# Date 2008-01-16 Time 03:49:25 PST -0800 (1200484165.18 s)
#phil __OFF__

Command line arguments: "../61.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2688
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 61

-------------------------------------------------------------------------------
  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: (68.4938, 46.93, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.38, per 1000 atoms: 1.20


================================== 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: (68.4938, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7371 1.95082
Completeness in resolution range: 0.934501
Completeness with d_max=infinity: 0.931656

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7371
                             d_min =   1.9508

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: (68.4938, 46.93, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7371 1.95082
Completeness in resolution range: 0.934501
Completeness with d_max=infinity: 0.931656

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7375 -  4.1741 [2210/2238]  1987   223  10.1%
  bin  2:  4.1741 -  3.3256 [2104/2127]  1891   213  10.1%
  bin  3:  3.3256 -  2.9089 [2068/2090]  1866   202   9.8%
  bin  4:  2.9089 -  2.6446 [2090/2109]  1881   209  10.0%
  bin  5:  2.6446 -  2.4560 [2030/2059]  1821   209  10.3%
  bin  6:  2.4560 -  2.3118 [2055/2097]  1852   203   9.9%
  bin  7:  2.3118 -  2.1964 [2027/2063]  1829   198   9.8%
  bin  8:  2.1964 -  2.1010 [2031/2072]  1821   210  10.3%
  bin  9:  2.1010 -  2.0204 [2022/2051]  1828   194   9.6%
  bin 10:  2.0204 -  1.9508 [ 952/2056]   854    98  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_61/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 18
        2.02 -     2.74: 292
        2.74 -     3.46: 4672
        3.46 -     4.18: 9527
        4.18 -     4.90: 14184
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.304 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.342 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.476 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.561 3.040 -x+1,y-1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.589 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28688 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_61/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_61/model_refine_001.geo

CPU time processing inputs: 9.26


============================ 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 = 68.49375 46.93 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3424   r_free= 0.3410   ksol= 0.00   Bsol= 0.00   scale= 0.967    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.110015                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7375 -  4.6554 0.99   1430  158 0.2921 0.2884      6.3924      6.4281|
|  2:  4.6554 -  3.7146 0.99   1385  154 0.2668 0.2496      6.4852      6.4924|
|  3:  3.7146 -  3.2508 0.99   1341  149 0.3022 0.3126      6.4161      6.5097|
|  4:  3.2508 -  2.9562 0.99   1340  146 0.3160 0.3504      6.2915      6.3701|
|  5:  2.9562 -  2.7458 0.98   1316  151 0.3469 0.3619      6.1605      6.1958|
|  6:  2.7458 -  2.5848 0.98   1337  143 0.3575 0.3850      6.0962      6.0163|
|  7:  2.5848 -  2.4560 0.99   1297  155 0.3656 0.3018      6.0647      5.9587|
|  8:  2.4560 -  2.3495 0.99   1338  138 0.3799 0.3764      6.0243      6.0547|
|  9:  2.3495 -  2.2594 0.98   1311  147 0.3935 0.3920      5.9956      6.0208|
| 10:  2.2594 -  2.1817 0.98   1309  144 0.3859 0.3579      5.9668      5.8911|
| 11:  2.1817 -  2.1137 0.98   1283  152 0.3913 0.3871       5.899      5.9106|
| 12:  2.1137 -  2.0534 0.99   1306  142 0.4049 0.4056      5.8498      5.8853|
| 13:  2.0534 -  1.9995 0.94   1268  128 0.4026 0.4081      5.7741      5.6946|
| 14:  1.9995 -  1.9508 0.29    369   52 0.4803 0.4636      5.8999      5.7238|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7375 -  4.6554  1430   158  0.77  27.91   0.87     0.78      48173.25|
|  2:  4.6554 -  3.7146  1385   154  0.81  25.33   0.98     0.89      58998.56|
|  3:  3.7146 -  3.2508  1341   149  0.75  30.72   0.99     0.92      60407.72|
|  4:  3.2508 -  2.9562  1340   146  0.71  34.92   0.99     0.89      53586.99|
|  5:  2.9562 -  2.7458  1316   151  0.65  39.60   0.98     0.86      44345.55|
|  6:  2.7458 -  2.5848  1337   143  0.66  39.42   0.97     0.86      37196.96|
|  7:  2.5848 -  2.4560  1297   155  0.67  38.39   1.00     0.88      32070.74|
|  8:  2.4560 -  2.3495  1338   138  0.66  38.85   1.01     0.89      28758.33|
|  9:  2.3495 -  2.2594  1311   147  0.67  38.54   1.00     0.91      26721.97|
| 10:  2.2594 -  2.1817  1309   144  0.66  38.98   1.02     0.90      25003.29|
| 11:  2.1817 -  2.1137  1283   152  0.64  40.86   1.01     0.93      24563.63|
| 12:  2.1137 -  2.0534  1306   142  0.61  43.61   1.05     0.91      23861.35|
| 13:  2.0534 -  1.9995  1268   128  0.58  45.94   1.04     0.87      22186.85|
| 14:  1.9995 -  1.9508   369    52  0.60  44.58   0.98     0.76      18865.92|
|alpha:            min =        0.76 max =            0.93 mean =         0.88|
|beta:             min =    18865.92 max =        60407.72 mean =     37272.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           89.99 mean =        37.16|
|phase err.(test): min =        0.00 max =           89.77 mean =        37.02|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.290173              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.797   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.728439              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.833   (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 |  1.304 -  1.664:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.664 -  2.023:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.023 -  2.383:       27 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.383 -  2.743:      265 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.743 -  3.102:     2348 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.102 -  3.462:     2324 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.462 -  3.821:     4319 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.821 -  4.181:     5208 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.181 -  4.540:     6370 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.540 -  4.900:     7814 |
|-----------------------------------------------------------------------------|
|-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 |        0.211 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.304 |       0.923 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.559)------------------------------------------|
|    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: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3424   r_free= 0.3410   ksol= 0.00   Bsol= 0.00   scale= 0.967    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.110015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3284   r_free= 0.3303   ksol= 0.32   Bsol= 35.16   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.76,-2.83,-0.99,-0.00,-0.00,-0.00); trace/3= -0.69                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.087957                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.748936              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.496   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.403627              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.529   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3284      final r-factor (work) = 0.2077          |
| start r-factor (free) = 0.3303      final r-factor (free) = 0.2362          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6943 = 4.75 * 0.50 * 6.0996 + 1.00 * 0.2110                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9438 = 4.75 * 0.50 * 5.8376 + 1.00 * 0.0825                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2077      final r-factor (work) = 0.1888          |
| start r-factor (free) = 0.2362      final r-factor (free) = 0.2399          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3624 = 0.40 * 1.00 * 5.8376 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2655 = 0.40 * 1.00 * 5.5894 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.559)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.09   17.45    None  None   None       |
|    all(noH): 2823   0      0.00    77.09   17.45    None  None   None       |
|    Sol.    : 438    0      6.57    74.67   39.30    None  None   None       |
|    Mac.    : 2385   0      0.00    77.09   13.44    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 -   7.709:  525   |   5:    38.543 -  46.251:  126        |
|      1:     7.709 -  15.417: 1256   |   6:    46.251 -  53.960:   89        |
|      2:    15.417 -  23.126:  452   |   7:    53.960 -  61.668:   68        |
|      3:    23.126 -  30.834:  165   |   8:    61.668 -  69.377:   17        |
|      4:    30.834 -  38.543:  122   |   9:    69.377 -  77.085:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1888 r_free = 0.2399             target_work(ml) = 5.599         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1886 r_free = 0.2398             target_work(ml) = 5.598         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1886   r_free= 0.2398   ksol= 0.32   Bsol= 35.16   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.76,-2.83,-0.99,-0.00,-0.00,-0.00); trace/3= -0.69                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.598263                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1826   r_free= 0.2335   ksol= 0.32   Bsol= 42.70   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.74,-1.43,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.575317                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.816393              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.311   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.188013              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.201  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1826      final r-factor (work) = 0.1361          |
| start r-factor (free) = 0.2335      final r-factor (free) = 0.1752          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9536 = 2.82 * 0.50 * 5.5895 + 1.00 * 0.0825                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7431 = 2.82 * 0.50 * 5.4583 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1361      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1752      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0356 = 0.19 * 1.00 * 5.4583 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9980 = 0.19 * 1.00 * 5.2693 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.559)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    82.05   17.17    None  None   None       |
|    all(noH): 2823   0      1.12    82.05   17.17    None  None   None       |
|    Sol.    : 438    0      6.34    70.05   38.58    None  None   None       |
|    Mac.    : 2385   0      1.12    82.05   13.24    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:     1.125 -   9.217:  745   |   5:    41.587 -  49.680:  127        |
|      1:     9.217 -  17.310: 1274   |   6:    49.680 -  57.772:   78        |
|      2:    17.310 -  25.402:  299   |   7:    57.772 -  65.865:   30        |
|      3:    25.402 -  33.495:  129   |   8:    65.865 -  73.957:    8        |
|      4:    33.495 -  41.587:  131   |   9:    73.957 -  82.050:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1285 r_free = 0.1676             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1283 r_free = 0.1673             target_work(ml) = 5.244         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1673   ksol= 0.32   Bsol= 42.70   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.74,-1.43,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.244017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1279   r_free= 0.1669   ksol= 0.32   Bsol= 42.70   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.59,-1.38,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.240112                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.887658              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.678  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.182777              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.797  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1279      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0282 = 1.89 * 0.50 * 5.2677 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9582 = 1.89 * 0.50 * 5.1949 + 1.00 * 0.0551                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9568 = 0.18 * 1.00 * 5.1949 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9496 = 0.18 * 1.00 * 5.1563 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.559)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.07    83.78   17.01    None  None   None       |
|    all(noH): 2823   0      2.07    83.78   17.01    None  None   None       |
|    Sol.    : 438    0      3.63    70.08   38.24    None  None   None       |
|    Mac.    : 2385   0      2.07    83.78   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.072 -  10.243: 1004   |   5:    42.926 -  51.097:  118        |
|      1:    10.243 -  18.414: 1111   |   6:    51.097 -  59.268:   72        |
|      2:    18.414 -  26.584:  247   |   7:    59.268 -  67.439:   20        |
|      3:    26.584 -  34.755:  115   |   8:    67.439 -  75.609:    5        |
|      4:    34.755 -  42.926:  129   |   9:    75.609 -  83.780:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1554             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1554             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1554   ksol= 0.32   Bsol= 42.70   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.59,-1.38,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154218                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1555   ksol= 0.32   Bsol= 42.70   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,-2.53,-1.31,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153996                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.647785              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.340  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.151584              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.855  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3029 = 1.65 * 0.50 * 5.1557 + 1.00 * 0.0551                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2918 = 1.65 * 0.50 * 5.1447 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7870 = 0.15 * 1.00 * 5.1447 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7856 = 0.15 * 1.00 * 5.1383 + 1.00 * 0.0067                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.559)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.39    84.03   16.77    None  None   None       |
|    all(noH): 2823   0      2.39    84.03   16.77    None  None   None       |
|    Sol.    : 438    0      2.95    69.55   37.31    None  None   None       |
|    Mac.    : 2385   0      2.39    84.03   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.394 -  10.558: 1085   |   5:    43.214 -  51.378:  108        |
|      1:    10.558 -  18.722: 1059   |   6:    51.378 -  59.542:   56        |
|      2:    18.722 -  26.886:  227   |   7:    59.542 -  67.706:   17        |
|      3:    26.886 -  35.050:  122   |   8:    67.706 -  75.870:    4        |
|      4:    35.050 -  43.214:  143   |   9:    75.870 -  84.034:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1534             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1534             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1534   ksol= 0.32   Bsol= 42.70   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,-2.53,-1.31,-0.00,-0.00,-0.00); trace/3= -2.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137855                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1534   ksol= 0.32   Bsol= 42.70   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,-2.43,-1.21,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.137830                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.265058              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.396  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.296888              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.651  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4415 = 3.27 * 0.50 * 5.1382 + 1.00 * 0.0532                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4257 = 3.27 * 0.50 * 5.1166 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1059          |
| start r-factor (free) = 0.1528      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5258 = 0.30 * 1.00 * 5.1166 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5243 = 0.30 * 1.00 * 5.1096 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.559)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.99    84.17   16.72    None  None   None       |
|    all(noH): 2823   0      1.99    84.17   16.72    None  None   None       |
|    Sol.    : 438    0      4.39    69.69   37.70    None  None   None       |
|    Mac.    : 2385   0      1.99    84.17   12.87    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:     1.991 -  10.209: 1036   |   5:    43.082 -  51.300:  106        |
|      1:    10.209 -  18.427: 1091   |   6:    51.300 -  59.518:   65        |
|      2:    18.427 -  26.645:  237   |   7:    59.518 -  67.736:   19        |
|      3:    26.645 -  34.864:  125   |   8:    67.736 -  75.955:    5        |
|      4:    34.864 -  43.082:  137   |   9:    75.955 -  84.173:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1059 r_free = 0.1532             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1058 r_free = 0.1533             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1058   r_free= 0.1533   ksol= 0.32   Bsol= 42.70   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.33,-2.43,-1.21,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111662                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7375 -  4.6554 0.99   1430  158 0.1004 0.1317      5.4036       5.566|
|  2:  4.6554 -  3.7146 0.99   1385  154 0.0832 0.1100      5.4116      5.5993|
|  3:  3.7146 -  3.2508 0.99   1341  149 0.1010 0.1500      5.4198      5.8141|
|  4:  3.2508 -  2.9562 0.99   1340  146 0.1142 0.1461      5.3925       5.545|
|  5:  2.9562 -  2.7458 0.98   1316  151 0.1211 0.1553       5.254      5.4654|
|  6:  2.7458 -  2.5848 0.98   1337  143 0.1159 0.1967      5.1608      5.4496|
|  7:  2.5848 -  2.4560 0.99   1297  155 0.1163 0.1589      5.1165      5.3343|
|  8:  2.4560 -  2.3495 0.99   1338  138 0.1077 0.1582       5.035      5.2355|
|  9:  2.3495 -  2.2594 0.98   1311  147 0.1111 0.1853      4.9857      5.3275|
| 10:  2.2594 -  2.1817 0.98   1309  144 0.1024 0.1685      4.9005      5.1415|
| 11:  2.1817 -  2.1137 0.98   1283  152 0.1056 0.1734      4.8734      5.2398|
| 12:  2.1137 -  2.0534 0.99   1306  142 0.1059 0.1556      4.8191      5.0674|
| 13:  2.0534 -  1.9995 0.94   1268  128 0.1010 0.1665      4.7294      4.9435|
| 14:  1.9995 -  1.9508 0.29    369   52 0.0985 0.1677      4.6641      4.9274|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7375 -  4.6554  1430   158  0.94   9.38   0.98     0.95       7451.01|
|  2:  4.6554 -  3.7146  1385   154  0.95   7.73   1.02     1.01       8750.98|
|  3:  3.7146 -  3.2508  1341   149  0.94  10.87   1.03     1.02       9450.46|
|  4:  3.2508 -  2.9562  1340   146  0.92  13.09   1.01     1.01       9443.64|
|  5:  2.9562 -  2.7458  1316   151  0.91  14.95   0.99     0.97       7437.96|
|  6:  2.7458 -  2.5848  1337   143  0.90  15.80   0.98     0.95       6453.98|
|  7:  2.5848 -  2.4560  1297   155  0.91  15.00   0.98     0.95       5802.39|
|  8:  2.4560 -  2.3495  1338   138  0.91  15.02   1.00     0.97       5218.78|
|  9:  2.3495 -  2.2594  1311   147  0.91  15.15   1.00     0.97       4666.35|
| 10:  2.2594 -  2.1817  1309   144  0.91  15.17   0.99     0.96       4150.73|
| 11:  2.1817 -  2.1137  1283   152  0.91  15.52   1.00     0.97       3998.40|
| 12:  2.1137 -  2.0534  1306   142  0.91  15.35   1.01     1.00       3615.18|
| 13:  2.0534 -  1.9995  1268   128  0.91  15.35   1.00     0.99       3091.76|
| 14:  1.9995 -  1.9508   369    52  0.92  13.58   0.98     0.94       2496.19|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2496.19 max =         9450.46 mean =      6084.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.66|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.29|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1525   ksol= 0.32   Bsol= 42.46   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,-2.24,-1.00,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109782                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.74 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1525   ksol= 0.32   Bsol= 42.46   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.17,-2.24,-1.00,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109782                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7375 -  4.6554 0.99   1430  158 0.0988 0.1270      5.3856      5.5304|
|  2:  4.6554 -  3.7146 0.99   1385  154 0.0834 0.1101      5.4083      5.6028|
|  3:  3.7146 -  3.2508 0.99   1341  149 0.1013 0.1492      5.4203      5.8039|
|  4:  3.2508 -  2.9562 0.99   1340  146 0.1144 0.1452      5.3897      5.5373|
|  5:  2.9562 -  2.7458 0.98   1316  151 0.1209 0.1551      5.2512      5.4613|
|  6:  2.7458 -  2.5848 0.98   1337  143 0.1160 0.1968      5.1605      5.4518|
|  7:  2.5848 -  2.4560 0.99   1297  155 0.1161 0.1592      5.1166      5.3355|
|  8:  2.4560 -  2.3495 0.99   1338  138 0.1077 0.1578      5.0349       5.234|
|  9:  2.3495 -  2.2594 0.98   1311  147 0.1109 0.1848      4.9853      5.3276|
| 10:  2.2594 -  2.1817 0.98   1309  144 0.1023 0.1684      4.9014      5.1443|
| 11:  2.1817 -  2.1137 0.98   1283  152 0.1057 0.1736       4.875      5.2409|
| 12:  2.1137 -  2.0534 0.99   1306  142 0.1058 0.1566      4.8196      5.0699|
| 13:  2.0534 -  1.9995 0.94   1268  128 0.1010 0.1666      4.7305      4.9441|
| 14:  1.9995 -  1.9508 0.29    369   52 0.0984 0.1682      4.6632      4.9283|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7375 -  4.6554  1430   158  0.94   9.12   0.98     0.96       7147.14|
|  2:  4.6554 -  3.7146  1385   154  0.95   7.69   1.02     1.01       8603.02|
|  3:  3.7146 -  3.2508  1341   149  0.94  10.83   1.03     1.02       9409.74|
|  4:  3.2508 -  2.9562  1340   146  0.92  12.95   1.01     1.01       9281.07|
|  5:  2.9562 -  2.7458  1316   151  0.91  14.83   1.00     0.97       7353.34|
|  6:  2.7458 -  2.5848  1337   143  0.90  15.78   0.98     0.96       6447.60|
|  7:  2.5848 -  2.4560  1297   155  0.91  14.99   0.99     0.96       5811.68|
|  8:  2.4560 -  2.3495  1338   138  0.91  15.01   1.00     0.98       5216.32|
|  9:  2.3495 -  2.2594  1311   147  0.91  15.14   1.01     0.97       4661.93|
| 10:  2.2594 -  2.1817  1309   144  0.91  15.18   1.00     0.96       4153.77|
| 11:  2.1817 -  2.1137  1283   152  0.91  15.56   1.01     0.98       4014.36|
| 12:  2.1137 -  2.0534  1306   142  0.91  15.40   1.02     1.01       3630.95|
| 13:  2.0534 -  1.9995  1268   128  0.91  15.39   1.01     0.99       3102.65|
| 14:  1.9995 -  1.9508   369    52  0.92  13.59   0.99     0.95       2497.38|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2497.38 max =         9409.74 mean =      6029.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.75 mean =        13.61|
|phase err.(test): min =        0.00 max =           89.51 mean =        13.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.559)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.92    84.10   16.65    None  None   None       |
|    all(noH): 2823   0      1.92    84.10   16.65    None  None   None       |
|    Sol.    : 438    0      4.32    69.62   37.63    None  None   None       |
|    Mac.    : 2385   0      1.92    84.10   12.80    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:     1.919 -  10.137: 1036   |   5:    43.010 -  51.228:  106        |
|      1:    10.137 -  18.355: 1091   |   6:    51.228 -  59.446:   65        |
|      2:    18.355 -  26.574:  237   |   7:    59.446 -  67.665:   19        |
|      3:    26.574 -  34.792:  125   |   8:    67.665 -  75.883:    5        |
|      4:    34.792 -  43.010:  137   |   9:    75.883 -  84.101:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 268         
Filter by distance & map next to the model:
   mapped sites are within: 0.436 - 5.479
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 265 from: 268
   mapped sites are within: 0.779 - 5.479

peak=    5.778 closest distance to " NH2 ARG A  56 " =    2.180
peak=    5.730 closest distance to " CB  ARG A 275 " =    0.926
peak=    5.335 closest distance to " O   HOH Z 142 " =    1.633
peak=    5.313 closest distance to " O   HOH Z 126 " =    1.853
peak=    5.299 closest distance to " NE2 GLN A  11 " =    1.149
peak=    4.983 closest distance to " CB  GLN A 183 " =    1.250
peak=    4.823 closest distance to " CB  SER A  63 " =    1.130
peak=    4.763 closest distance to " O   HOH Z 232 " =    2.376
peak=    4.745 closest distance to " CG  PRO A  54 " =    1.205
peak=    4.725 closest distance to " O   HOH Z 250 " =    1.519
peak=    4.724 closest distance to " O   HOH Z 417 " =    1.507
peak=    4.706 closest distance to " O   HOH Z 126 " =    1.889
peak=    4.659 closest distance to " CB  GLU A 152 " =    1.198
peak=    4.640 closest distance to " O   HOH Z  40 " =    1.760
peak=    4.625 closest distance to " CB  ARG A  79 " =    1.412
peak=    4.598 closest distance to " O   HOH Z 298 " =    1.821
peak=    4.556 closest distance to " O   HOH Z 402 " =    1.428
peak=    4.551 closest distance to " O   SER A  87 " =    2.187
peak=    4.548 closest distance to " CB  GLN A 223 " =    1.470
peak=    4.547 closest distance to " O   HOH Z 369 " =    2.244
peak=    4.529 closest distance to " CD2 TRP A 179 " =    1.348
peak=    4.410 closest distance to " O   HOH Z 272 " =    1.843
peak=    4.402 closest distance to " CB  ASN A 148 " =    1.505
peak=    4.390 closest distance to " O   HOH Z 209 " =    2.251
peak=    4.390 closest distance to " O   HOH Z 287 " =    1.924
peak=    4.367 closest distance to " O   HOH Z 109 " =    1.548
peak=    4.330 closest distance to " ND2 ASN A 187 " =    1.492
peak=    4.300 closest distance to " O   HOH Z 193 " =    1.768
peak=    4.283 closest distance to " O   HOH Z 346 " =    1.604
peak=    4.269 closest distance to " CA  TYR A  30 " =    0.915
peak=    4.262 closest distance to " C   PRO A 198 " =    1.443
peak=    4.259 closest distance to " O   HOH Z 427 " =    2.875
peak=    4.243 closest distance to " O   HOH Z 403 " =    1.715
peak=    4.228 closest distance to " O   HOH Z 368 " =    2.004
peak=    4.205 closest distance to " O   HOH Z  54 " =    1.693
peak=    4.192 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.188 closest distance to " O   HOH Z 303 " =    2.189
peak=    4.176 closest distance to " O   HOH Z 234 " =    3.560
peak=    4.156 closest distance to " O   HOH Z  43 " =    1.888
peak=    4.150 closest distance to " O   HOH Z  78 " =    1.742
peak=    4.130 closest distance to " O   HOH Z  44 " =    1.911
peak=    4.114 closest distance to " O   HOH Z 128 " =    1.887
peak=    4.113 closest distance to " O   HOH Z  61 " =    1.624
peak=    4.096 closest distance to " CB  PRO A  54 " =    0.923
peak=    4.089 closest distance to " O   HOH Z 392 " =    2.789
peak=    4.088 closest distance to " O   HOH Z 406 " =    1.566
peak=    4.079 closest distance to " O   HOH Z  97 " =    2.333
peak=    4.047 closest distance to " O   HOH Z  97 " =    1.932
peak=    4.038 closest distance to " CG  ARG A  66 " =    2.569
peak=    4.036 closest distance to " O   HOH Z  15 " =    2.176
peak=    4.005 closest distance to " O   HOH Z  66 " =    2.263
peak=    4.003 closest distance to " CB  ARG A 190 " =    1.676
peak=    4.001 closest distance to " O   HOH Z 203 " =    1.754
peak=    3.992 closest distance to " NH2BARG A 145 " =    1.950
peak=    3.961 closest distance to " CB  VAL A 265 " =    1.228
peak=    3.953 closest distance to " OE1 GLU A   2 " =    2.272
peak=    3.949 closest distance to " O   HOH Z  61 " =    1.497
peak=    3.932 closest distance to " OG ASER A 258 " =    3.022
peak=    3.900 closest distance to " O   HOH Z 327 " =    1.603
peak=    3.898 closest distance to " NZ  LYS A 117 " =    3.066
peak=    3.887 closest distance to " CB  VAL A 202 " =    1.544
peak=    3.882 closest distance to " O   HOH Z 158 " =    3.054
peak=    3.878 closest distance to " O   HOH Z 245 " =    1.401
peak=    3.873 closest distance to " CB  TRP A 266 " =    1.010
peak=    3.849 closest distance to " O   HOH Z 189 " =    2.388
peak=    3.845 closest distance to " O   HOH Z 365 " =    2.751
peak=    3.841 closest distance to " O   HOH Z 423 " =    2.006
peak=    3.797 closest distance to " O   HOH Z 416 " =    2.645
peak=    3.795 closest distance to " O   HOH Z  47 " =    1.639
peak=    3.788 closest distance to " CB  SER A  26 " =    1.671
peak=    3.782 closest distance to " O   HOH Z 415 " =    3.586
peak=    3.771 closest distance to " O   HOH Z 425 " =    2.026
peak=    3.761 closest distance to " CA  ALA A  84 " =    1.181
peak=    3.738 closest distance to " O   HOH Z 173 " =    2.031
peak=    3.715 closest distance to " O   HOH Z  59 " =    1.956
peak=    3.707 closest distance to " CB  ASN A  39 " =    0.813
peak=    3.702 closest distance to " CB  SER A   3 " =    1.207
peak=    3.676 closest distance to " O   HOH Z 353 " =    2.620
peak=    3.667 closest distance to " O   HOH Z   1 " =    1.919
peak=    3.663 closest distance to " CG  MET A 185 " =    1.082
peak=    3.660 closest distance to " CG2 VAL A 257 " =    0.811
peak=    3.656 closest distance to " CB  ASN A 110 " =    1.046
peak=    3.656 closest distance to " O   HOH Z  10 " =    1.824
peak=    3.653 closest distance to " CG2 ILE A  20 " =    1.363
peak=    3.652 closest distance to " O  BHOH Z 338 " =    2.306
peak=    3.651 closest distance to " O   HOH Z 344 " =    3.102
peak=    3.641 closest distance to " CB  GLU A 277 " =    3.491
peak=    3.641 closest distance to " CD2 LEU A 297 " =    0.948
peak=    3.632 closest distance to " O   HOH Z 128 " =    2.145
peak=    3.628 closest distance to " CA  ALA A  21 " =    1.105
peak=    3.628 closest distance to " CZ  PHE A 218 " =    1.107
peak=    3.628 closest distance to " O   HOH Z 286 " =    2.242
peak=    3.627 closest distance to " CG2 ILE A 120 " =    1.209
peak=    3.622 closest distance to " O   HOH Z 368 " =    3.611
peak=    3.611 closest distance to " O   HOH Z 261 " =    2.073
peak=    3.609 closest distance to " CG  GLN A  77 " =    2.087
peak=    3.607 closest distance to " O   HOH Z 273 " =    2.695
peak=    3.604 closest distance to " OG BSER A 164 " =    2.104
peak=    3.603 closest distance to " NH2AARG A 190 " =    1.948
peak=    3.602 closest distance to " O   HOH Z 214 " =    2.112
peak=    3.601 closest distance to " CG AARG A 275 " =    1.078
peak=    3.598 closest distance to " N   ASN A  39 " =    1.198
peak=    3.594 closest distance to " O   HOH Z 255 " =    1.646
peak=    3.582 closest distance to " O   HOH Z 132 " =    2.814
peak=    3.577 closest distance to " O  BHOH Z  74 " =    1.385
peak=    3.574 closest distance to " O   HOH Z 357 " =    1.946
peak=    3.569 closest distance to " CB  THR A  31 " =    1.604
peak=    3.564 closest distance to " O   HOH Z 291 " =    1.478
peak=    3.562 closest distance to " O   HOH Z 183 " =    1.707
peak=    3.556 closest distance to " O   HOH Z 299 " =    4.248
peak=    3.553 closest distance to " O   HOH Z 265 " =    2.203
peak=    3.537 closest distance to " CG1 ILE A  33 " =    1.187
peak=    3.537 closest distance to " O   HOH Z 389 " =    1.790
peak=    3.535 closest distance to " CD  ARG A  66 " =    2.673
peak=    3.529 closest distance to " N   PHE A 130 " =    1.328
peak=    3.527 closest distance to " CB  HIS A 108 " =    0.868
peak=    3.526 closest distance to " O   HOH Z  85 " =    1.448
peak=    3.526 closest distance to " CA  ARG A 195 " =    1.310
peak=    3.517 closest distance to " CB  GLU A  46 " =    1.010
peak=    3.514 closest distance to " N   ARG A 156 " =    1.308
peak=    3.513 closest distance to " O   HOH Z 280 " =    3.013
peak=    3.512 closest distance to " CB  ILE A 120 " =    1.278
peak=    3.508 closest distance to " O   HOH Z 380 " =    1.987
peak=    3.508 closest distance to " O   HOH Z 261 " =    1.758
peak=    3.506 closest distance to " O   HOH Z 337 " =    3.436
peak=    3.506 closest distance to " O   HOH Z  88 " =    2.622
peak=    3.500 closest distance to " O   HOH Z 345 " =    3.047
peak=    3.499 closest distance to " O   HOH Z 305 " =    3.598
peak=    3.497 closest distance to " O   HOH Z  21 " =    1.863
peak=    3.478 closest distance to " NH1AARG A 145 " =    1.154
peak=    3.476 closest distance to " CA  ALA A  51 " =    0.887
peak=    3.476 closest distance to " CD  ARG A 269 " =    0.922
peak=    3.475 closest distance to " O   HOH Z 180 " =    2.205
peak=    3.474 closest distance to " OD1 ASN A  69 " =    2.559
peak=    3.472 closest distance to " CB  TRP A 179 " =    1.189
peak=    3.470 closest distance to " CB  TYR A 169 " =    0.790
peak=    3.469 closest distance to " O   HOH Z 433 " =    1.866
peak=    3.464 closest distance to " O   HOH Z 213 " =    1.710
peak=    3.464 closest distance to " O   HOH Z 126 " =    1.577
peak=    3.462 closest distance to " O   HOH Z   3 " =    1.920
peak=    3.457 closest distance to " CB  GLN A  88 " =    1.161
peak=    3.456 closest distance to " O   HOH Z 147 " =    1.804
peak=    3.454 closest distance to " CA  ASN A 215 " =    0.996
peak=    3.451 closest distance to " CD  LYS A 166 " =    1.282
peak=    3.450 closest distance to " O   HOH Z 234 " =    2.198
peak=    3.447 closest distance to " CA  ARG A  36 " =    0.990
peak=    3.444 closest distance to " CB  ASP A 140 " =    1.071
peak=    3.442 closest distance to " O   HOH Z 132 " =    2.383
peak=    3.440 closest distance to " CD  LYS A  76 " =    1.547
peak=    3.440 closest distance to " O   HOH Z 435 " =    1.872
peak=    3.437 closest distance to " O   HOH Z 172 " =    3.703
peak=    3.433 closest distance to " NE2 GLN A  73 " =    3.892
peak=    3.428 closest distance to " O   HOH Z 102 " =    1.252
peak=    3.416 closest distance to " O   HOH Z 371 " =    3.101
peak=    3.415 closest distance to " O   HOH Z 227 " =    2.169
peak=    3.414 closest distance to " O   HOH Z 248 " =    1.558
peak=    3.409 closest distance to " CA  LYS A 117 " =    1.222
peak=    3.408 closest distance to " CD  GLN A 194 " =    1.431
peak=    3.407 closest distance to " O   HOH Z 227 " =    1.609
peak=    3.405 closest distance to " O   ALA A   1 " =    1.650
peak=    3.401 closest distance to " CG  PRO A  90 " =    1.240
peak=    3.397 closest distance to " O   HOH Z 261 " =    2.395
peak=    3.396 closest distance to " OG1 THR A 294 " =    2.318
peak=    3.393 closest distance to " O   HOH Z 148 " =    3.325
peak=    3.387 closest distance to " O   HOH Z 342 " =    0.960
peak=    3.387 closest distance to " O   HOH Z 380 " =    1.911
peak=    3.386 closest distance to " CE  LYS A 119 " =    1.204
peak=    3.382 closest distance to " OD2 ASP A 286 " =    2.761
peak=    3.382 closest distance to " CG2 THR A 294 " =    1.585
peak=    3.380 closest distance to " O   HOH Z  88 " =    2.505
peak=    3.376 closest distance to " O   HOH Z 411 " =    3.856
peak=    3.376 closest distance to " O   HOH Z 272 " =    2.341
peak=    3.374 closest distance to " CB  TYR A 169 " =    0.928
peak=    3.372 closest distance to " CG  PRO A 243 " =    1.053
peak=    3.370 closest distance to " N   TYR A 116 " =    1.597
peak=    3.366 closest distance to " CA  MET A  40 " =    1.133
peak=    3.366 closest distance to " CB  ARG A 139 " =    1.148
peak=    3.361 closest distance to " CG1BVAL A  72 " =    1.566
peak=    3.361 closest distance to " CB  ALA A 114 " =    1.233
peak=    3.353 closest distance to " O   HOH Z 329 " =    3.933
peak=    3.348 closest distance to " N   ASP A 162 " =    1.129
peak=    3.347 closest distance to " O   HOH Z  49 " =    2.132
peak=    3.346 closest distance to " N   HIS A 108 " =    1.848
peak=    3.341 closest distance to " O   ALA A 165 " =    1.458
peak=    3.340 closest distance to " O   HOH Z 124 " =    1.277
peak=    3.330 closest distance to " O   HOH Z 371 " =    1.588
peak=    3.324 closest distance to " O   HOH Z 427 " =    3.140
peak=    3.322 closest distance to " CB  LYS A 290 " =    0.995
peak=    3.320 closest distance to " CA  ASN A 176 " =    1.088
peak=    3.311 closest distance to " CB  LEU A  83 " =    0.785
peak=    3.307 closest distance to " CB  ALA A   9 " =    1.548
peak=    3.304 closest distance to " O   HOH Z  85 " =    2.417
peak=    3.291 closest distance to " CB  ALA A 291 " =    1.276
peak=    3.283 closest distance to " O   HOH Z 426 " =    1.468
peak=    3.275 closest distance to " OG BSER A  99 " =    2.401
peak=    3.271 closest distance to " CG  LEU A 167 " =    1.294
peak=    3.267 closest distance to " OG ASER A  99 " =    1.390
peak=    3.263 closest distance to " CB  ASN A 215 " =    1.091
peak=    3.263 closest distance to " O   HOH Z 250 " =    1.518
peak=    3.259 closest distance to " O   HOH Z 193 " =    2.006
peak=    3.254 closest distance to " O   HOH Z 286 " =    2.367
peak=    3.254 closest distance to " O   HOH Z 421 " =    1.836
peak=    3.253 closest distance to " CB  SER A 141 " =    1.048
peak=    3.252 closest distance to " O   HOH Z  94 " =    2.019
peak=    3.251 closest distance to " CA  ALA A 233 " =    1.112
peak=    3.251 closest distance to " CA  ILE A 234 " =    0.961
peak=    3.248 closest distance to " O   HOH Z 298 " =    2.295
peak=    3.242 closest distance to " O   HOH Z  96 " =    2.017
peak=    3.241 closest distance to " CA  TYR A 116 " =    1.389
peak=    3.236 closest distance to " N   SER A 135 " =    1.271
peak=    3.234 closest distance to " CE BLYS A 290 " =    1.124
peak=    3.231 closest distance to " O   HOH Z 411 " =    1.586
peak=    3.229 closest distance to " O   HOH Z 267 " =    2.044
peak=    3.227 closest distance to " CB  GLN A  89 " =    1.382
peak=    3.224 closest distance to " O   HOH Z 234 " =    1.924
peak=    3.215 closest distance to " O   HOH Z   1 " =    1.525
peak=    3.214 closest distance to " O   HOH Z  63 " =    2.195
peak=    3.213 closest distance to " CA  VAL A 125 " =    1.044
peak=    3.209 closest distance to " CA  ASP A 140 " =    1.072
peak=    3.207 closest distance to " CD  ARG A  79 " =    2.041
peak=    3.207 closest distance to " CG  LYS A 119 " =    1.178
peak=    3.206 closest distance to " O   HOH Z 236 " =    1.394
peak=    3.206 closest distance to " CB  ALA A 248 " =    1.412
peak=    3.203 closest distance to " O   HOH Z 419 " =    1.963
peak=    3.202 closest distance to " CG  PRO A 198 " =    1.354
peak=    3.195 closest distance to " NE2 HIS A 207 " =    1.363
peak=    3.195 closest distance to " O   TRP A 274 " =    1.922
peak=    3.194 closest distance to " OG  SER A  62 " =    2.707
peak=    3.187 closest distance to " CG  LYS A  76 " =    0.981
peak=    3.186 closest distance to " NH2 ARG A 219 " =    1.822
peak=    3.185 closest distance to " CB  ALA A  34 " =    1.026
peak=    3.175 closest distance to " O   HOH Z 303 " =    1.606
peak=    3.174 closest distance to " CA  MET A 105 " =    1.007
peak=    3.170 closest distance to " ND2 ASN A 110 " =    1.634
peak=    3.167 closest distance to " CB  GLN A 205 " =    1.152
peak=    3.165 closest distance to " CD1 ILE A 106 " =    0.938
peak=    3.165 closest distance to " CA  ARG A 159 " =    1.259
peak=    3.164 closest distance to " CA  SER A  32 " =    1.628
peak=    3.160 closest distance to " OE1 GLN A  11 " =    2.001
peak=    3.157 closest distance to " O   HOH Z 358 " =    3.620
peak=    3.153 closest distance to " CA  ASN A 217 " =    1.257
peak=    3.150 closest distance to " O   HOH Z 128 " =    1.874
peak=    3.146 closest distance to " O   HOH Z 394 " =    3.749
peak=    3.144 closest distance to " O   HOH Z 293 " =    1.813
peak=    3.142 closest distance to " OE1 GLU A 236 " =    1.383
peak=    3.141 closest distance to " O   HOH Z 188 " =    1.366
peak=    3.141 closest distance to " O   ASN A  74 " =    1.512
peak=    3.140 closest distance to " O   THR A 220 " =    1.293
peak=    3.140 closest distance to " CZ2 TRP A 179 " =    1.836
peak=    3.134 closest distance to " O   HOH Z 257 " =    2.132
peak=    3.134 closest distance to " OG1 THR A 264 " =    0.779
peak=    3.131 closest distance to " OG  SER A  62 " =    3.557
peak=    3.128 closest distance to " CG  MET A 113 " =    1.067
peak=    3.128 closest distance to " O   HOH Z  19 " =    2.231
peak=    3.120 closest distance to " OE2 GLU A   2 " =    1.718
peak=    3.119 closest distance to " O   HOH Z  88 " =    3.133
peak=    3.118 closest distance to " CD1 ILE A 239 " =    1.275
peak=    3.108 closest distance to " CB  ASN A 285 " =    1.008
peak=    3.098 closest distance to " O   HOH Z 430 " =    5.479
peak=    3.088 closest distance to " O   HOH Z 263 " =    1.793
peak=    3.082 closest distance to " CB  GLU A 175 " =    1.370
peak=    3.080 closest distance to " ND2 ASN A 249 " =    0.921
peak=    3.077 closest distance to " CB  ASN A 142 " =    1.140
peak=    3.073 closest distance to " O   HOH Z  48 " =    1.544
peak=    3.060 closest distance to " O   HOH Z 251 " =    1.546

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.409 - 5.874
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 204
   mapped sites are within: 0.801 - 5.874

peak=   -4.638 closest distance to " O   HOH Z 266 " =    5.072
peak=   -4.594 closest distance to " CG  GLN A  58 " =    1.034
peak=   -4.453 closest distance to " C   HIS A 108 " =    1.168
peak=   -4.412 closest distance to " CB  PRO A 243 " =    2.645
peak=   -4.327 closest distance to " CD  ARG A  14 " =    3.352
peak=   -4.297 closest distance to " OG BSER A 134 " =    1.358
peak=   -4.251 closest distance to " N   ALA A 248 " =    1.750
peak=   -4.218 closest distance to " CG  GLN A 223 " =    2.093
peak=   -4.211 closest distance to " O   VAL A  67 " =    2.662
peak=   -4.210 closest distance to " CA  VAL A  67 " =    2.840
peak=   -4.207 closest distance to " CD  ARG A 156 " =    2.082
peak=   -4.138 closest distance to " CG1 VAL A 112 " =    2.760
peak=   -4.087 closest distance to " C   ILE A 239 " =    2.218
peak=   -4.063 closest distance to " O   HOH Z 290 " =    1.181
peak=   -4.007 closest distance to " CB  ASN A  39 " =    2.269
peak=   -4.000 closest distance to " CZ  TYR A 169 " =    1.824
peak=   -3.957 closest distance to " N   GLN A  58 " =    1.694
peak=   -3.945 closest distance to " O   PRO A 198 " =    1.253
peak=   -3.931 closest distance to " CB  ALA A 184 " =    2.384
peak=   -3.883 closest distance to " CE  MET A 105 " =    2.399
peak=   -3.881 closest distance to " O   HOH Z 185 " =    2.329
peak=   -3.877 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -3.874 closest distance to " O   HOH Z 351 " =    1.396
peak=   -3.863 closest distance to " CZ3 TRP A 179 " =    1.235
peak=   -3.849 closest distance to " O   HOH Z 211 " =    1.750
peak=   -3.831 closest distance to " OD2 ASP A 171 " =    2.320
peak=   -3.826 closest distance to " CD  ARG A 139 " =    1.576
peak=   -3.803 closest distance to " CB  PHE A 192 " =    1.976
peak=   -3.795 closest distance to " OXT GLY A 302 " =    2.802
peak=   -3.789 closest distance to " CB  ALA A 291 " =    2.261
peak=   -3.786 closest distance to " O   HOH Z  15 " =    1.481
peak=   -3.774 closest distance to " O   HOH Z 429 " =    1.947
peak=   -3.766 closest distance to " N   ALA A 248 " =    2.192
peak=   -3.765 closest distance to " O   VAL A 174 " =    2.245
peak=   -3.765 closest distance to " O   HOH Z 313 " =    1.876
peak=   -3.762 closest distance to " O   HOH Z 198 " =    1.668
peak=   -3.748 closest distance to " O   HOH Z 165 " =    2.027
peak=   -3.748 closest distance to " O   PRO A 163 " =    2.001
peak=   -3.745 closest distance to " O   HOH Z 407 " =    2.601
peak=   -3.742 closest distance to " C   GLN A 205 " =    1.795
peak=   -3.738 closest distance to " O   HOH Z 362 " =    5.762
peak=   -3.726 closest distance to " CD1 LEU A 101 " =    2.355
peak=   -3.694 closest distance to " O   HOH Z 372 " =    2.180
peak=   -3.691 closest distance to " CB  PRO A 163 " =    2.503
peak=   -3.678 closest distance to " O   HOH Z 102 " =    1.604
peak=   -3.676 closest distance to " OG  SER A  97 " =    2.164
peak=   -3.674 closest distance to " CG1 VAL A  78 " =    3.181
peak=   -3.667 closest distance to " O   SER A 210 " =    1.967
peak=   -3.666 closest distance to " O   PHE A 218 " =    1.677
peak=   -3.640 closest distance to " CD1 LEU A 255 " =    2.717
peak=   -3.635 closest distance to " ND2 ASN A 187 " =    1.465
peak=   -3.629 closest distance to " O   HOH Z 317 " =    1.525
peak=   -3.628 closest distance to " O   HOH Z  13 " =    1.653
peak=   -3.612 closest distance to " CB  ASP A 132 " =    2.260
peak=   -3.611 closest distance to " CB  PHE A 208 " =    2.247
peak=   -3.611 closest distance to " O   HOH Z 196 " =    2.083
peak=   -3.604 closest distance to " OD2 ASP A 191 " =    1.391
peak=   -3.592 closest distance to " CD1 PHE A  59 " =    2.005
peak=   -3.583 closest distance to " O   ALA A 161 " =    1.651
peak=   -3.572 closest distance to " CG2 ILE A 263 " =    2.160
peak=   -3.563 closest distance to " O   LEU A 167 " =    1.546
peak=   -3.527 closest distance to " CB  ALA A 161 " =    2.441
peak=   -3.522 closest distance to " O   HOH Z 281 " =    2.686
peak=   -3.521 closest distance to " O   HOH Z 389 " =    1.866
peak=   -3.521 closest distance to " CG  ARG A  66 " =    2.552
peak=   -3.506 closest distance to " CG  PHE A 283 " =    2.580
peak=   -3.504 closest distance to " CB  ALA A 248 " =    2.278
peak=   -3.493 closest distance to " OD1 ASN A 301 " =    1.911
peak=   -3.491 closest distance to " CE  MET A 105 " =    2.286
peak=   -3.491 closest distance to " O   PRO A 198 " =    1.233
peak=   -3.491 closest distance to " CZ  ARG A  66 " =    1.168
peak=   -3.490 closest distance to " O   HOH Z  38 " =    1.681
peak=   -3.486 closest distance to " O   HOH Z 139 " =    5.089
peak=   -3.484 closest distance to " CG1 VAL A 230 " =    1.900
peak=   -3.483 closest distance to " NE  ARG A 156 " =    1.914
peak=   -3.479 closest distance to " OXT GLY A 302 " =    3.415
peak=   -3.471 closest distance to " CD2 TYR A 247 " =    2.493
peak=   -3.464 closest distance to " O   HOH Z 126 " =    1.929
peak=   -3.453 closest distance to " OG BSER A 134 " =    1.676
peak=   -3.453 closest distance to " OD1 ASP A 191 " =    1.831
peak=   -3.450 closest distance to " O   SER A  95 " =    1.506
peak=   -3.445 closest distance to " O   HOH Z 394 " =    1.453
peak=   -3.445 closest distance to " CA  ASP A 298 " =    1.089
peak=   -3.444 closest distance to " OD1 ASP A 171 " =    1.594
peak=   -3.442 closest distance to " N   ALA A  43 " =    2.515
peak=   -3.439 closest distance to " NH1 ARG A 195 " =    2.606
peak=   -3.438 closest distance to " O   HOH Z   6 " =    2.073
peak=   -3.435 closest distance to " N   THR A 220 " =    2.247
peak=   -3.430 closest distance to " O   HOH Z 243 " =    1.902
peak=   -3.430 closest distance to " O   HOH Z 183 " =    1.543
peak=   -3.424 closest distance to " O   HOH Z  11 " =    1.782
peak=   -3.422 closest distance to " O   HOH Z 421 " =    3.262
peak=   -3.420 closest distance to " O   GLY A 241 " =    2.355
peak=   -3.415 closest distance to " ND2 ASN A  45 " =    1.086
peak=   -3.413 closest distance to " CD2 TYR A 293 " =    2.046
peak=   -3.406 closest distance to " ND2 ASN A  45 " =    1.590
peak=   -3.404 closest distance to " CA  GLY A 241 " =    3.105
peak=   -3.400 closest distance to " O   MET A  40 " =    2.761
peak=   -3.400 closest distance to " CB  ASP A 132 " =    2.395
peak=   -3.394 closest distance to " O   HOH Z 417 " =    2.164
peak=   -3.393 closest distance to " N   ASP A 286 " =    2.130
peak=   -3.392 closest distance to " CG  GLU A 152 " =    0.870
peak=   -3.388 closest distance to " O   HOH Z 114 " =    3.196
peak=   -3.386 closest distance to " N   GLY A  23 " =    2.445
peak=   -3.379 closest distance to " O   GLN A  89 " =    1.554
peak=   -3.379 closest distance to " CA  GLY A 203 " =    2.338
peak=   -3.378 closest distance to " O   HOH Z  63 " =    1.623
peak=   -3.377 closest distance to " CG2 THR A 178 " =    2.192
peak=   -3.375 closest distance to " C   ASP A 231 " =    2.594
peak=   -3.373 closest distance to " N   PRO A 163 " =    1.537
peak=   -3.365 closest distance to " CB  ALA A 291 " =    2.163
peak=   -3.360 closest distance to " OH  TYR A 186 " =    2.602
peak=   -3.356 closest distance to " OE1 GLN A 183 " =    1.468
peak=   -3.354 closest distance to " CE3 TRP A 274 " =    2.320
peak=   -3.350 closest distance to " CG1 VAL A 265 " =    2.537
peak=   -3.331 closest distance to " ND2 ASN A 249 " =    2.323
peak=   -3.328 closest distance to " SG ACYS A 201 " =    1.872
peak=   -3.328 closest distance to " C   MET A 188 " =    1.523
peak=   -3.327 closest distance to " CB  ASP A 286 " =    2.102
peak=   -3.327 closest distance to " O   HOH Z 134 " =    3.104
peak=   -3.320 closest distance to " O   HOH Z 377 " =    1.412
peak=   -3.319 closest distance to " ND2 ASN A  39 " =    1.136
peak=   -3.317 closest distance to " N   THR A  52 " =    1.737
peak=   -3.317 closest distance to " NE2 GLN A 194 " =    1.792
peak=   -3.302 closest distance to " O   TRP A  70 " =    1.454
peak=   -3.289 closest distance to " O   HOH Z 166 " =    1.957
peak=   -3.286 closest distance to " O   TRP A  92 " =    1.801
peak=   -3.284 closest distance to " O   ALA A  34 " =    2.335
peak=   -3.284 closest distance to " O   VAL A 189 " =    2.622
peak=   -3.281 closest distance to " CG  PHE A 225 " =    1.286
peak=   -3.281 closest distance to " OG  SER A   3 " =    1.713
peak=   -3.280 closest distance to " C   ALA A 114 " =    2.210
peak=   -3.275 closest distance to " CD  GLN A  88 " =    1.034
peak=   -3.274 closest distance to " CE BMET A  47 " =    1.448
peak=   -3.272 closest distance to " NE2 GLN A 278 " =    1.711
peak=   -3.271 closest distance to " N   PHE A  59 " =    1.771
peak=   -3.256 closest distance to " CE3 TRP A 274 " =    1.142
peak=   -3.254 closest distance to " O   ALA A 292 " =    2.186
peak=   -3.250 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.249 closest distance to " CB  TYR A  15 " =    2.222
peak=   -3.248 closest distance to " ND2 ASN A  60 " =    1.369
peak=   -3.242 closest distance to " O   ARG A 145 " =    1.643
peak=   -3.240 closest distance to " OE2 GLU A 152 " =    1.295
peak=   -3.239 closest distance to " NE2 GLN A  11 " =    1.926
peak=   -3.238 closest distance to " CZ  ARG A 259 " =    0.939
peak=   -3.230 closest distance to " O   ASN A 187 " =    1.508
peak=   -3.227 closest distance to " O   HOH Z   6 " =    1.491
peak=   -3.224 closest distance to " O   HOH Z  97 " =    1.392
peak=   -3.222 closest distance to " CG  GLU A   2 " =    1.954
peak=   -3.221 closest distance to " O   ILE A 106 " =    1.991
peak=   -3.219 closest distance to " O   HOH Z 414 " =    1.542
peak=   -3.213 closest distance to " O   HOH Z 119 " =    2.345
peak=   -3.209 closest distance to " OH  TYR A 172 " =    1.802
peak=   -3.209 closest distance to " O   HOH Z 191 " =    5.874
peak=   -3.208 closest distance to " O   HOH Z  33 " =    2.518
peak=   -3.205 closest distance to " C   ILE A 234 " =    1.352
peak=   -3.205 closest distance to " O   HOH Z 139 " =    3.157
peak=   -3.202 closest distance to " O   SER A   3 " =    1.000
peak=   -3.194 closest distance to " O   HOH Z  89 " =    2.671
peak=   -3.189 closest distance to " NH2AARG A 275 " =    5.055
peak=   -3.189 closest distance to " OD1 ASN A 148 " =    1.552
peak=   -3.188 closest distance to " NE2 GLN A  88 " =    1.757
peak=   -3.186 closest distance to " CG1AVAL A  41 " =    2.670
peak=   -3.184 closest distance to " O   ALA A 248 " =    1.654
peak=   -3.184 closest distance to " O   HOH Z 193 " =    1.663
peak=   -3.183 closest distance to " CD2 LEU A 237 " =    2.686
peak=   -3.181 closest distance to " NH2 ARG A  79 " =    2.050
peak=   -3.181 closest distance to " O   HOH Z 200 " =    4.865
peak=   -3.179 closest distance to " O   HOH Z 369 " =    2.172
peak=   -3.177 closest distance to " O   HOH Z 311 " =    3.612
peak=   -3.172 closest distance to " O   HOH Z 187 " =    1.725
peak=   -3.171 closest distance to " O   SER A 146 " =    1.169
peak=   -3.167 closest distance to " CD1 ILE A 109 " =    2.563
peak=   -3.167 closest distance to " O   HOH Z 197 " =    5.084
peak=   -3.163 closest distance to " O   GLU A 152 " =    1.394
peak=   -3.157 closest distance to " CB  SER A 210 " =    1.341
peak=   -3.156 closest distance to " O   HOH Z 174 " =    4.081
peak=   -3.154 closest distance to " CB  TRP A  85 " =    2.560
peak=   -3.153 closest distance to " CG  GLU A 277 " =    1.277
peak=   -3.153 closest distance to " O   HOH Z 422 " =    1.523
peak=   -3.152 closest distance to " O   HOH Z  43 " =    1.780
peak=   -3.151 closest distance to " C   SER A 206 " =    1.561
peak=   -3.150 closest distance to " CZ2 TRP A 274 " =    1.101
peak=   -3.144 closest distance to " CB  ALA A  64 " =    2.705
peak=   -3.138 closest distance to " CD1 ILE A 106 " =    2.191
peak=   -3.137 closest distance to " O   HOH Z 357 " =    2.079
peak=   -3.129 closest distance to " CG  GLN A 278 " =    2.030
peak=   -3.119 closest distance to " O   HOH Z 174 " =    2.313
peak=   -3.118 closest distance to " CD2 PHE A  61 " =    2.545
peak=   -3.104 closest distance to " O   HOH Z 135 " =    4.935
peak=   -3.103 closest distance to " O   ALA A   1 " =    1.829
peak=   -3.103 closest distance to " CG  GLU A  53 " =    1.554
peak=   -3.102 closest distance to " O   SER A 135 " =    1.498
peak=   -3.100 closest distance to " O   HOH Z 198 " =    1.565
peak=   -3.100 closest distance to " C   ALA A 158 " =    1.315
peak=   -3.088 closest distance to " O   HOH Z 137 " =    1.503
peak=   -3.087 closest distance to " N   ALA A 226 " =    1.925
peak=   -3.079 closest distance to " O   HOH Z 427 " =    1.498
peak=   -3.070 closest distance to " O   HOH Z 326 " =    1.657
peak=   -3.062 closest distance to " CD2 LEU A 237 " =    2.319
peak=   -3.048 closest distance to " ND2 ASN A 209 " =    1.511
peak=   -3.042 closest distance to " CE3 TRP A 150 " =    2.260

================= 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    :  0.3424 0.3410   6.110015e+00   6.107477e+00
   1_bss:  0.3284 0.3303   6.087957e+00   6.085661e+00
   1_xyz:  0.2077 0.2362   5.653648e+00   5.758368e+00
   1_adp:  0.1888 0.2399   5.598909e+00   5.780551e+00
   1_occ:  0.1886 0.2398   5.598263e+00   5.779899e+00
   2_bss:  0.1826 0.2335   5.575317e+00   5.759556e+00
   2_xyz:  0.1361 0.1752   5.297134e+00   5.494751e+00
   2_adp:  0.1285 0.1676   5.245515e+00   5.446217e+00
   2_occ:  0.1283 0.1673   5.244017e+00   5.444874e+00
   3_bss:  0.1279 0.1669   5.240112e+00   5.438875e+00
   3_xyz:  0.1164 0.1562   5.163837e+00   5.379577e+00
   3_adp:  0.1147 0.1554   5.154449e+00   5.374322e+00
   3_occ:  0.1146 0.1554   5.154218e+00   5.374499e+00
   4_bss:  0.1145 0.1555   5.153996e+00   5.374152e+00
   4_xyz:  0.1118 0.1537   5.138027e+00   5.363820e+00
   4_adp:  0.1119 0.1534   5.137929e+00   5.362373e+00
   4_occ:  0.1118 0.1534   5.137855e+00   5.362736e+00
   5_bss:  0.1118 0.1534   5.137830e+00   5.362624e+00
   5_xyz:  0.1066 0.1528   5.113562e+00   5.357650e+00
   5_adp:  0.1059 0.1532   5.111510e+00   5.359534e+00
   5_occ:  0.1058 0.1533   5.111662e+00   5.359878e+00
   5_bss:  0.1056 0.1525   5.109782e+00   5.356316e+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:  0.315  35.157   1.761  -2.831  -0.990  -0.000  -0.000  -0.000
   1_xyz:  0.315  35.157   1.761  -2.831  -0.990  -0.000  -0.000  -0.000
   1_adp:  0.315  35.157   1.761  -2.831  -0.990  -0.000  -0.000  -0.000
   1_occ:  0.315  35.157   1.761  -2.831  -0.990  -0.000  -0.000  -0.000
   2_bss:  0.321  42.703  -2.252  -2.737  -1.433  -0.000  -0.000  -0.000
   2_xyz:  0.321  42.703  -2.252  -2.737  -1.433  -0.000  -0.000  -0.000
   2_adp:  0.321  42.703  -2.252  -2.737  -1.433  -0.000  -0.000  -0.000
   2_occ:  0.321  42.703  -2.252  -2.737  -1.433  -0.000  -0.000  -0.000
   3_bss:  0.320  42.702  -3.151  -2.591  -1.376  -0.000  -0.000  -0.000
   3_xyz:  0.320  42.702  -3.151  -2.591  -1.376  -0.000  -0.000  -0.000
   3_adp:  0.320  42.702  -3.151  -2.591  -1.376  -0.000  -0.000  -0.000
   3_occ:  0.320  42.702  -3.151  -2.591  -1.376  -0.000  -0.000  -0.000
   4_bss:  0.322  42.702  -3.334  -2.532  -1.311  -0.000  -0.000  -0.000
   4_xyz:  0.322  42.702  -3.334  -2.532  -1.311  -0.000  -0.000  -0.000
   4_adp:  0.322  42.702  -3.334  -2.532  -1.311  -0.000  -0.000  -0.000
   4_occ:  0.322  42.702  -3.334  -2.532  -1.311  -0.000  -0.000  -0.000
   5_bss:  0.322  42.702  -3.329  -2.435  -1.215  -0.000  -0.000  -0.000
   5_xyz:  0.322  42.702  -3.329  -2.435  -1.215  -0.000  -0.000  -0.000
   5_adp:  0.322  42.702  -3.329  -2.435  -1.215  -0.000  -0.000  -0.000
   5_occ:  0.322  42.702  -3.329  -2.435  -1.215  -0.000  -0.000  -0.000
   5_bss:  0.320  42.462  -3.167  -2.238  -0.998  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.150 0.6797  0.8801    37268.976
   1_bss:  35.990 0.6916  0.8804    33980.797
   1_xyz:  22.980 0.8330  1.0029    14403.983
   1_adp:  23.761 0.8243  1.0020    15030.328
   1_occ:  23.768 0.8243  1.0019    15025.878
   2_bss:  23.054 0.8312  0.9550    14203.560
   2_xyz:  16.459 0.8939  0.9887     7897.667
   2_adp:  15.352 0.9038  0.9913     7267.808
   2_occ:  15.317 0.9041  0.9914     7239.236
   3_bss:  15.220 0.9048  0.9821     7128.126
   3_xyz:  14.079 0.9141  0.9853     6291.415
   3_adp:  13.959 0.9153  0.9825     6249.879
   3_occ:  13.963 0.9152  0.9823     6243.807
   4_bss:  13.961 0.9152  0.9813     6240.612
   4_xyz:  13.687 0.9175  0.9822     6110.974
   4_adp:  13.645 0.9180  0.9800     6105.971
   4_occ:  13.647 0.9179  0.9798     6106.586
   5_bss:  13.648 0.9179  0.9821     6105.571
   5_xyz:  13.574 0.9184  0.9823     6074.103
   5_adp:  13.614 0.9181  0.9778     6081.879
   5_occ:  13.619 0.9181  0.9777     6084.016
   5_bss:  13.579 0.9183  0.9821     6029.046
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.1104e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.1104e-01
   1_xyz:   1.218  0.009  0.078 15.164  0.005  4.110   8.2519e-02
   1_adp:   1.218  0.009  0.078 15.164  0.005  4.110   8.2519e-02
   1_occ:   1.218  0.009  0.078 15.164  0.005  4.110   8.2519e-02
   2_bss:   1.218  0.009  0.078 15.164  0.005  4.110   8.2519e-02
   2_xyz:   1.001  0.006  0.071 14.443  0.004  4.116   5.6669e-02
   2_adp:   1.001  0.006  0.071 14.443  0.004  4.116   5.6669e-02
   2_occ:   1.001  0.006  0.071 14.443  0.004  4.116   5.6669e-02
   3_bss:   1.001  0.006  0.071 14.443  0.004  4.116   5.6669e-02
   3_xyz:   0.970  0.006  0.072 14.610  0.004  4.113   5.5103e-02
   3_adp:   0.970  0.006  0.072 14.610  0.004  4.113   5.5103e-02
   3_occ:   0.970  0.006  0.072 14.610  0.004  4.113   5.5103e-02
   4_bss:   0.970  0.006  0.072 14.610  0.004  4.113   5.5103e-02
   4_xyz:   0.950  0.006  0.071 14.450  0.004  4.109   5.3158e-02
   4_adp:   0.950  0.006  0.071 14.450  0.004  4.109   5.3158e-02
   4_occ:   0.950  0.006  0.071 14.450  0.004  4.109   5.3158e-02
   5_bss:   0.950  0.006  0.071 14.450  0.004  4.109   5.3158e-02
   5_xyz:   1.133  0.009  0.084 14.954  0.005  4.109   7.2688e-02
   5_adp:   1.133  0.009  0.084 14.954  0.005  4.109   7.2688e-02
   5_occ:   1.133  0.009  0.084 14.954  0.005  4.109   7.2688e-02
   5_bss:   1.133  0.009  0.084 14.954  0.005  4.109   7.2688e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.304   2.4180e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.304   2.4180e-01
   1_xyz:   7.967  0.056  0.299 82.225  0.047  2.182   8.5736e-02
   1_adp:   7.967  0.056  0.299 82.225  0.047  2.182   8.5736e-02
   1_occ:   7.967  0.056  0.299 82.225  0.047  2.182   8.5736e-02
   2_bss:   7.967  0.056  0.299 82.225  0.047  2.182   8.5736e-02
   2_xyz:   7.287  0.038  0.220 80.393  0.038  2.298   4.6390e-02
   2_adp:   7.287  0.038  0.220 80.393  0.038  2.298   4.6390e-02
   2_occ:   7.287  0.038  0.220 80.393  0.038  2.298   4.6390e-02
   3_bss:   7.287  0.038  0.220 80.393  0.038  2.298   4.6390e-02
   3_xyz:   6.648  0.044  0.231 83.234  0.038  2.367   4.7162e-02
   3_adp:   6.648  0.044  0.231 83.234  0.038  2.367   4.7162e-02
   3_occ:   6.648  0.044  0.231 83.234  0.038  2.367   4.7162e-02
   4_bss:   6.648  0.044  0.231 83.234  0.038  2.367   4.7162e-02
   4_xyz:   6.480  0.042  0.230 82.751  0.037  2.370   3.3472e-02
   4_adp:   6.480  0.042  0.230 82.751  0.037  2.370   3.3472e-02
   4_occ:   6.480  0.042  0.230 82.751  0.037  2.370   3.3472e-02
   5_bss:   6.480  0.042  0.230 82.751  0.037  2.370   3.3472e-02
   5_xyz:   7.517  0.055  0.285 83.789  0.040  2.258   5.8065e-02
   5_adp:   7.517  0.055  0.285 83.789  0.040  2.258   5.8065e-02
   5_occ:   7.517  0.055  0.285 83.789  0.040  2.258   5.8065e-02
   5_bss:   7.517  0.055  0.285 83.789  0.040  2.258   5.8065e-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:  77.09   0.00  17.45  77.09   0.00  13.44  74.67   6.57  39.30
   1_occ:  77.09   0.00  17.45  77.09   0.00  13.44  74.67   6.57  39.30
   2_bss:  77.09   0.00  17.45  77.09   0.00  13.44  74.67   6.57  39.30
   2_xyz:  77.09   0.00  17.45  77.09   0.00  13.44  74.67   6.57  39.30
   2_adp:  82.05   1.12  17.17  82.05   1.12  13.24  70.05   6.34  38.58
   2_occ:  82.05   1.12  17.17  82.05   1.12  13.24  70.05   6.34  38.58
   3_bss:  82.05   1.12  17.17  82.05   1.12  13.24  70.05   6.34  38.58
   3_xyz:  82.05   1.12  17.17  82.05   1.12  13.24  70.05   6.34  38.58
   3_adp:  83.78   2.07  17.01  83.78   2.07  13.11  70.08   3.63  38.24
   3_occ:  83.78   2.07  17.01  83.78   2.07  13.11  70.08   3.63  38.24
   4_bss:  83.78   2.07  17.01  83.78   2.07  13.11  70.08   3.63  38.24
   4_xyz:  83.78   2.07  17.01  83.78   2.07  13.11  70.08   3.63  38.24
   4_adp:  84.03   2.39  16.77  84.03   2.39  12.99  69.55   2.95  37.31
   4_occ:  84.03   2.39  16.77  84.03   2.39  12.99  69.55   2.95  37.31
   5_bss:  84.03   2.39  16.77  84.03   2.39  12.99  69.55   2.95  37.31
   5_xyz:  84.03   2.39  16.77  84.03   2.39  12.99  69.55   2.95  37.31
   5_adp:  84.17   1.99  16.72  84.17   1.99  12.87  69.69   4.39  37.70
   5_occ:  84.17   1.99  16.72  84.17   1.99  12.87  69.69   4.39  37.70
   5_bss:  84.10   1.92  16.65  84.10   1.92  12.80  69.62   4.32  37.63
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.903    0.012    0.342
   1_adp:    1.903    0.012    0.342
   1_occ:    1.903    0.012    0.342
   2_bss:    1.903    0.012    0.342
   2_xyz:    1.837    0.021    0.401
   2_adp:    1.837    0.021    0.401
   2_occ:    1.837    0.021    0.401
   3_bss:    1.837    0.021    0.401
   3_xyz:    1.871    0.011    0.435
   3_adp:    1.871    0.011    0.435
   3_occ:    1.871    0.011    0.435
   4_bss:    1.871    0.011    0.435
   4_xyz:    1.841    0.015    0.445
   4_adp:    1.841    0.015    0.445
   4_occ:    1.841    0.015    0.445
   5_bss:    1.841    0.015    0.445
   5_xyz:    1.793    0.017    0.453
   5_adp:    1.793    0.017    0.453
   5_occ:    1.793    0.017    0.453
   5_bss:    1.793    0.017    0.453
------------------------------------------------------------------------

CPU time actual refinement: 339.00


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_61/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_61/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_61/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_61/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_61/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.86 
  Macro-tasks:
    bulk solvent and scale       = 35.92  
    individual site refinement   = 144.61 
    weights calculation          = 29.74  
    collect and process          = 6.60   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 216.98 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 110.08 
    alpha_beta                      = 8.01   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 119.81 
    fmodel                         = 6.43   
    r_factors                      = 0.20   
    phase_errors                   = 11.22  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 258.94 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.711 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    673 calls, 109.68 s
gradients_fft:          618 calls, 105.39 s

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

# Date 2008-01-16 Time 03:55:17 PST -0800 (1200484517.48 s)
Start R-work = 0.3424, R-free = 0.3410 (no bulk solvent and anisotropic scale)
Final R-work = 0.1334, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.3284, R-free = 0.3303
Final R-work = 0.1056, R-free = 0.1525