
peak=    4.005 closest distance to " CB  SER A 216 " =    0.766
peak=    4.000 closest distance to " O   HOH Z 193 " =    1.936
peak=    3.998 closest distance to " O   HOH Z 427 " =    2.983
peak=    3.993 closest distance to " CB  ARG A 190 " =    1.611
peak=    3.990 closest distance to " O   HOH Z 189 " =    2.426
peak=    3.967 closest distance to " CB  ASP A 124 " =    0.720
peak=    3.958 closest distance to " O   HOH Z 368 " =    1.926
peak=    3.952 closest distance to " CA  ASN A 215 " =    1.169
peak=    3.945 closest distance to " CB  ASN A  39 " =    0.930
peak=    3.944 closest distance to " CB  VAL A 265 " =    1.269
peak=    3.932 closest distance to " O   HOH Z 346 " =    1.621
peak=    3.926 closest distance to " OD2 ASP A 286 " =    2.900
peak=    3.918 closest distance to " NH2 ARG A 156 " =    1.230
peak=    3.911 closest distance to " NH1AARG A 145 " =    1.193
peak=    3.906 closest distance to " CB  LEU A 143 " =    1.126
peak=    3.896 closest distance to " O   HOH Z 316 " =    3.134
peak=    3.877 closest distance to " O   HOH Z  68 " =    2.159
peak=    3.871 closest distance to " O   HOH Z 132 " =    2.561
peak=    3.867 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.853 closest distance to " O   HOH Z 158 " =    3.026
peak=    3.851 closest distance to " O   HOH Z 193 " =    1.766
peak=    3.846 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.840 closest distance to " O   HOH Z 214 " =    2.037
peak=    3.839 closest distance to " CG1 ILE A  33 " =    1.292
peak=    3.832 closest distance to " O   HOH Z 344 " =    3.163
peak=    3.827 closest distance to " CD  ARG A  66 " =    2.252
peak=    3.821 closest distance to " O   HOH Z 203 " =    1.894
peak=    3.807 closest distance to " ND2 ASN A 249 " =    1.974
peak=    3.805 closest distance to " O   HOH Z  21 " =    1.755
peak=    3.805 closest distance to " CG  LEU A 167 " =    1.205
peak=    3.796 closest distance to " O   HOH Z  61 " =    1.622
peak=    3.789 closest distance to " O   HOH Z  10 " =    1.862
peak=    3.780 closest distance to " ND1 HIS A  86 " =    1.694
peak=    3.739 closest distance to " NZ  LYS A 117 " =    3.240
peak=    3.739 closest distance to " CB  SER A 212 " =    1.173
peak=    3.725 closest distance to " O   HOH Z 135 " =    1.702
peak=    3.724 closest distance to " CG2 THR A 221 " =    1.013
peak=    3.724 closest distance to " CB  ASN A 142 " =    0.959
peak=    3.721 closest distance to " CD  ARG A 269 " =    0.916
peak=    3.714 closest distance to " O   HOH Z 180 " =    2.116
peak=    3.711 closest distance to " CA  TYR A  30 " =    1.066
peak=    3.709 closest distance to " O   HOH Z   1 " =    2.000
peak=    3.708 closest distance to " CA  ALA A  21 " =    1.188
peak=    3.688 closest distance to " CZ  PHE A 192 " =    0.885
peak=    3.679 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.670 closest distance to " ND2 ASN A 110 " =    1.843
peak=    3.666 closest distance to " CB  MET A  40 " =    0.795
peak=    3.658 closest distance to " OD1BASN A 224 " =    2.323
peak=    3.654 closest distance to " N   ARG A 156 " =    1.358
peak=    3.653 closest distance to " O   HOH Z 368 " =    3.596
peak=    3.652 closest distance to " CB  ALA A  34 " =    0.941
peak=    3.633 closest distance to " CA  SER A  87 " =    1.027
peak=    3.625 closest distance to " O   HOH Z 197 " =    3.197
peak=    3.622 closest distance to " CB  ASP A 140 " =    0.874
peak=    3.609 closest distance to " CD  ARG A 219 " =    1.076
peak=    3.608 closest distance to " O   HOH Z  40 " =    1.808
peak=    3.606 closest distance to " O   HOH Z  54 " =    2.438
peak=    3.602 closest distance to " O   HOH Z 213 " =    1.838
peak=    3.600 closest distance to " O   HOH Z 133 " =    1.686
peak=    3.579 closest distance to " CB  MET A  47 " =    1.024
peak=    3.579 closest distance to " O   HOH Z 219 " =    2.128
peak=    3.578 closest distance to " CD BLYS A 290 " =    1.056
peak=    3.575 closest distance to " CA  MET A  40 " =    1.107
peak=    3.572 closest distance to " CD  LYS A 166 " =    1.249
peak=    3.571 closest distance to " CZ  PHE A 208 " =    1.123
peak=    3.566 closest distance to " O   HOH Z 305 " =    3.668
peak=    3.566 closest distance to " CB  TRP A 179 " =    1.385
peak=    3.547 closest distance to " O   HOH Z 273 " =    2.673
peak=    3.537 closest distance to " CB  GLU A 277 " =    3.630
peak=    3.536 closest distance to " N   ASN A 127 " =    1.244
peak=    3.535 closest distance to " O   MET A 105 " =    1.783
peak=    3.535 closest distance to " N   ASN A  39 " =    1.287
peak=    3.534 closest distance to " CG1BVAL A  72 " =    1.589
peak=    3.530 closest distance to " O   HOH Z 419 " =    1.987
peak=    3.522 closest distance to " O   TYR A 116 " =    1.266
peak=    3.519 closest distance to " CG2 ILE A 120 " =    1.134
peak=    3.517 closest distance to " O   HOH Z 147 " =    1.751
peak=    3.515 closest distance to " CG1 VAL A 153 " =    0.886
peak=    3.513 closest distance to " O   HOH Z 426 " =    1.620
peak=    3.513 closest distance to " NH2BARG A 145 " =    2.108
peak=    3.513 closest distance to " O   SER A  87 " =    2.189
peak=    3.493 closest distance to " O   HOH Z  88 " =    3.407
peak=    3.493 closest distance to " CB  GLU A  46 " =    0.954
peak=    3.492 closest distance to " N   PHE A 130 " =    1.232
peak=    3.491 closest distance to " CD2 LEU A 255 " =    1.603
peak=    3.490 closest distance to " CA  ALA A  51 " =    0.883
peak=    3.489 closest distance to " CA  THR A 221 " =    0.959
peak=    3.488 closest distance to " O   HOH Z 402 " =    1.466
peak=    3.479 closest distance to " CB  ILE A 120 " =    1.163
peak=    3.477 closest distance to " O   HOH Z 403 " =    1.678
peak=    3.475 closest distance to " O   HOH Z 291 " =    1.647
peak=    3.470 closest distance to " O   HOH Z 128 " =    2.160
peak=    3.467 closest distance to " O   HOH Z 128 " =    2.243
peak=    3.462 closest distance to " O   HOH Z 193 " =    1.941
peak=    3.462 closest distance to " O   HOH Z  43 " =    1.823
peak=    3.461 closest distance to " CB  TYR A 116 " =    0.843
peak=    3.460 closest distance to " O   HOH Z 133 " =    2.426
peak=    3.456 closest distance to " O   HOH Z 411 " =    3.847
peak=    3.454 closest distance to " CD1 ILE A 106 " =    0.799
peak=    3.448 closest distance to " CA  ALA A 154 " =    0.970
peak=    3.446 closest distance to " O   HOH Z 425 " =    1.269
peak=    3.444 closest distance to " OG  SER A 206 " =    1.270
peak=    3.428 closest distance to " O   HOH Z 425 " =    2.057
peak=    3.427 closest distance to " CD2 TRP A 179 " =    1.289
peak=    3.427 closest distance to " O   HOH Z 437 " =    1.475
peak=    3.426 closest distance to " CB  HIS A 108 " =    0.789
peak=    3.421 closest distance to " CA  ARG A 195 " =    1.195
peak=    3.420 closest distance to " O   HOH Z 406 " =    1.676
peak=    3.402 closest distance to " CB  ALA A 291 " =    1.330
peak=    3.401 closest distance to " OG  SER A  22 " =    2.726
peak=    3.394 closest distance to " O   HOH Z 280 " =    3.118
peak=    3.391 closest distance to " CB  SER A 141 " =    0.977
peak=    3.388 closest distance to " O   HOH Z 245 " =    1.319
peak=    3.386 closest distance to " O   HOH Z 234 " =    1.716
peak=    3.383 closest distance to " O   HOH Z  61 " =    1.517
peak=    3.378 closest distance to " CB  ARG A 139 " =    0.913
peak=    3.374 closest distance to " O   HOH Z 371 " =    2.981
peak=    3.371 closest distance to " CA  ALA A 233 " =    1.320
peak=    3.351 closest distance to " CB  THR A 157 " =    1.122
peak=    3.348 closest distance to " CG  MET A 113 " =    1.265
peak=    3.347 closest distance to " O   HOH Z 327 " =    2.045
peak=    3.345 closest distance to " O   HOH Z 411 " =    1.815
peak=    3.341 closest distance to " CA  ARG A  36 " =    1.132
peak=    3.338 closest distance to " O   HOH Z  40 " =    1.860
peak=    3.337 closest distance to " CA  ASP A 140 " =    1.239
peak=    3.334 closest distance to " O   HOH Z 295 " =    1.526
peak=    3.332 closest distance to " O   HOH Z 172 " =    3.274
peak=    3.328 closest distance to " O   HOH Z   1 " =    1.758
peak=    3.328 closest distance to " CA  ALA A 291 " =    0.947
peak=    3.326 closest distance to " O   HOH Z  44 " =    3.134
peak=    3.326 closest distance to " CB  ALA A 248 " =    1.017
peak=    3.321 closest distance to " CB  ALA A   1 " =    4.626
peak=    3.320 closest distance to " CB  ALA A 242 " =    0.808
peak=    3.316 closest distance to " CB  SER A  62 " =    1.197
peak=    3.316 closest distance to " N   GLN A 278 " =    1.006
peak=    3.315 closest distance to " O   HOH Z 353 " =    2.707
peak=    3.315 closest distance to " CB  LYS A 193 " =    0.982
peak=    3.313 closest distance to " O   HOH Z 108 " =    2.421
peak=    3.311 closest distance to " CB  PHE A  16 " =    1.039
peak=    3.309 closest distance to " O   HOH Z 166 " =    3.732
peak=    3.307 closest distance to " O   HOH Z 409 " =    2.830
peak=    3.301 closest distance to " CA  ALA A 158 " =    1.172
peak=    3.293 closest distance to " O   HOH Z  93 " =    2.641
peak=    3.290 closest distance to " CB  ALA A 248 " =    1.287
peak=    3.289 closest distance to " CG1 ILE A 151 " =    0.996
peak=    3.288 closest distance to " O   HOH Z 213 " =    2.197
peak=    3.287 closest distance to " O   HOH Z  64 " =    2.123
peak=    3.287 closest distance to " OD1 ASN A 217 " =    1.655
peak=    3.286 closest distance to " O   THR A 251 " =    1.159
peak=    3.285 closest distance to " N   SER A 135 " =    1.293
peak=    3.282 closest distance to " CB  PRO A 198 " =    0.954
peak=    3.281 closest distance to " O  BHOH Z 338 " =    2.388
peak=    3.281 closest distance to " CA  ASP A 191 " =    0.733
peak=    3.280 closest distance to " O   HOH Z 271 " =    2.299
peak=    3.275 closest distance to " O   HOH Z 313 " =    1.968
peak=    3.274 closest distance to " CA  ILE A 234 " =    0.915
peak=    3.274 closest distance to " O   HOH Z 294 " =    1.522
peak=    3.271 closest distance to " CB  SER A 210 " =    0.768
peak=    3.268 closest distance to " O   ASN A 209 " =    1.310
peak=    3.264 closest distance to " NE2 HIS A 207 " =    1.356
peak=    3.258 closest distance to " O   THR A 220 " =    1.309
peak=    3.257 closest distance to " O   HOH Z 285 " =    2.977
peak=    3.249 closest distance to " O   HOH Z 175 " =    2.134
peak=    3.247 closest distance to " ND1 HIS A  81 " =    1.627
peak=    3.246 closest distance to " CG1 ILE A 120 " =    1.061
peak=    3.244 closest distance to " O   HOH Z  97 " =    1.955
peak=    3.243 closest distance to " CA  GLY A 267 " =    1.163
peak=    3.242 closest distance to " O   HOH Z 435 " =    1.962
peak=    3.242 closest distance to " CG  ARG A 159 " =    0.892
peak=    3.240 closest distance to " CA  LEU A 282 " =    1.034
peak=    3.240 closest distance to " C   TYR A 214 " =    1.570
peak=    3.240 closest distance to " CD1 LEU A  96 " =    0.767
peak=    3.240 closest distance to " CB  ALA A 184 " =    0.911
peak=    3.239 closest distance to " O   HOH Z  59 " =    1.931
peak=    3.238 closest distance to " O   HOH Z  53 " =    2.556
peak=    3.235 closest distance to " O   HOH Z 329 " =    3.746
peak=    3.228 closest distance to " O   HOH Z 261 " =    2.172
peak=    3.225 closest distance to " CA  GLN A 223 " =    0.948
peak=    3.222 closest distance to " CB  GLU A 236 " =    1.094
peak=    3.216 closest distance to " CG  GLN A  11 " =    1.801
peak=    3.215 closest distance to " O   HOH Z 183 " =    1.410
peak=    3.215 closest distance to " CZ3 TRP A 123 " =    1.240
peak=    3.213 closest distance to " O   HOH Z 188 " =    2.148
peak=    3.212 closest distance to " O   HOH Z 345 " =    3.519
peak=    3.209 closest distance to " O   HOH Z 383 " =    1.835
peak=    3.206 closest distance to " O   HOH Z 423 " =    1.566
peak=    3.205 closest distance to " CA  ASN A 127 " =    1.051
peak=    3.204 closest distance to " CG BARG A 275 " =    1.484
peak=    3.204 closest distance to " CA  ALA A  84 " =    1.391
peak=    3.199 closest distance to " CD  LYS A 119 " =    1.278
peak=    3.196 closest distance to " O   HOH Z 152 " =    2.123
peak=    3.196 closest distance to " O   HOH Z 403 " =    1.363
peak=    3.192 closest distance to " CG  GLN A 278 " =    1.344
peak=    3.191 closest distance to " O   HOH Z  49 " =    2.957
peak=    3.190 closest distance to " O   HOH Z  88 " =    1.874
peak=    3.190 closest distance to " ND2 ASN A 249 " =    0.863
peak=    3.190 closest distance to " N   TYR A  15 " =    0.715
peak=    3.188 closest distance to " CZ2 TRP A 179 " =    1.736
peak=    3.187 closest distance to " O   HOH Z 238 " =    3.710
peak=    3.185 closest distance to " CB  ARG A 145 " =    0.815
peak=    3.182 closest distance to " CB  ALA A 114 " =    1.098
peak=    3.181 closest distance to " CA  ASN A 217 " =    1.289
peak=    3.179 closest distance to " CD  PRO A 243 " =    1.569
peak=    3.178 closest distance to " CG  LYS A  76 " =    0.941
peak=    3.177 closest distance to " CB  LYS A 117 " =    1.184
peak=    3.177 closest distance to " NH1BARG A 145 " =    1.107
peak=    3.174 closest distance to " N   VAL A 126 " =    1.353
peak=    3.170 closest distance to " CB  ASN A 224 " =    1.088
peak=    3.165 closest distance to " OD1 ASP A 171 " =    1.256
peak=    3.163 closest distance to " O   TRP A 274 " =    1.829
peak=    3.157 closest distance to " O   HOH Z 148 " =    3.312
peak=    3.149 closest distance to " CA  TYR A 116 " =    1.386
peak=    3.148 closest distance to " CA  LYS A 290 " =    1.280
peak=    3.139 closest distance to " N   ASN A 252 " =    1.427
peak=    3.135 closest distance to " CB  TRP A 150 " =    1.419
peak=    3.133 closest distance to " NH1 ARG A 138 " =    1.060
peak=    3.132 closest distance to " O   HOH Z 359 " =    3.922
peak=    3.132 closest distance to " O   HOH Z 379 " =    3.451
peak=    3.131 closest distance to " CB  GLN A  88 " =    1.255
peak=    3.129 closest distance to " CA  MET A 105 " =    0.962
peak=    3.122 closest distance to " CB  GLN A 103 " =    0.825
peak=    3.120 closest distance to " CB  GLU A 152 " =    1.398
peak=    3.119 closest distance to " CB  ALA A   9 " =    1.543
peak=    3.115 closest distance to " O   HOH Z 144 " =    1.771
peak=    3.112 closest distance to " O   HOH Z 216 " =    2.807
peak=    3.112 closest distance to " CB  ALA A 137 " =    1.031
peak=    3.110 closest distance to " CG  MET A 185 " =    1.025
peak=    3.103 closest distance to " O   HOH Z 391 " =    2.920
peak=    3.102 closest distance to " O   HOH Z 386 " =    2.800
peak=    3.101 closest distance to " CG  MET A 185 " =    1.133
peak=    3.097 closest distance to " CD2 HIS A  81 " =    1.178
peak=    3.093 closest distance to " OD1 ASP A 238 " =    1.009
peak=    3.087 closest distance to " CA  GLU A  46 " =    0.747
peak=    3.080 closest distance to " CA  ALA A 248 " =    1.259
peak=    3.071 closest distance to " O   HOH Z 371 " =    1.690
peak=    3.071 closest distance to " OG BSER A 164 " =    2.392
peak=    3.070 closest distance to " OG1 THR A 246 " =    3.234
peak=    3.069 closest distance to " O   HOH Z 292 " =    1.823
peak=    3.067 closest distance to " CB  ASP A 171 " =    0.730
peak=    3.057 closest distance to " CB  ARG A 138 " =    1.010
peak=    3.035 closest distance to " O   ALA A 158 " =    1.309
peak=    3.034 closest distance to " O   HOH Z 365 " =    2.946
peak=    3.029 closest distance to " O   HOH Z 175 " =    2.303

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.506 - 5.535
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 191
   mapped sites are within: 0.763 - 5.535

peak=   -4.625 closest distance to " CB  PRO A 243 " =    2.611
peak=   -4.442 closest distance to " O   HOH Z 266 " =    4.985
peak=   -4.428 closest distance to " O   HOH Z 290 " =    1.128
peak=   -4.279 closest distance to " O   VAL A  67 " =    2.639
peak=   -4.270 closest distance to " CD  ARG A 156 " =    2.031
peak=   -4.185 closest distance to " CG  GLN A 223 " =    1.828
peak=   -4.131 closest distance to " O   HOH Z 377 " =    1.980
peak=   -4.121 closest distance to " CZ3 TRP A 179 " =    1.110
peak=   -4.113 closest distance to " CE2 TYR A  30 " =    2.835
peak=   -4.073 closest distance to " O   HOH Z 389 " =    1.907
peak=   -4.028 closest distance to " O   HOH Z 435 " =    2.797
peak=   -4.022 closest distance to " O   ILE A 109 " =    2.667
peak=   -4.015 closest distance to " O   HOH Z 372 " =    2.425
peak=   -3.985 closest distance to " CD  ARG A  14 " =    3.324
peak=   -3.944 closest distance to " O   HOH Z 231 " =    2.109
peak=   -3.935 closest distance to " O   PRO A 198 " =    1.228
peak=   -3.920 closest distance to " O   HOH Z 118 " =    3.175
peak=   -3.883 closest distance to " O   HOH Z 126 " =    1.856
peak=   -3.877 closest distance to " CG  ASP A 231 " =    0.770
peak=   -3.862 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.840 closest distance to " OG BSER A 134 " =    1.196
peak=   -3.828 closest distance to " O   HOH Z  43 " =    1.659
peak=   -3.823 closest distance to " ND2 ASN A  45 " =    1.482
peak=   -3.821 closest distance to " CD  GLN A  58 " =    1.005
peak=   -3.808 closest distance to " C   ALA A 158 " =    1.419
peak=   -3.800 closest distance to " O   HOH Z 185 " =    2.295
peak=   -3.788 closest distance to " O   HOH Z 198 " =    2.030
peak=   -3.787 closest distance to " N   ALA A  43 " =    2.559
peak=   -3.787 closest distance to " O   HOH Z  38 " =    1.420
peak=   -3.780 closest distance to " CG1 VAL A 112 " =    2.899
peak=   -3.778 closest distance to " O   HOH Z 313 " =    2.028
peak=   -3.777 closest distance to " C   HIS A 108 " =    1.078
peak=   -3.772 closest distance to " NH2AARG A 275 " =    5.483
peak=   -3.761 closest distance to " C   ASN A 285 " =    2.511
peak=   -3.740 closest distance to " CG  MET A 105 " =    0.960
peak=   -3.732 closest distance to " O   HOH Z  52 " =    1.226
peak=   -3.721 closest distance to " O   HOH Z 353 " =    2.144
peak=   -3.714 closest distance to " CZ  TYR A 169 " =    1.674
peak=   -3.707 closest distance to " CB  ALA A 291 " =    2.211
peak=   -3.705 closest distance to " CG2 ILE A 263 " =    2.361
peak=   -3.696 closest distance to " O   HOH Z 407 " =    3.230
peak=   -3.694 closest distance to " O   GLY A 211 " =    1.378
peak=   -3.687 closest distance to " O   HOH Z  10 " =    1.505
peak=   -3.682 closest distance to " CD2 PHE A 192 " =    2.045
peak=   -3.676 closest distance to " ND2 ASN A  45 " =    1.055
peak=   -3.628 closest distance to " CG  PHE A 283 " =    2.799
peak=   -3.610 closest distance to " CD1 ILE A 263 " =    3.190
peak=   -3.608 closest distance to " O   HOH Z 211 " =    1.635
peak=   -3.598 closest distance to " O   VAL A 189 " =    2.530
peak=   -3.581 closest distance to " CB  ASN A  39 " =    2.229
peak=   -3.577 closest distance to " CB  CYS A 201 " =    2.640
peak=   -3.576 closest distance to " CD1 PHE A  59 " =    1.802
peak=   -3.571 closest distance to " CE  MET A 105 " =    2.276
peak=   -3.567 closest distance to " CG1 VAL A 112 " =    2.598
peak=   -3.557 closest distance to " CB  ALA A  43 " =    2.560
peak=   -3.550 closest distance to " CD1 LEU A 228 " =    2.364
peak=   -3.545 closest distance to " CZ  PHE A  59 " =    1.567
peak=   -3.541 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.539 closest distance to " O   HOH Z 198 " =    1.339
peak=   -3.535 closest distance to " OG  SER A  97 " =    2.207
peak=   -3.533 closest distance to " ND2 ASN A 249 " =    2.180
peak=   -3.529 closest distance to " CG  GLU A 152 " =    0.797
peak=   -3.524 closest distance to " CD  ARG A 139 " =    1.602
peak=   -3.522 closest distance to " OE1 GLN A  88 " =    1.154
peak=   -3.515 closest distance to " O   HOH Z  60 " =    2.500
peak=   -3.513 closest distance to " NH1 ARG A 195 " =    2.567
peak=   -3.512 closest distance to " OXT GLY A 302 " =    2.901
peak=   -3.505 closest distance to " CE2 PHE A 218 " =    2.508
peak=   -3.504 closest distance to " CB  ALA A 248 " =    2.019
peak=   -3.500 closest distance to " O   HOH Z  11 " =    1.824
peak=   -3.492 closest distance to " CA  GLY A 241 " =    2.302
peak=   -3.489 closest distance to " OD1 ASN A 187 " =    1.596
peak=   -3.486 closest distance to " CA  GLY A  98 " =    1.931
peak=   -3.484 closest distance to " CB  ALA A 291 " =    2.217
peak=   -3.481 closest distance to " N   GLN A  58 " =    1.935
peak=   -3.470 closest distance to " C   LEU A 222 " =    0.763
peak=   -3.457 closest distance to " O   HOH Z 426 " =    1.654
peak=   -3.453 closest distance to " CD1 LEU A 101 " =    2.369
peak=   -3.444 closest distance to " CD  ARG A 195 " =    5.184
peak=   -3.442 closest distance to " N   SER A 212 " =    1.841
peak=   -3.440 closest distance to " OD1 ASN A 148 " =    1.642
peak=   -3.435 closest distance to " O   HOH Z  47 " =    1.611
peak=   -3.426 closest distance to " CG1 VAL A 250 " =    2.670
peak=   -3.410 closest distance to " O   HOH Z 394 " =    1.419
peak=   -3.406 closest distance to " O   PRO A 163 " =    2.018
peak=   -3.401 closest distance to " CZ BARG A 275 " =    1.822
peak=   -3.400 closest distance to " O   HOH Z  73 " =    2.152
peak=   -3.397 closest distance to " O   HOH Z 222 " =    1.129
peak=   -3.391 closest distance to " C   LEU A 143 " =    1.268
peak=   -3.389 closest distance to " O   VAL A  67 " =    2.751
peak=   -3.387 closest distance to " NH2 ARG A  79 " =    1.942
peak=   -3.385 closest distance to " NH2 ARG A  79 " =    1.549
peak=   -3.379 closest distance to " OD1 ASP A 191 " =    1.695
peak=   -3.377 closest distance to " CA  GLY A 203 " =    2.304
peak=   -3.375 closest distance to " CB  ALA A 248 " =    2.502
peak=   -3.374 closest distance to " CD2 LEU A 237 " =    2.790
peak=   -3.371 closest distance to " N   ASP A 171 " =    2.425
peak=   -3.371 closest distance to " CA  GLY A 241 " =    3.114
peak=   -3.370 closest distance to " O   HOH Z 298 " =    2.497
peak=   -3.354 closest distance to " OD1 ASP A 171 " =    1.578
peak=   -3.354 closest distance to " O   GLY A 196 " =    1.147
peak=   -3.349 closest distance to " OD2 ASP A 171 " =    1.868
peak=   -3.348 closest distance to " CG  ARG A 269 " =    2.578
peak=   -3.348 closest distance to " CG  TRP A 266 " =    1.797
peak=   -3.345 closest distance to " OG BSER A 134 " =    1.726
peak=   -3.340 closest distance to " CD2 TYR A 293 " =    1.987
peak=   -3.338 closest distance to " O   LEU A 101 " =    2.723
peak=   -3.334 closest distance to " O   HOH Z  51 " =    1.232
peak=   -3.334 closest distance to " NE2 GLN A  88 " =    1.920
peak=   -3.329 closest distance to " CE BMET A  47 " =    1.934
peak=   -3.323 closest distance to " CD  GLN A  88 " =    0.881
peak=   -3.320 closest distance to " C   MET A 188 " =    1.498
peak=   -3.318 closest distance to " CG1 VAL A 197 " =    2.232
peak=   -3.318 closest distance to " CD1 ILE A 239 " =    2.123
peak=   -3.315 closest distance to " CB  ASP A 286 " =    2.068
peak=   -3.313 closest distance to " CD  GLU A 236 " =    1.058
peak=   -3.310 closest distance to " O   HOH Z 317 " =    1.527
peak=   -3.301 closest distance to " CD1 LEU A 297 " =    2.469
peak=   -3.299 closest distance to " O   HOH Z 111 " =    2.095
peak=   -3.298 closest distance to " O   HOH Z 241 " =    1.285
peak=   -3.295 closest distance to " CB  CYS A 254 " =    2.298
peak=   -3.289 closest distance to " O   HOH Z 311 " =    3.639
peak=   -3.287 closest distance to " SG ACYS A 201 " =    1.970
peak=   -3.284 closest distance to " N   ALA A 226 " =    2.184
peak=   -3.281 closest distance to " N   THR A 157 " =    1.503
peak=   -3.280 closest distance to " O   HOH Z 417 " =    2.498
peak=   -3.278 closest distance to " O   HOH Z 298 " =    1.218
peak=   -3.273 closest distance to " CD1 ILE A 199 " =    2.620
peak=   -3.271 closest distance to " O   HOH Z  51 " =    1.522
peak=   -3.269 closest distance to " CB  TYR A  15 " =    2.152
peak=   -3.269 closest distance to " O   HOH Z  13 " =    1.452
peak=   -3.264 closest distance to " NE2 GLN A 278 " =    1.791
peak=   -3.262 closest distance to " ND2 ASN A  60 " =    1.381
peak=   -3.256 closest distance to " O   PRO A 243 " =    2.605
peak=   -3.248 closest distance to " O   HOH Z 196 " =    2.136
peak=   -3.235 closest distance to " N   THR A 264 " =    1.137
peak=   -3.229 closest distance to " O   HOH Z 114 " =    1.704
peak=   -3.228 closest distance to " O   HOH Z 388 " =    2.085
peak=   -3.224 closest distance to " CA  ASP A 298 " =    1.102
peak=   -3.221 closest distance to " O   HOH Z  93 " =    2.381
peak=   -3.219 closest distance to " O   HOH Z 253 " =    3.977
peak=   -3.216 closest distance to " C   PHE A  59 " =    1.373
peak=   -3.216 closest distance to " O   HOH Z 423 " =    1.102
peak=   -3.214 closest distance to " O   HOH Z 322 " =    1.482
peak=   -3.210 closest distance to " O   HOH Z 210 " =    0.986
peak=   -3.208 closest distance to " O   TRP A  70 " =    1.494
peak=   -3.206 closest distance to " O   GLN A 240 " =    2.122
peak=   -3.201 closest distance to " O   HOH Z 281 " =    2.681
peak=   -3.200 closest distance to " CE1 TYR A 169 " =    2.544
peak=   -3.199 closest distance to " O   SER A 135 " =    1.444
peak=   -3.198 closest distance to " OG  SER A  62 " =    1.619
peak=   -3.187 closest distance to " CG  GLU A 277 " =    1.183
peak=   -3.185 closest distance to " O   PHE A 218 " =    1.522
peak=   -3.181 closest distance to " O   HOH Z  63 " =    1.574
peak=   -3.181 closest distance to " O   SER A  22 " =    2.392
peak=   -3.179 closest distance to " O   HOH Z  44 " =    2.240
peak=   -3.178 closest distance to " O   HOH Z 393 " =    1.434
peak=   -3.177 closest distance to " O   ALA A 161 " =    1.604
peak=   -3.176 closest distance to " O   HOH Z 252 " =    4.263
peak=   -3.166 closest distance to " CE  LYS A  76 " =    2.774
peak=   -3.164 closest distance to " O   HOH Z 282 " =    1.139
peak=   -3.162 closest distance to " CB  ASP A 132 " =    2.353
peak=   -3.162 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.159 closest distance to " C   GLY A  13 " =    0.967
peak=   -3.159 closest distance to " CE3 TRP A 150 " =    2.004
peak=   -3.147 closest distance to " O   HOH Z 359 " =    3.262
peak=   -3.140 closest distance to " CB  PHE A 208 " =    2.287
peak=   -3.139 closest distance to " CB  TRP A  85 " =    2.355
peak=   -3.138 closest distance to " O   HOH Z 244 " =    2.054
peak=   -3.137 closest distance to " O   SER A  62 " =    2.129
peak=   -3.133 closest distance to " CE3 TRP A 274 " =    2.493
peak=   -3.119 closest distance to " O   ALA A 180 " =    1.347
peak=   -3.118 closest distance to " CG1 VAL A 125 " =    1.916
peak=   -3.114 closest distance to " CG  ASP A 132 " =    2.292
peak=   -3.108 closest distance to " CA  GLY A 241 " =    2.799
peak=   -3.103 closest distance to " O   HOH Z 417 " =    2.586
peak=   -3.099 closest distance to " O   GLY A  17 " =    1.315
peak=   -3.096 closest distance to " O   HOH Z 168 " =    1.816
peak=   -3.091 closest distance to " CH2 TRP A 177 " =    2.100
peak=   -3.087 closest distance to " CA  SER A 135 " =    1.336
peak=   -3.077 closest distance to " CA  ASP A  27 " =    2.457
peak=   -3.068 closest distance to " O   HOH Z 166 " =    1.957
peak=   -3.063 closest distance to " CD1 TRP A 179 " =    0.902
peak=   -3.062 closest distance to " OD1AASN A 224 " =    1.713
peak=   -3.054 closest distance to " CD  GLN A  11 " =    0.938
peak=   -3.044 closest distance to " N   ALA A 248 " =    1.577
peak=   -3.016 closest distance to " O   HOH Z 283 " =    5.535

================= 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    :  0.2950 0.2973   5.958452e+00   5.964525e+00
   1_bss:  0.2807 0.2829   5.932689e+00   5.933852e+00
   1_xyz:  0.1569 0.1773   5.392279e+00   5.504282e+00
   1_adp:  0.1455 0.1818   5.342567e+00   5.528597e+00
   1_occ:  0.1451 0.1818   5.340188e+00   5.527856e+00
   2_bss:  0.1439 0.1799   5.336496e+00   5.523510e+00
   2_xyz:  0.1200 0.1599   5.184546e+00   5.406806e+00
   2_adp:  0.1155 0.1561   5.152821e+00   5.384283e+00
   2_occ:  0.1153 0.1561   5.152612e+00   5.384405e+00
   3_bss:  0.1152 0.1559   5.151806e+00   5.383382e+00
   3_xyz:  0.1117 0.1554   5.137509e+00   5.378323e+00
   3_adp:  0.1109 0.1551   5.133513e+00   5.377690e+00
   3_occ:  0.1108 0.1551   5.133619e+00   5.378031e+00
   4_bss:  0.1111 0.1548   5.133686e+00   5.376289e+00
   4_xyz:  0.1082 0.1553   5.119235e+00   5.374347e+00
   4_adp:  0.1072 0.1563   5.117374e+00   5.377634e+00
   4_occ:  0.1071 0.1563   5.117331e+00   5.377681e+00
   5_bss:  0.1070 0.1562   5.117094e+00   5.377483e+00
   5_xyz:  0.1103 0.1576   5.139500e+00   5.390946e+00
   5_adp:  0.1115 0.1568   5.141611e+00   5.387746e+00
   5_occ:  0.1115 0.1568   5.141503e+00   5.387731e+00
   5_bss:  0.1115 0.1568   5.141560e+00   5.387745e+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:  0.328  50.000   0.194  -2.315  -1.519  -0.000  -0.000  -0.000
   1_xyz:  0.328  50.000   0.194  -2.315  -1.519  -0.000  -0.000  -0.000
   1_adp:  0.328  50.000   0.194  -2.315  -1.519  -0.000  -0.000  -0.000
   1_occ:  0.328  50.000   0.194  -2.315  -1.519  -0.000  -0.000  -0.000
   2_bss:  0.332  54.529  -1.916  -2.952  -1.927  -0.000  -0.000  -0.000
   2_xyz:  0.332  54.529  -1.916  -2.952  -1.927  -0.000  -0.000  -0.000
   2_adp:  0.332  54.529  -1.916  -2.952  -1.927  -0.000  -0.000  -0.000
   2_occ:  0.332  54.529  -1.916  -2.952  -1.927  -0.000  -0.000  -0.000
   3_bss:  0.332  54.529  -2.240  -2.754  -1.707  -0.000  -0.000  -0.000
   3_xyz:  0.332  54.529  -2.240  -2.754  -1.707  -0.000  -0.000  -0.000
   3_adp:  0.332  54.529  -2.240  -2.754  -1.707  -0.000  -0.000  -0.000
   3_occ:  0.332  54.529  -2.240  -2.754  -1.707  -0.000  -0.000  -0.000
   4_bss:  0.332  54.529  -2.317  -2.662  -1.616  -0.000  -0.000  -0.000
   4_xyz:  0.332  54.529  -2.317  -2.662  -1.616  -0.000  -0.000  -0.000
   4_adp:  0.332  54.529  -2.317  -2.662  -1.616  -0.000  -0.000  -0.000
   4_occ:  0.332  54.529  -2.317  -2.662  -1.616  -0.000  -0.000  -0.000
   5_bss:  0.326  54.529  -2.103  -2.427  -1.381  -0.000  -0.000  -0.000
   5_xyz:  0.326  54.529  -2.103  -2.427  -1.381  -0.000  -0.000  -0.000
   5_adp:  0.326  54.529  -2.103  -2.427  -1.381  -0.000  -0.000  -0.000
   5_occ:  0.326  54.529  -2.103  -2.427  -1.381  -0.000  -0.000  -0.000
   5_bss:  0.326  54.487  -2.042  -2.317  -1.262  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  29.790 0.7640  0.9370    24945.282
   1_bss:  28.597 0.7752  0.9134    22125.435
   1_xyz:  16.210 0.8978  1.0024     8191.447
   1_adp:  16.786 0.8924  1.0018     8539.770
   1_occ:  16.765 0.8925  1.0016     8499.009
   2_bss:  16.630 0.8936  0.9652     8407.406
   2_xyz:  14.232 0.9132  0.9763     6593.084
   2_adp:  13.730 0.9173  0.9772     6262.633
   2_occ:  13.732 0.9173  0.9770     6261.034
   3_bss:  13.716 0.9174  0.9782     6246.480
   3_xyz:  13.575 0.9187  0.9764     6190.494
   3_adp:  13.541 0.9191  0.9715     6184.434
   3_occ:  13.550 0.9190  0.9714     6187.614
   4_bss:  13.553 0.9189  0.9722     6157.113
   4_xyz:  13.528 0.9190  0.9730     6133.606
   4_adp:  13.618 0.9183  0.9672     6152.044
   4_occ:  13.619 0.9182  0.9672     6152.967
   5_bss:  13.614 0.9183  0.9751     6146.005
   5_xyz:  13.834 0.9167  0.9734     6308.025
   5_adp:  13.751 0.9174  0.9693     6292.235
   5_occ:  13.753 0.9174  0.9693     6290.085
   5_bss:  13.754 0.9174  0.9712     6290.196
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6074e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6074e-01
   1_xyz:   1.004  0.008  0.073 14.916  0.004  4.117   6.0838e-02
   1_adp:   1.004  0.008  0.073 14.916  0.004  4.117   6.0838e-02
   1_occ:   1.004  0.008  0.073 14.916  0.004  4.117   6.0838e-02
   2_bss:   1.004  0.008  0.073 14.916  0.004  4.117   6.0838e-02
   2_xyz:   0.996  0.007  0.075 14.629  0.004  4.120   5.9188e-02
   2_adp:   0.996  0.007  0.075 14.629  0.004  4.120   5.9188e-02
   2_occ:   0.996  0.007  0.075 14.629  0.004  4.120   5.9188e-02
   3_bss:   0.996  0.007  0.075 14.629  0.004  4.120   5.9188e-02
   3_xyz:   0.958  0.007  0.074 14.563  0.004  4.123   5.6517e-02
   3_adp:   0.958  0.007  0.074 14.563  0.004  4.123   5.6517e-02
   3_occ:   0.958  0.007  0.074 14.563  0.004  4.123   5.6517e-02
   4_bss:   0.958  0.007  0.074 14.563  0.004  4.123   5.6517e-02
   4_xyz:   1.038  0.009  0.079 14.701  0.004  4.125   6.5448e-02
   4_adp:   1.038  0.009  0.079 14.701  0.004  4.125   6.5448e-02
   4_occ:   1.038  0.009  0.079 14.701  0.004  4.125   6.5448e-02
   5_bss:   1.038  0.009  0.079 14.701  0.004  4.125   6.5448e-02
   5_xyz:   0.904  0.006  0.070 14.406  0.004  4.123   5.0510e-02
   5_adp:   0.904  0.006  0.070 14.406  0.004  4.123   5.0510e-02
   5_occ:   0.904  0.006  0.070 14.406  0.004  4.123   5.0510e-02
   5_bss:   0.904  0.006  0.070 14.406  0.004  4.123   5.0510e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4145e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4145e-01
   1_xyz:   8.945  0.043  0.277 83.473  0.037  2.330   6.2284e-02
   1_adp:   8.945  0.043  0.277 83.473  0.037  2.330   6.2284e-02
   1_occ:   8.945  0.043  0.277 83.473  0.037  2.330   6.2284e-02
   2_bss:   8.945  0.043  0.277 83.473  0.037  2.330   6.2284e-02
   2_xyz:   7.832  0.041  0.230 82.999  0.042  2.329   4.1637e-02
   2_adp:   7.832  0.041  0.230 82.999  0.042  2.329   4.1637e-02
   2_occ:   7.832  0.041  0.230 82.999  0.042  2.329   4.1637e-02
   3_bss:   7.832  0.041  0.230 82.999  0.042  2.329   4.1637e-02
   3_xyz:   7.682  0.041  0.228 83.712  0.038  2.341   4.2772e-02
   3_adp:   7.682  0.041  0.228 83.712  0.038  2.341   4.2772e-02
   3_occ:   7.682  0.041  0.228 83.712  0.038  2.341   4.2772e-02
   4_bss:   7.682  0.041  0.228 83.712  0.038  2.341   4.2772e-02
   4_xyz:   7.187  0.043  0.249 84.029  0.037  2.274   5.3038e-02
   4_adp:   7.187  0.043  0.249 84.029  0.037  2.274   5.3038e-02
   4_occ:   7.187  0.043  0.249 84.029  0.037  2.274   5.3038e-02
   5_bss:   7.187  0.043  0.249 84.029  0.037  2.274   5.3038e-02
   5_xyz:   7.465  0.039  0.219 83.623  0.034  2.383   3.1659e-02
   5_adp:   7.465  0.039  0.219 83.623  0.034  2.383   3.1659e-02
   5_occ:   7.465  0.039  0.219 83.623  0.034  2.383   3.1659e-02
   5_bss:   7.465  0.039  0.219 83.623  0.034  2.383   3.1659e-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:  62.96   0.00  16.57  55.27   0.00  12.74  62.96   5.57  37.42
   1_occ:  62.96   0.00  16.57  55.27   0.00  12.74  62.96   5.57  37.42
   2_bss:  62.96   0.00  16.57  55.27   0.00  12.74  62.96   5.57  37.42
   2_xyz:  62.96   0.00  16.57  55.27   0.00  12.74  62.96   5.57  37.42
   2_adp:  69.25   1.63  16.83  68.08   1.63  12.98  69.25   5.57  37.77
   2_occ:  69.25   1.63  16.83  68.08   1.63  12.98  69.25   5.57  37.77
   3_bss:  69.25   1.63  16.83  68.08   1.63  12.98  69.25   5.57  37.77
   3_xyz:  69.25   1.63  16.83  68.08   1.63  12.98  69.25   5.57  37.77
   3_adp:  71.17   1.44  16.77  70.40   1.44  12.92  71.17   5.30  37.73
   3_occ:  71.17   1.44  16.77  70.40   1.44  12.92  71.17   5.30  37.73
   4_bss:  71.17   1.44  16.77  70.40   1.44  12.92  71.17   5.30  37.73
   4_xyz:  71.17   1.44  16.77  70.40   1.44  12.92  71.17   5.30  37.73
   4_adp:  83.00   0.60  17.04  83.00   0.60  12.94  75.73   6.58  39.37
   4_occ:  83.00   0.60  17.04  83.00   0.60  12.94  75.73   6.58  39.37
   5_bss:  83.00   0.60  17.04  83.00   0.60  12.94  75.73   6.58  39.37
   5_xyz:  83.00   0.60  17.04  83.00   0.60  12.94  75.73   6.58  39.37
   5_adp:  80.96   1.20  16.49  80.96   1.20  12.69  74.54   6.50  37.17
   5_occ:  80.96   1.20  16.49  80.96   1.20  12.69  74.54   6.50  37.17
   5_bss:  80.91   1.16  16.44  80.91   1.16  12.65  74.50   6.46  37.13
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.872    0.010    0.276
   1_adp:    0.872    0.010    0.276
   1_occ:    0.872    0.010    0.276
   2_bss:    0.872    0.010    0.276
   2_xyz:    0.688    0.027    0.315
   2_adp:    0.688    0.027    0.315
   2_occ:    0.688    0.027    0.315
   3_bss:    0.688    0.027    0.315
   3_xyz:    0.783    0.040    0.335
   3_adp:    0.783    0.040    0.335
   3_occ:    0.783    0.040    0.335
   4_bss:    0.783    0.040    0.335
   4_xyz:    0.900    0.054    0.344
   4_adp:    0.900    0.054    0.344
   4_occ:    0.900    0.054    0.344
   5_bss:    0.900    0.054    0.344
   5_xyz:    0.991    0.048    0.346
   5_adp:    0.991    0.048    0.346
   5_occ:    0.991    0.048    0.346
   5_bss:    0.991    0.048    0.346
------------------------------------------------------------------------

CPU time actual refinement: 330.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1016/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_1016/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1016/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1016/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1016/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.35 
  Macro-tasks:
    bulk solvent and scale       = 37.02  
    individual site refinement   = 136.83 
    weights calculation          = 29.98  
    collect and process          = 6.75   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 210.67 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 105.96 
    alpha_beta                      = 8.19   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 115.41 
    fmodel                         = 6.62   
    r_factors                      = 0.16   
    phase_errors                   = 11.29  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 250.21 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.641 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    661 calls, 105.72 s
gradients_fft:          606 calls, 101.34 s

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

# Date 2008-01-16 Time 06:12:42 PST -0800 (1200492762.51 s)
Start R-work = 0.2950, R-free = 0.2973 (no bulk solvent and anisotropic scale)
Final R-work = 0.1357, R-free = 0.1773 (no bulk solvent and anisotropic scale)

Start R-work = 0.2807, R-free = 0.2829
Final R-work = 0.1115, R-free = 0.1568