# Date 2008-01-16 Time 04:20:53 PST -0800 (1200486053.53 s)
#phil __OFF__

Command line arguments: "../277.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15245
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 277

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.4607, 85.0941, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7691 1.97043
Completeness in resolution range: 0.981511
Completeness with d_max=infinity: 0.978374

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7691
                             d_min =   1.9704

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7691 1.97043
Completeness in resolution range: 0.981511
Completeness with d_max=infinity: 0.978374

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7695 -  4.2153 [2093/2118]  1884   209  10.0%
  bin  2:  4.2153 -  3.3588 [2024/2042]  1822   202  10.0%
  bin  3:  3.3588 -  2.9380 [1983/2002]  1784   199  10.0%
  bin  4:  2.9380 -  2.6711 [1956/1986]  1761   195  10.0%
  bin  5:  2.6711 -  2.4806 [1960/1979]  1764   196  10.0%
  bin  6:  2.4806 -  2.3350 [1949/1974]  1751   198  10.2%
  bin  7:  2.3350 -  2.2184 [1944/1972]  1755   189   9.7%
  bin  8:  2.2184 -  2.1222 [1941/1977]  1744   197  10.1%
  bin  9:  2.1222 -  2.0407 [1902/1944]  1711   191  10.0%
  bin 10:  2.0407 -  1.9704 [1837/1964]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_277/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:
        1.33 -     2.04: 10
        2.04 -     2.76: 437
        2.76 -     3.47: 4678
        3.47 -     4.19: 9587
        4.19 -     4.90: 14181
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.328 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.613 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.755 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.857 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28888 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_277/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_277/model_refine_001.geo

CPU time processing inputs: 9.53


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.4607 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3984   r_free= 0.3978   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.177727                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7011 0.99   1370  153 0.3219 0.3234      6.4328      6.4158|
|  2:  4.7011 -  3.7516 0.99   1304  145 0.3220 0.3138      6.6041      6.5924|
|  3:  3.7516 -  3.2833 0.99   1280  142 0.3532 0.3646       6.522      6.6293|
|  4:  3.2833 -  2.9858 0.99   1280  140 0.3701 0.3885        6.39      6.4271|
|  5:  2.9858 -  2.7733 0.99   1257  142 0.4016 0.4114      6.2536      6.2079|
|  6:  2.7733 -  2.6107 0.99   1275  140 0.4255 0.4336      6.1963      6.1767|
|  7:  2.6107 -  2.4806 0.99   1249  139 0.4264 0.3908      6.1499      6.0592|
|  8:  2.4806 -  2.3731 0.98   1254  140 0.4400 0.4518       6.123      6.1753|
|  9:  2.3731 -  2.2821 0.98   1241  140 0.4605 0.4474      6.0679      6.0248|
| 10:  2.2821 -  2.2036 0.99   1238  137 0.4532 0.4762      6.0426      6.0552|
| 11:  2.2036 -  2.1349 0.98   1251  137 0.4537 0.4687      5.9844      6.0354|
| 12:  2.1349 -  2.0741 0.97   1238  138 0.4695 0.4237      5.9623      5.9436|
| 13:  2.0741 -  2.0196 1.00   1228  134 0.4583 0.4363      5.8495      5.8211|
| 14:  2.0196 -  1.9704 0.91   1165  132 0.4671 0.4275      5.8184      5.6974|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7695 -  4.7011  1370   153  0.75  30.15   0.86     0.78      54974.99|
|  2:  4.7011 -  3.7516  1304   145  0.78  27.66   0.96     0.89      71406.01|
|  3:  3.7516 -  3.2833  1280   142  0.72  33.91   0.99     0.90      74917.57|
|  4:  3.2833 -  2.9858  1280   140  0.66  38.95   0.98     0.87      68004.24|
|  5:  2.9858 -  2.7733  1257   142  0.61  42.94   0.96     0.82      54177.30|
|  6:  2.7733 -  2.6107  1275   140  0.61  43.53   0.96     0.83      46629.92|
|  7:  2.6107 -  2.4806  1249   139  0.60  43.89   0.96     0.83      41892.66|
|  8:  2.4806 -  2.3731  1254   140  0.58  46.04   0.99     0.80      40394.27|
|  9:  2.3731 -  2.2821  1241   140  0.55  48.09   0.97     0.76      37463.12|
| 10:  2.2821 -  2.2036  1238   137  0.54  48.83   1.03     0.76      35232.92|
| 11:  2.2036 -  2.1349  1251   137  0.54  49.09   1.00     0.79      32479.15|
| 12:  2.1349 -  2.0741  1238   138  0.56  47.63   1.03     0.82      28960.73|
| 13:  2.0741 -  2.0196  1228   134  0.57  46.92   1.01     0.83      24097.36|
| 14:  2.0196 -  1.9704  1165   132  0.61  43.87   1.00     0.81      17877.17|
|alpha:            min =        0.76 max =            0.90 mean =         0.82|
|beta:             min =    17877.17 max =        74917.57 mean =     45315.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.98 mean =        42.08|
|phase err.(test): min =        0.00 max =           89.76 mean =        42.05|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.018461              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.790   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.143163              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.040   (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 |  1.328 -  1.685:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.685 -  2.043:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.043 -  2.400:       32 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.400 -  2.757:      405 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.757 -  3.114:     2276 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.114 -  3.471:     2402 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.471 -  3.828:     4443 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.828 -  4.186:     5144 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.186 -  4.543:     6401 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.543 -  4.900:     7780 |
|-----------------------------------------------------------------------------|
|-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 |        0.181 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.328 |       0.489 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3984   r_free= 0.3978   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.177727                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3877   r_free= 0.3843   ksol= 0.33   Bsol= 19.74   scale= 0.975   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.30,-0.23,0.82,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.165035                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.401421              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.639   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.621904              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.964   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3877      final r-factor (work) = 0.2469          |
| start r-factor (free) = 0.3843      final r-factor (free) = 0.2743          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6694 = 3.40 * 0.50 * 6.1672 + 1.00 * 0.1807                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1843 = 3.40 * 0.50 * 5.9395 + 1.00 * 0.0830                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2469      final r-factor (work) = 0.2254          |
| start r-factor (free) = 0.2743      final r-factor (free) = 0.2809          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6998 = 0.62 * 1.00 * 5.9395 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5768 = 0.62 * 1.00 * 5.7308 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.85   17.86    None  None   None       |
|    all(noH): 2823   0      0.00    78.85   17.86    None  None   None       |
|    Sol.    : 438    0      5.13    78.85   39.81    None  None   None       |
|    Mac.    : 2385   0      0.00    76.79   13.82    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 -   7.885:  614   |   5:    39.424 -  47.309:  118        |
|      1:     7.885 -  15.770: 1103   |   6:    47.309 -  55.193:   91        |
|      2:    15.770 -  23.654:  489   |   7:    55.193 -  63.078:   58        |
|      3:    23.654 -  31.539:  187   |   8:    63.078 -  70.963:   27        |
|      4:    31.539 -  39.424:  130   |   9:    70.963 -  78.848:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2254 r_free = 0.2809             target_work(ml) = 5.745         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2250 r_free = 0.2811             target_work(ml) = 5.744         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2250   r_free= 0.2811   ksol= 0.33   Bsol= 19.74   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.30,-0.23,0.82,-0.00,0.00,0.00); trace/3= -0.24                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.743846                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2226   r_free= 0.2792   ksol= 0.31   Bsol= 32.09   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.71,-0.98,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.740485                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.919371              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.208   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.188113              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.846  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2226      final r-factor (work) = 0.1500          |
| start r-factor (free) = 0.2792      final r-factor (free) = 0.1977          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1962 = 4.92 * 0.50 * 5.7378 + 1.00 * 0.0830                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7893 = 4.92 * 0.50 * 5.5810 + 1.00 * 0.0617                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1500      final r-factor (work) = 0.1345          |
| start r-factor (free) = 0.1977      final r-factor (free) = 0.1768          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0623 = 0.19 * 1.00 * 5.5810 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0096 = 0.19 * 1.00 * 5.3289 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    76.99   17.11    None  None   None       |
|    all(noH): 2823   0      1.30    76.99   17.11    None  None   None       |
|    Sol.    : 438    0      6.35    70.80   38.70    None  None   None       |
|    Mac.    : 2385   0      1.30    76.99   13.14    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:     1.303 -   8.872:  685   |   5:    39.148 -  46.717:  114        |
|      1:     8.872 -  16.441: 1277   |   6:    46.717 -  54.286:  101        |
|      2:    16.441 -  24.010:  335   |   7:    54.286 -  61.855:   44        |
|      3:    24.010 -  31.579:  124   |   8:    61.855 -  69.424:   17        |
|      4:    31.579 -  39.148:  120   |   9:    69.424 -  76.993:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1345 r_free = 0.1768             target_work(ml) = 5.271         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1342 r_free = 0.1768             target_work(ml) = 5.270         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1342   r_free= 0.1768   ksol= 0.31   Bsol= 32.09   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.71,-0.98,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.269871                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1760   ksol= 0.32   Bsol= 36.40   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.29,-1.46,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.268018                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.063350              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.484  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.395473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.397  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1760      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5609 = 2.06 * 0.50 * 5.3310 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4237 = 2.06 * 0.50 * 5.2055 + 1.00 * 0.0534                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0658 = 0.40 * 1.00 * 5.2055 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0413 = 0.40 * 1.00 * 5.1414 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.87   17.17    None  None   None       |
|    all(noH): 2823   0      0.00    82.87   17.17    None  None   None       |
|    Sol.    : 438    0      2.31    75.03   39.75    None  None   None       |
|    Mac.    : 2385   0      0.00    82.87   13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.287:  557   |   5:    41.434 -  49.721:  114        |
|      1:     8.287 -  16.574: 1424   |   6:    49.721 -  58.007:   86        |
|      2:    16.574 -  24.860:  335   |   7:    58.007 -  66.294:   45        |
|      3:    24.860 -  33.147:  128   |   8:    66.294 -  74.581:   13        |
|      4:    33.147 -  41.434:  116   |   9:    74.581 -  82.868:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1568             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1567             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1567   ksol= 0.32   Bsol= 36.40   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.29,-1.46,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.135178                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1566   ksol= 0.32   Bsol= 37.84   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.44,-1.63,-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: 5.134808                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.247404              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.637  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.389944              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.984  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2601 = 1.25 * 0.50 * 5.1414 + 1.00 * 0.0534                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2464 = 1.25 * 0.50 * 5.1306 + 1.00 * 0.0464                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0087 = 0.39 * 1.00 * 5.1306 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0049 = 0.39 * 1.00 * 5.1205 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    85.91   17.06    None  None   None       |
|    all(noH): 2823   0      1.12    85.91   17.06    None  None   None       |
|    Sol.    : 438    0      3.61    77.10   39.45    None  None   None       |
|    Mac.    : 2385   0      1.12    85.91   12.95    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:     1.120 -   9.600:  922   |   5:    43.516 -  51.996:  116        |
|      1:     9.600 -  18.079: 1178   |   6:    51.996 -  60.475:   64        |
|      2:    18.079 -  26.558:  254   |   7:    60.475 -  68.954:   32        |
|      3:    26.558 -  35.037:  120   |   8:    68.954 -  77.433:   10        |
|      4:    35.037 -  43.516:  124   |   9:    77.433 -  85.912:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1549             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1549             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1549   ksol= 0.32   Bsol= 37.84   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.44,-1.63,-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: 5.122297                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1549   ksol= 0.32   Bsol= 37.84   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.35,-1.53,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122205                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.875644              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.145  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.270441              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.322  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1045          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4078 = 2.88 * 0.50 * 5.1198 + 1.00 * 0.0464                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3906 = 2.88 * 0.50 * 5.0950 + 1.00 * 0.0649                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1045      final r-factor (work) = 0.1044          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3861 = 0.27 * 1.00 * 5.0950 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3836 = 0.27 * 1.00 * 5.0874 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    86.92   16.74    None  None   None       |
|    all(noH): 2823   0      1.36    86.92   16.74    None  None   None       |
|    Sol.    : 438    0      5.52    78.68   38.36    None  None   None       |
|    Mac.    : 2385   0      1.36    86.92   12.77    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:     1.358 -   9.914: 1018   |   5:    44.139 -  52.695:  102        |
|      1:     9.914 -  18.470: 1118   |   6:    52.695 -  61.251:   55        |
|      2:    18.470 -  27.026:  236   |   7:    61.251 -  69.807:   22        |
|      3:    27.026 -  35.583:  127   |   8:    69.807 -  78.363:    8        |
|      4:    35.583 -  44.139:  133   |   9:    78.363 -  86.919:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1044 r_free = 0.1527             target_work(ml) = 5.085         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1043 r_free = 0.1527             target_work(ml) = 5.085         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1043   r_free= 0.1527   ksol= 0.32   Bsol= 37.84   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-2.35,-1.53,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.085444                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7011 0.99   1370  153 0.0968 0.1245      5.3575      5.4959|
|  2:  4.7011 -  3.7516 0.99   1304  145 0.0820 0.1124      5.4096      5.6093|
|  3:  3.7516 -  3.2833 0.99   1280  142 0.1001 0.1520      5.4402      5.8594|
|  4:  3.2833 -  2.9858 0.99   1280  140 0.1152 0.1501      5.4184      5.5659|
|  5:  2.9858 -  2.7733 0.99   1257  142 0.1172 0.1688      5.2567      5.4829|
|  6:  2.7733 -  2.6107 0.99   1275  140 0.1102 0.1621      5.1441      5.3513|
|  7:  2.6107 -  2.4806 0.99   1249  139 0.1139 0.1616      5.0844      5.3378|
|  8:  2.4806 -  2.3731 0.98   1254  140 0.1066 0.1662      5.0059      5.3237|
|  9:  2.3731 -  2.2821 0.98   1241  140 0.1080 0.1640       4.966      5.2095|
| 10:  2.2821 -  2.2036 0.99   1238  137 0.1032 0.1796      4.9115      5.2103|
| 11:  2.2036 -  2.1349 0.98   1251  137 0.1047 0.1634      4.8909      5.1968|
| 12:  2.1349 -  2.0741 0.97   1238  138 0.1047 0.1666      4.8336      5.1939|
| 13:  2.0741 -  2.0196 1.00   1228  134 0.1022 0.1570      4.7466           5|
| 14:  2.0196 -  1.9704 0.91   1165  132 0.1008 0.1719      4.6308      4.9189|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7695 -  4.7011  1370   153  0.94   8.79   0.99     0.96       6709.68|
|  2:  4.7011 -  3.7516  1304   145  0.95   7.72   1.03     1.02       8712.36|
|  3:  3.7516 -  3.2833  1280   142  0.94  10.61   1.04     1.02       9810.32|
|  4:  3.2833 -  2.9858  1280   140  0.93  12.80   1.02     1.01       9649.46|
|  5:  2.9858 -  2.7733  1257   142  0.91  14.48   1.00     0.97       7390.77|
|  6:  2.7733 -  2.6107  1275   140  0.91  14.74   0.99     0.96       6230.06|
|  7:  2.6107 -  2.4806  1249   139  0.91  14.52   0.99     0.96       5376.24|
|  8:  2.4806 -  2.3731  1254   140  0.92  13.39   1.00     0.98       4625.36|
|  9:  2.3731 -  2.2821  1241   140  0.92  14.19   1.01     0.99       4419.34|
| 10:  2.2821 -  2.2036  1238   137  0.91  14.33   1.00     0.97       3969.77|
| 11:  2.2036 -  2.1349  1251   137  0.91  15.32   1.00     0.98       4083.62|
| 12:  2.1349 -  2.0741  1238   138  0.92  14.44   1.02     1.01       3630.12|
| 13:  2.0741 -  2.0196  1228   134  0.92  14.46   1.01     1.01       3078.80|
| 14:  2.0196 -  1.9704  1165   132  0.92  13.79   0.99     0.96       2362.59|
|alpha:            min =        0.96 max =            1.02 mean =         0.99|
|beta:             min =     2362.59 max =         9810.32 mean =      5771.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.06|
|phase err.(test): min =        0.00 max =           89.24 mean =        12.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1043   r_free= 0.1527   ksol= 0.32   Bsol= 37.80   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-2.20,-1.34,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.085731                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1043   r_free= 0.1527   ksol= 0.32   Bsol= 37.80   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-2.20,-1.34,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.085731                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7011 0.99   1370  153 0.0969 0.1248      5.3605      5.5001|
|  2:  4.7011 -  3.7516 0.99   1304  145 0.0819 0.1123      5.4098      5.6083|
|  3:  3.7516 -  3.2833 0.99   1280  142 0.1000 0.1520      5.4398      5.8593|
|  4:  3.2833 -  2.9858 0.99   1280  140 0.1152 0.1501      5.4183       5.566|
|  5:  2.9858 -  2.7733 0.99   1257  142 0.1172 0.1688      5.2567       5.483|
|  6:  2.7733 -  2.6107 0.99   1275  140 0.1102 0.1621      5.1442      5.3512|
|  7:  2.6107 -  2.4806 0.99   1249  139 0.1139 0.1616      5.0845      5.3379|
|  8:  2.4806 -  2.3731 0.98   1254  140 0.1066 0.1662       5.006      5.3238|
|  9:  2.3731 -  2.2821 0.98   1241  140 0.1080 0.1640      4.9661      5.2094|
| 10:  2.2821 -  2.2036 0.99   1238  137 0.1032 0.1796      4.9117      5.2105|
| 11:  2.2036 -  2.1349 0.98   1251  137 0.1047 0.1635      4.8911      5.1971|
| 12:  2.1349 -  2.0741 0.97   1238  138 0.1046 0.1666      4.8336      5.1941|
| 13:  2.0741 -  2.0196 1.00   1228  134 0.1022 0.1570      4.7466      5.0001|
| 14:  2.0196 -  1.9704 0.91   1165  132 0.1009 0.1719      4.6308      4.9187|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7695 -  4.7011  1370   153  0.94   8.83   0.99     0.96       6775.82|
|  2:  4.7011 -  3.7516  1304   145  0.95   7.74   1.03     1.03       8741.71|
|  3:  3.7516 -  3.2833  1280   142  0.94  10.60   1.04     1.03       9802.78|
|  4:  3.2833 -  2.9858  1280   140  0.93  12.80   1.02     1.01       9648.61|
|  5:  2.9858 -  2.7733  1257   142  0.91  14.48   1.01     0.98       7389.58|
|  6:  2.7733 -  2.6107  1275   140  0.91  14.74   0.99     0.97       6230.60|
|  7:  2.6107 -  2.4806  1249   139  0.91  14.52   0.99     0.97       5377.12|
|  8:  2.4806 -  2.3731  1254   140  0.92  13.39   1.00     0.99       4626.39|
|  9:  2.3731 -  2.2821  1241   140  0.92  14.19   1.02     1.00       4420.38|
| 10:  2.2821 -  2.2036  1238   137  0.91  14.33   1.01     0.97       3970.98|
| 11:  2.2036 -  2.1349  1251   137  0.91  15.32   1.01     0.98       4085.43|
| 12:  2.1349 -  2.0741  1238   138  0.92  14.44   1.03     1.01       3630.69|
| 13:  2.0741 -  2.0196  1228   134  0.92  14.45   1.02     1.02       3078.51|
| 14:  2.0196 -  1.9704  1165   132  0.92  13.79   1.00     0.97       2361.82|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2361.82 max =         9802.78 mean =      5778.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.06|
|phase err.(test): min =        0.00 max =           89.24 mean =        12.75|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.430)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    86.87   16.69    None  None   None       |
|    all(noH): 2823   0      1.31    86.87   16.69    None  None   None       |
|    Sol.    : 438    0      5.47    78.63   38.31    None  None   None       |
|    Mac.    : 2385   0      1.31    86.87   12.72    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:     1.310 -   9.866: 1018   |   5:    44.091 -  52.647:  102        |
|      1:     9.866 -  18.422: 1118   |   6:    52.647 -  61.203:   55        |
|      2:    18.422 -  26.978:  236   |   7:    61.203 -  69.759:   22        |
|      3:    26.978 -  35.535:  127   |   8:    69.759 -  78.315:    8        |
|      4:    35.535 -  44.091:  133   |   9:    78.315 -  86.871:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 285         
Filter by distance & map next to the model:
   mapped sites are within: 0.560 - 4.562
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 280 from: 285
   mapped sites are within: 0.715 - 4.562

peak=    6.286 closest distance to " O   HOH Z 144 " =    1.852
peak=    6.002 closest distance to " NE2 GLN A  11 " =    1.161
peak=    5.813 closest distance to " O   HOH Z 126 " =    1.898
peak=    5.603 closest distance to " NH2 ARG A  56 " =    2.127
peak=    5.367 closest distance to " CB  ARG A 275 " =    0.907
peak=    5.224 closest distance to " O   HOH Z 236 " =    1.469
peak=    5.075 closest distance to " CG  PRO A  54 " =    1.187
peak=    4.976 closest distance to " CB  GLN A 183 " =    1.209
peak=    4.924 closest distance to " C   PRO A 198 " =    1.449
peak=    4.875 closest distance to " CB  SER A  63 " =    1.106
peak=    4.795 closest distance to " O   HOH Z 427 " =    2.706
peak=    4.788 closest distance to " CB  GLU A 152 " =    1.232
peak=    4.769 closest distance to " O   HOH Z 209 " =    2.244
peak=    4.758 closest distance to " O   HOH Z 193 " =    1.747
peak=    4.742 closest distance to " CG  PRO A 213 " =    1.263
peak=    4.722 closest distance to " O   HOH Z  78 " =    1.737
peak=    4.647 closest distance to " CB  GLN A 223 " =    1.511
peak=    4.625 closest distance to " O   HOH Z 272 " =    1.839
peak=    4.589 closest distance to " O   HOH Z 232 " =    2.376
peak=    4.439 closest distance to " O   HOH Z 203 " =    1.704
peak=    4.415 closest distance to " O   HOH Z 369 " =    2.123
peak=    4.378 closest distance to " CB  ARG A  79 " =    1.498
peak=    4.307 closest distance to " ND2 ASN A 187 " =    1.474
peak=    4.304 closest distance to " O   HOH Z 234 " =    3.580
peak=    4.304 closest distance to " CB  SER A   3 " =    1.284
peak=    4.281 closest distance to " OG ASER A 258 " =    3.007
peak=    4.260 closest distance to " O   HOH Z 124 " =    1.369
peak=    4.249 closest distance to " O   HOH Z  15 " =    2.380
peak=    4.206 closest distance to " O   HOH Z 368 " =    1.932
peak=    4.171 closest distance to " OG BSER A 164 " =    2.326
peak=    4.160 closest distance to " OD1 ASN A  69 " =    2.595
peak=    4.153 closest distance to " O   HOH Z 402 " =    1.442
peak=    4.140 closest distance to " O   HOH Z 298 " =    1.791
peak=    4.137 closest distance to " NZ  LYS A 117 " =    3.154
peak=    4.136 closest distance to " CA  TYR A  30 " =    0.910
peak=    4.118 closest distance to " CB  ASN A 148 " =    1.768
peak=    4.117 closest distance to " O   HOH Z 303 " =    2.161
peak=    4.116 closest distance to " O   HOH Z  66 " =    2.040
peak=    4.113 closest distance to " O   HOH Z  59 " =    1.741
peak=    4.093 closest distance to " O   HOH Z 344 " =    3.110
peak=    4.080 closest distance to " O   SER A  87 " =    2.265
peak=    4.062 closest distance to " CB  PRO A  54 " =    0.946
peak=    4.061 closest distance to " CD2 TRP A 179 " =    1.366
peak=    4.053 closest distance to " O   HOH Z 346 " =    1.673
peak=    4.048 closest distance to " O   HOH Z 250 " =    1.394
peak=    4.033 closest distance to " CB  VAL A 265 " =    1.325
peak=    4.030 closest distance to " O   HOH Z 425 " =    1.969
peak=    4.027 closest distance to " CB  ARG A 139 " =    1.022
peak=    4.025 closest distance to " CB  SER A  26 " =    1.590
peak=    4.020 closest distance to " O   HOH Z   1 " =    1.775
peak=    4.016 closest distance to " O   HOH Z   6 " =    2.252
peak=    4.010 closest distance to " NH1BARG A 145 " =    1.364
peak=    4.006 closest distance to " O   HOH Z 189 " =    1.834
peak=    3.981 closest distance to " O   HOH Z  44 " =    1.854
peak=    3.948 closest distance to " O   HOH Z 403 " =    1.705
peak=    3.941 closest distance to " O   HOH Z 144 " =    2.096
peak=    3.941 closest distance to " O   HOH Z  61 " =    1.535
peak=    3.918 closest distance to " O   HOH Z  54 " =    1.664
peak=    3.917 closest distance to " O   HOH Z 371 " =    1.627
peak=    3.916 closest distance to " O   HOH Z 287 " =    1.928
peak=    3.911 closest distance to " O   HOH Z 407 " =    2.287
peak=    3.896 closest distance to " O   HOH Z  43 " =    2.070
peak=    3.895 closest distance to " CB  TYR A 169 " =    0.860
peak=    3.890 closest distance to " NH2BARG A 145 " =    2.026
peak=    3.869 closest distance to " CG  ARG A  66 " =    2.705
peak=    3.866 closest distance to " O   HOH Z 128 " =    2.023
peak=    3.855 closest distance to " O   HOH Z   3 " =    1.880
peak=    3.850 closest distance to " O   HOH Z  61 " =    1.687
peak=    3.838 closest distance to " CB  GLU A 128 " =    1.008
peak=    3.832 closest distance to " O   HOH Z  97 " =    1.933
peak=    3.826 closest distance to " O   HOH Z 327 " =    1.606
peak=    3.817 closest distance to " O   HOH Z 389 " =    3.045
peak=    3.809 closest distance to " O   HOH Z 132 " =    2.227
peak=    3.802 closest distance to " O   HOH Z 419 " =    1.945
peak=    3.801 closest distance to " O   HOH Z 365 " =    2.825
peak=    3.791 closest distance to " O   HOH Z 368 " =    3.626
peak=    3.791 closest distance to " CB  VAL A 202 " =    1.523
peak=    3.790 closest distance to " O   HOH Z 173 " =    2.003
peak=    3.784 closest distance to " O   HOH Z  10 " =    1.776
peak=    3.783 closest distance to " O   HOH Z  93 " =    2.091
peak=    3.779 closest distance to " O   HOH Z 207 " =    1.750
peak=    3.771 closest distance to " O   HOH Z 283 " =    2.237
peak=    3.757 closest distance to " CG1 ILE A  33 " =    1.213
peak=    3.754 closest distance to " O   HOH Z 128 " =    2.014
peak=    3.748 closest distance to " CG2 VAL A 257 " =    0.825
peak=    3.728 closest distance to " O   HOH Z  89 " =    2.120
peak=    3.726 closest distance to " O   HOH Z 286 " =    2.204
peak=    3.715 closest distance to " CA  ALA A  21 " =    1.057
peak=    3.714 closest distance to " CA  ASN A 215 " =    1.136
peak=    3.702 closest distance to " O   HOH Z 417 " =    3.200
peak=    3.698 closest distance to " O   HOH Z 263 " =    2.349
peak=    3.695 closest distance to " O   HOH Z 371 " =    3.004
peak=    3.692 closest distance to " OD2 ASP A 286 " =    2.680
peak=    3.690 closest distance to " O   HOH Z 423 " =    1.954
peak=    3.670 closest distance to " CB  TRP A 266 " =    1.033
peak=    3.664 closest distance to " O   HOH Z   9 " =    2.059
peak=    3.652 closest distance to " O   HOH Z  21 " =    1.742
peak=    3.642 closest distance to " O   HOH Z 345 " =    3.259
peak=    3.641 closest distance to " O   HOH Z 425 " =    1.286
peak=    3.638 closest distance to " OG  SER A  22 " =    2.580
peak=    3.632 closest distance to " O  BHOH Z 338 " =    2.367
peak=    3.622 closest distance to " CD BLYS A 290 " =    1.277
peak=    3.616 closest distance to " O   HOH Z 248 " =    1.614
peak=    3.614 closest distance to " O   HOH Z 426 " =    1.517
peak=    3.609 closest distance to " N   ARG A 156 " =    1.269
peak=    3.600 closest distance to " O   HOH Z  64 " =    2.153
peak=    3.598 closest distance to " O   HOH Z  71 " =    1.849
peak=    3.597 closest distance to " O   HOH Z 158 " =    2.978
peak=    3.591 closest distance to " OE2 GLU A  53 " =    2.096
peak=    3.586 closest distance to " N   ASN A  39 " =    1.135
peak=    3.574 closest distance to " CB  ARG A 190 " =    1.707
peak=    3.569 closest distance to " CB  LEU A 228 " =    1.121
peak=    3.564 closest distance to " O   HOH Z 433 " =    1.857
peak=    3.563 closest distance to " O   HOH Z 234 " =    1.801
peak=    3.560 closest distance to " CA  PHE A 283 " =    1.246
peak=    3.558 closest distance to " O   HOH Z 213 " =    1.757
peak=    3.518 closest distance to " O   HOH Z 250 " =    1.916
peak=    3.517 closest distance to " CG AARG A 275 " =    1.058
peak=    3.517 closest distance to " O   HOH Z 183 " =    1.485
peak=    3.506 closest distance to " O   HOH Z 336 " =    1.830
peak=    3.504 closest distance to " CB  TRP A 179 " =    1.277
peak=    3.504 closest distance to " CA  ALA A 233 " =    1.077
peak=    3.498 closest distance to " O   HOH Z 406 " =    1.652
peak=    3.494 closest distance to " CA  THR A 264 " =    0.885
peak=    3.492 closest distance to " O   HOH Z 245 " =    1.335
peak=    3.487 closest distance to " CG  PRO A  90 " =    1.170
peak=    3.479 closest distance to " O   HOH Z  88 " =    2.529
peak=    3.479 closest distance to " O   HOH Z 357 " =    1.740
peak=    3.477 closest distance to " OD1BASN A 224 " =    2.254
peak=    3.477 closest distance to " O   HOH Z 353 " =    2.500
peak=    3.470 closest distance to " N   PHE A 130 " =    1.389
peak=    3.466 closest distance to " CG  GLN A  77 " =    2.249
peak=    3.466 closest distance to " O   HOH Z 291 " =    1.580
peak=    3.465 closest distance to " CG  MET A 185 " =    1.230
peak=    3.462 closest distance to " OG BSER A  99 " =    2.200
peak=    3.462 closest distance to " O   HOH Z 437 " =    1.514
peak=    3.461 closest distance to " CG2 ILE A 120 " =    1.076
peak=    3.460 closest distance to " CG  PRO A 243 " =    1.089
peak=    3.456 closest distance to " O   HOH Z 163 " =    1.761
peak=    3.453 closest distance to " CB  ALA A  34 " =    1.035
peak=    3.451 closest distance to " O   MET A 105 " =    1.864
peak=    3.450 closest distance to " CB  ASN A  39 " =    0.819
peak=    3.449 closest distance to " O   HOH Z 112 " =    2.403
peak=    3.441 closest distance to " CB  ILE A 120 " =    1.266
peak=    3.436 closest distance to " O   HOH Z  40 " =    1.495
peak=    3.436 closest distance to " O   HOH Z 299 " =    4.263
peak=    3.431 closest distance to " O   HOH Z 193 " =    1.958
peak=    3.424 closest distance to " O   HOH Z 192 " =    1.987
peak=    3.423 closest distance to " CB  TYR A 169 " =    0.894
peak=    3.416 closest distance to " CB  THR A  31 " =    1.764
peak=    3.415 closest distance to " O   ALA A   1 " =    1.684
peak=    3.414 closest distance to " CA  ASP A 162 " =    1.051
peak=    3.405 closest distance to " O   HOH Z   1 " =    1.522
peak=    3.399 closest distance to " CB  SER A  62 " =    1.358
peak=    3.399 closest distance to " NH1AARG A 145 " =    1.160
peak=    3.394 closest distance to " CD2 LEU A 297 " =    0.994
peak=    3.394 closest distance to " CA  ALA A  84 " =    1.294
peak=    3.391 closest distance to " O   HOH Z 147 " =    1.655
peak=    3.389 closest distance to " CB  GLN A  89 " =    1.388
peak=    3.388 closest distance to " O   HOH Z 411 " =    3.706
peak=    3.376 closest distance to " CB  GLU A 277 " =    3.436
peak=    3.371 closest distance to " CG  GLU A 277 " =    2.067
peak=    3.368 closest distance to " CG  PRO A 198 " =    1.239
peak=    3.366 closest distance to " O   HOH Z 261 " =    2.136
peak=    3.362 closest distance to " CE BLYS A 290 " =    1.140
peak=    3.360 closest distance to " CE  LYS A  76 " =    0.878
peak=    3.353 closest distance to " O   HOH Z 435 " =    1.853
peak=    3.344 closest distance to " O   HOH Z 337 " =    3.538
peak=    3.343 closest distance to " CB  THR A 157 " =    1.076
peak=    3.341 closest distance to " O   HOH Z 291 " =    1.773
peak=    3.341 closest distance to " CB  ALA A 291 " =    1.399
peak=    3.340 closest distance to " O   HOH Z 180 " =    2.223
peak=    3.337 closest distance to " NE2 GLN A  73 " =    3.647
peak=    3.333 closest distance to " CG2 ILE A  20 " =    1.513
peak=    3.332 closest distance to " O   HOH Z 380 " =    1.723
peak=    3.324 closest distance to " O   HOH Z 305 " =    3.515
peak=    3.319 closest distance to " O   HOH Z 108 " =    2.220
peak=    3.315 closest distance to " O   HOH Z 374 " =    2.459
peak=    3.315 closest distance to " CB  ALA A  71 " =    1.369
peak=    3.313 closest distance to " O   HOH Z 193 " =    1.700
peak=    3.313 closest distance to " O   HOH Z 172 " =    3.376
peak=    3.313 closest distance to " CB  LYS A 290 " =    1.008
peak=    3.313 closest distance to " O   HOH Z  85 " =    2.366
peak=    3.312 closest distance to " N   ASP A 162 " =    1.204
peak=    3.303 closest distance to " CG2 THR A 221 " =    1.097
peak=    3.297 closest distance to " O   HOH Z 218 " =    2.315
peak=    3.295 closest distance to " O   HOH Z 273 " =    2.615
peak=    3.293 closest distance to " CE AMET A  47 " =    1.382
peak=    3.291 closest distance to " O   HOH Z 163 " =    1.853
peak=    3.287 closest distance to " O   HOH Z 409 " =    2.641
peak=    3.286 closest distance to " O   HOH Z 284 " =    2.857
peak=    3.283 closest distance to " CB  ALA A 248 " =    1.411
peak=    3.282 closest distance to " O   HOH Z 281 " =    4.562
peak=    3.281 closest distance to " CA  ALA A 291 " =    0.903
peak=    3.273 closest distance to " CG1BVAL A  72 " =    1.411
peak=    3.266 closest distance to " CD1 ILE A 106 " =    0.937
peak=    3.263 closest distance to " CB  VAL A 126 " =    1.129
peak=    3.263 closest distance to " OD1 ASP A 231 " =    1.953
peak=    3.259 closest distance to " O   HOH Z 148 " =    3.158
peak=    3.256 closest distance to " O   HOH Z  40 " =    2.172
peak=    3.251 closest distance to " CE BMET A  47 " =    1.417
peak=    3.250 closest distance to " CG  MET A 113 " =    1.031
peak=    3.249 closest distance to " CA  MET A  40 " =    1.083
peak=    3.249 closest distance to " O   HOH Z 389 " =    1.645
peak=    3.247 closest distance to " CE1 TYR A 186 " =    1.305
peak=    3.246 closest distance to " CD  PRO A 243 " =    1.549
peak=    3.244 closest distance to " N   SER A 134 " =    1.524
peak=    3.243 closest distance to " O   HOH Z 128 " =    2.025
peak=    3.242 closest distance to " O   HOH Z 257 " =    2.179
peak=    3.241 closest distance to " CB  ASN A 110 " =    1.068
peak=    3.240 closest distance to " O   HOH Z  39 " =    2.511
peak=    3.239 closest distance to " O   HOH Z 227 " =    1.780
peak=    3.239 closest distance to " CA  THR A 221 " =    0.987
peak=    3.238 closest distance to " CB  GLN A  88 " =    1.197
peak=    3.237 closest distance to " O   HOH Z 175 " =    2.012
peak=    3.235 closest distance to " CB  SER A 216 " =    0.715
peak=    3.233 closest distance to " CA  SER A 146 " =    1.789
peak=    3.231 closest distance to " NZ  LYS A  76 " =    1.346
peak=    3.231 closest distance to " O   HOH Z  73 " =    1.686
peak=    3.230 closest distance to " O   HOH Z 388 " =    1.817
peak=    3.230 closest distance to " O   HOH Z  15 " =    1.425
peak=    3.222 closest distance to " O   HOH Z 106 " =    2.542
peak=    3.218 closest distance to " O   HOH Z 214 " =    2.141
peak=    3.216 closest distance to " OG BSER A 258 " =    3.290
peak=    3.212 closest distance to " N   GLN A 278 " =    1.054
peak=    3.210 closest distance to " OE1 GLN A  11 " =    2.076
peak=    3.201 closest distance to " O   HOH Z 130 " =    2.798
peak=    3.196 closest distance to " OG  SER A  62 " =    2.787
peak=    3.195 closest distance to " CB  ASP A 140 " =    0.819
peak=    3.185 closest distance to " NH2AARG A 190 " =    1.829
peak=    3.185 closest distance to " O   HOH Z 132 " =    2.752
peak=    3.184 closest distance to " O   HOH Z 263 " =    1.643
peak=    3.184 closest distance to " O   HOH Z  40 " =    1.881
peak=    3.183 closest distance to " O   HOH Z 189 " =    2.232
peak=    3.175 closest distance to " O   HOH Z 261 " =    1.498
peak=    3.171 closest distance to " NE AARG A 275 " =    2.142
peak=    3.171 closest distance to " CG2 THR A 294 " =    1.545
peak=    3.166 closest distance to " NH2 ARG A 219 " =    1.946
peak=    3.165 closest distance to " O   HOH Z 341 " =    2.303
peak=    3.164 closest distance to " CG  LYS A  76 " =    0.966
peak=    3.162 closest distance to " CD2 LEU A 255 " =    1.312
peak=    3.161 closest distance to " O   HOH Z  47 " =    1.740
peak=    3.158 closest distance to " NH2AARG A 190 " =    1.060
peak=    3.158 closest distance to " CA  LEU A 300 " =    1.047
peak=    3.150 closest distance to " O   HOH Z 298 " =    2.614
peak=    3.150 closest distance to " CB  LYS A 290 " =    1.303
peak=    3.145 closest distance to " O   HOH Z 266 " =    3.097
peak=    3.143 closest distance to " O   HOH Z 112 " =    1.189
peak=    3.141 closest distance to " CG  ARG A  79 " =    2.344
peak=    3.140 closest distance to " O   HOH Z 361 " =    3.082
peak=    3.139 closest distance to " O   HOH Z 279 " =    2.147
peak=    3.136 closest distance to " O   LYS A 290 " =    2.402
peak=    3.135 closest distance to " CZ2 TRP A 179 " =    1.627
peak=    3.133 closest distance to " NE2 GLN A 223 " =    1.853
peak=    3.131 closest distance to " O   HOH Z 325 " =    3.652
peak=    3.114 closest distance to " O   SER A 164 " =    1.096
peak=    3.113 closest distance to " NZ  LYS A 119 " =    1.441
peak=    3.112 closest distance to " CA  ALA A 299 " =    0.936
peak=    3.108 closest distance to " O   HOH Z 438 " =    1.806
peak=    3.107 closest distance to " O   HOH Z 417 " =    2.030
peak=    3.103 closest distance to " CD2 HIS A  81 " =    1.194
peak=    3.102 closest distance to " CG BARG A 102 " =    1.727
peak=    3.092 closest distance to " O   HOH Z 271 " =    2.104
peak=    3.089 closest distance to " O   GLY A 229 " =    1.570
peak=    3.084 closest distance to " O   HOH Z  44 " =    3.139
peak=    3.084 closest distance to " CB  GLN A 278 " =    0.803
peak=    3.083 closest distance to " CB  ASN A 215 " =    1.107
peak=    3.083 closest distance to " O   HOH Z  19 " =    2.518
peak=    3.075 closest distance to " O   HOH Z 251 " =    1.630
peak=    3.073 closest distance to " O   HOH Z 175 " =    2.102
peak=    3.072 closest distance to " N   HIS A  86 " =    1.845
peak=    3.072 closest distance to " O   HOH Z 389 " =    1.326
peak=    3.065 closest distance to " O   GLY A 147 " =    1.465
peak=    3.056 closest distance to " O   HOH Z 125 " =    2.234
peak=    3.051 closest distance to " O   HOH Z 329 " =    3.708
peak=    3.038 closest distance to " CB  MET A 188 " =    1.592
peak=    3.023 closest distance to " O   HOH Z 423 " =    2.833
peak=    3.015 closest distance to " O   HOH Z 153 " =    3.759
peak=    3.004 closest distance to " ND1 HIS A  81 " =    1.530
peak=    3.001 closest distance to " O   HOH Z  66 " =    1.902

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.730 - 5.930
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 192
   mapped sites are within: 0.730 - 5.930

peak=   -4.743 closest distance to " O   HOH Z 266 " =    4.574
peak=   -4.566 closest distance to " C   HIS A 108 " =    1.127
peak=   -4.519 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.493 closest distance to " SG  CYS A 254 " =    3.332
peak=   -4.485 closest distance to " CB  PRO A 243 " =    2.582
peak=   -4.467 closest distance to " CA  VAL A  67 " =    2.810
peak=   -4.433 closest distance to " O   VAL A  67 " =    2.655
peak=   -4.399 closest distance to " O   HOH Z 290 " =    1.090
peak=   -4.298 closest distance to " N   GLN A  58 " =    1.701
peak=   -4.278 closest distance to " CG  GLN A 223 " =    1.802
peak=   -4.219 closest distance to " O   PRO A 198 " =    1.319
peak=   -4.138 closest distance to " OG BSER A 134 " =    1.251
peak=   -4.130 closest distance to " O   HOH Z 377 " =    2.140
peak=   -4.065 closest distance to " OXT GLY A 302 " =    2.767
peak=   -4.010 closest distance to " O   ALA A 161 " =    1.592
peak=   -3.982 closest distance to " CD1 PHE A  59 " =    1.920
peak=   -3.967 closest distance to " O   HOH Z 435 " =    2.797
peak=   -3.937 closest distance to " O   HOH Z 231 " =    2.236
peak=   -3.925 closest distance to " CG1 VAL A 112 " =    2.785
peak=   -3.905 closest distance to " O   HOH Z 351 " =    1.504
peak=   -3.904 closest distance to " CB  ASN A  39 " =    2.200
peak=   -3.890 closest distance to " O   HOH Z 407 " =    2.906
peak=   -3.866 closest distance to " O   HOH Z 389 " =    1.889
peak=   -3.851 closest distance to " O   HOH Z 198 " =    1.876
peak=   -3.847 closest distance to " NE  ARG A 156 " =    1.835
peak=   -3.828 closest distance to " O   HOH Z 385 " =    2.019
peak=   -3.821 closest distance to " OXT GLY A 302 " =    3.488
peak=   -3.818 closest distance to " O   PRO A 163 " =    1.932
peak=   -3.812 closest distance to " CB  ALA A 161 " =    2.458
peak=   -3.794 closest distance to " CZ  TYR A 169 " =    1.728
peak=   -3.788 closest distance to " C   ALA A 158 " =    1.217
peak=   -3.788 closest distance to " CB  TYR A  15 " =    2.140
peak=   -3.782 closest distance to " O   HOH Z 126 " =    1.889
peak=   -3.778 closest distance to " CE  MET A 105 " =    2.263
peak=   -3.772 closest distance to " O   HOH Z  47 " =    1.616
peak=   -3.770 closest distance to " CG  PHE A 283 " =    2.551
peak=   -3.762 closest distance to " N   ALA A 248 " =    1.601
peak=   -3.744 closest distance to " OG  SER A  97 " =    2.109
peak=   -3.735 closest distance to " CD1 LEU A 228 " =    2.016
peak=   -3.732 closest distance to " O   HOH Z 102 " =    1.602
peak=   -3.710 closest distance to " CB  ALA A 291 " =    2.182
peak=   -3.704 closest distance to " CB  ALA A 291 " =    2.353
peak=   -3.704 closest distance to " ND2 ASN A  45 " =    1.644
peak=   -3.698 closest distance to " N   ASP A 286 " =    2.369
peak=   -3.687 closest distance to " OG  SER A   3 " =    1.550
peak=   -3.686 closest distance to " O   HOH Z 211 " =    1.637
peak=   -3.686 closest distance to " O   HOH Z 362 " =    5.930
peak=   -3.674 closest distance to " O   HOH Z 313 " =    1.986
peak=   -3.671 closest distance to " CB  ALA A 248 " =    2.104
peak=   -3.667 closest distance to " O   HOH Z 198 " =    1.390
peak=   -3.661 closest distance to " CZ  PHE A  59 " =    1.468
peak=   -3.653 closest distance to " CG  ASP A 231 " =    0.730
peak=   -3.652 closest distance to " CB  ALA A 248 " =    2.269
peak=   -3.649 closest distance to " O   SER A 135 " =    1.493
peak=   -3.639 closest distance to " O   HOH Z  11 " =    1.821
peak=   -3.635 closest distance to " O   PRO A 198 " =    1.248
peak=   -3.625 closest distance to " CA  GLY A  98 " =    1.888
peak=   -3.617 closest distance to " O   HOH Z 185 " =    2.206
peak=   -3.617 closest distance to " N   HIS A 115 " =    2.074
peak=   -3.615 closest distance to " CG1 VAL A 230 " =    1.895
peak=   -3.613 closest distance to " OD2 ASP A 191 " =    1.435
peak=   -3.609 closest distance to " O   HOH Z 114 " =    2.930
peak=   -3.603 closest distance to " NH2 ARG A  79 " =    1.928
peak=   -3.603 closest distance to " O   HOH Z  13 " =    1.457
peak=   -3.601 closest distance to " O   HOH Z  43 " =    1.780
peak=   -3.597 closest distance to " CB  PHE A 192 " =    1.861
peak=   -3.591 closest distance to " O   HOH Z  24 " =    1.300
peak=   -3.587 closest distance to " O   SER A 146 " =    1.004
peak=   -3.586 closest distance to " O   ALA A  51 " =    1.297
peak=   -3.583 closest distance to " O   HOH Z 372 " =    2.353
peak=   -3.581 closest distance to " O   HOH Z 395 " =    5.161
peak=   -3.581 closest distance to " O   HOH Z 166 " =    1.455
peak=   -3.570 closest distance to " CG  GLU A   2 " =    1.981
peak=   -3.569 closest distance to " CD1 LEU A 101 " =    2.273
peak=   -3.565 closest distance to " O   VAL A 189 " =    2.505
peak=   -3.558 closest distance to " O   HOH Z  52 " =    1.230
peak=   -3.550 closest distance to " OD1 ASP A 171 " =    1.628
peak=   -3.545 closest distance to " O   HOH Z  63 " =    1.650
peak=   -3.538 closest distance to " O   SER A  95 " =    1.419
peak=   -3.525 closest distance to " O   HOH Z  11 " =    1.998
peak=   -3.522 closest distance to " C   PRO A  90 " =    1.488
peak=   -3.515 closest distance to " CG  GLN A  58 " =    1.178
peak=   -3.512 closest distance to " CG2 THR A 178 " =    2.212
peak=   -3.506 closest distance to " CB  ASP A 132 " =    2.346
peak=   -3.506 closest distance to " O   HOH Z 263 " =    2.874
peak=   -3.500 closest distance to " O   HOH Z 137 " =    1.487
peak=   -3.499 closest distance to " CB  PRO A 163 " =    2.514
peak=   -3.497 closest distance to " O   HOH Z 385 " =    1.961
peak=   -3.492 closest distance to " CD  ARG A 139 " =    1.573
peak=   -3.491 closest distance to " CE2 TYR A  30 " =    2.787
peak=   -3.478 closest distance to " CE  MET A 105 " =    1.946
peak=   -3.475 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.462 closest distance to " CG  GLU A 152 " =    0.994
peak=   -3.451 closest distance to " CD2 LEU A 300 " =    2.948
peak=   -3.443 closest distance to " ND2 ASN A  45 " =    1.030
peak=   -3.436 closest distance to " OD2 ASP A 171 " =    2.422
peak=   -3.407 closest distance to " O   HOH Z 193 " =    2.011
peak=   -3.403 closest distance to " O   HOH Z 388 " =    2.026
peak=   -3.401 closest distance to " CB  ALA A 244 " =    2.030
peak=   -3.390 closest distance to " OD2 ASP A  50 " =    1.436
peak=   -3.381 closest distance to " CG2 VAL A 189 " =    2.031
peak=   -3.379 closest distance to " O   HOH Z 421 " =    3.034
peak=   -3.377 closest distance to " O   PHE A 218 " =    1.452
peak=   -3.363 closest distance to " O   SER A  22 " =    2.424
peak=   -3.362 closest distance to " CA  TYR A  30 " =    2.903
peak=   -3.351 closest distance to " CG2 ILE A 263 " =    2.207
peak=   -3.346 closest distance to " CE3 TRP A 274 " =    2.316
peak=   -3.346 closest distance to " O   TRP A  92 " =    1.616
peak=   -3.344 closest distance to " OD1 ASP A 191 " =    1.439
peak=   -3.344 closest distance to " N   SER A 212 " =    1.971
peak=   -3.341 closest distance to " CA  GLY A 133 " =    1.934
peak=   -3.324 closest distance to " NH1 ARG A 195 " =    2.539
peak=   -3.320 closest distance to " O   HOH Z 131 " =    4.019
peak=   -3.320 closest distance to " CD1 ILE A 239 " =    2.532
peak=   -3.318 closest distance to " CG1 VAL A  78 " =    3.018
peak=   -3.315 closest distance to " C   LEU A 143 " =    1.017
peak=   -3.313 closest distance to " OD1 ASP A 191 " =    1.830
peak=   -3.312 closest distance to " O   HOH Z 200 " =    4.806
peak=   -3.308 closest distance to " CD2 LEU A 237 " =    2.559
peak=   -3.307 closest distance to " O   HOH Z 137 " =    1.418
peak=   -3.302 closest distance to " O   HOH Z 196 " =    2.047
peak=   -3.302 closest distance to " O   HOH Z 427 " =    1.399
peak=   -3.301 closest distance to " N   GLN A  77 " =    1.652
peak=   -3.295 closest distance to " ND2 ASN A 209 " =    1.788
peak=   -3.289 closest distance to " OE1 GLN A 223 " =    1.724
peak=   -3.286 closest distance to " CA  GLY A 203 " =    2.098
peak=   -3.284 closest distance to " C   GLN A 205 " =    1.822
peak=   -3.273 closest distance to " C   MET A 188 " =    1.484
peak=   -3.271 closest distance to " O   HOH Z  51 " =    1.279
peak=   -3.270 closest distance to " N   ALA A  43 " =    2.529
peak=   -3.270 closest distance to " O   VAL A 174 " =    2.079
peak=   -3.268 closest distance to " CD  GLN A  88 " =    0.961
peak=   -3.268 closest distance to " ND2 ASN A 187 " =    1.586
peak=   -3.268 closest distance to " OD1 ASN A 148 " =    1.609
peak=   -3.267 closest distance to " SG ACYS A 201 " =    1.830
peak=   -3.259 closest distance to " OG BSER A 134 " =    1.588
peak=   -3.258 closest distance to " O   HOH Z 265 " =    1.845
peak=   -3.254 closest distance to " O   MET A  40 " =    2.706
peak=   -3.254 closest distance to " NH2 ARG A  56 " =    1.855
peak=   -3.248 closest distance to " OH  TYR A 172 " =    1.677
peak=   -3.245 closest distance to " CB  ASP A 132 " =    2.207
peak=   -3.244 closest distance to " OG  SER A  87 " =    1.254
peak=   -3.242 closest distance to " O   HOH Z  60 " =    1.963
peak=   -3.241 closest distance to " CE2 PHE A 218 " =    2.412
peak=   -3.240 closest distance to " N   GLN A 122 " =    1.339
peak=   -3.236 closest distance to " O   TRP A  70 " =    1.489
peak=   -3.228 closest distance to " O   HOH Z 345 " =    1.709
peak=   -3.228 closest distance to " CG  ARG A  66 " =    2.486
peak=   -3.227 closest distance to " O   ILE A 120 " =    1.437
peak=   -3.226 closest distance to " CE1 TYR A 169 " =    2.493
peak=   -3.225 closest distance to " O   HOH Z 250 " =    1.418
peak=   -3.224 closest distance to " N   SER A 276 " =    1.177
peak=   -3.217 closest distance to " O   ASP A 162 " =    2.096
peak=   -3.217 closest distance to " CB  ALA A  43 " =    2.321
peak=   -3.213 closest distance to " OD1 ASN A 176 " =    1.311
peak=   -3.207 closest distance to " O   HOH Z 353 " =    2.188
peak=   -3.207 closest distance to " OG1 THR A 178 " =    1.196
peak=   -3.205 closest distance to " O   HOH Z 423 " =    2.251
peak=   -3.204 closest distance to " O   GLN A 240 " =    1.807
peak=   -3.198 closest distance to " O   HOH Z  10 " =    1.272
peak=   -3.191 closest distance to " O   HOH Z 281 " =    2.732
peak=   -3.191 closest distance to " OE2 GLU A 152 " =    1.229
peak=   -3.185 closest distance to " CB  ASP A 286 " =    2.189
peak=   -3.183 closest distance to " CE  LYS A  76 " =    2.922
peak=   -3.178 closest distance to " O   ALA A  34 " =    2.369
peak=   -3.172 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.171 closest distance to " O   HOH Z 134 " =    2.963
peak=   -3.165 closest distance to " O   ALA A 292 " =    1.912
peak=   -3.160 closest distance to " O   VAL A 153 " =    2.339
peak=   -3.143 closest distance to " OD1 ASN A 249 " =    1.796
peak=   -3.143 closest distance to " O   GLY A  80 " =    2.517
peak=   -3.142 closest distance to " O   HOH Z 311 " =    3.475
peak=   -3.142 closest distance to " ND2 ASN A  39 " =    1.275
peak=   -3.134 closest distance to " O   LYS A 289 " =    2.878
peak=   -3.131 closest distance to " O   HOH Z 213 " =    1.336
peak=   -3.128 closest distance to " OD1 ASN A 301 " =    1.933
peak=   -3.116 closest distance to " O   HOH Z 174 " =    4.287
peak=   -3.109 closest distance to " OH  TYR A 214 " =    1.254
peak=   -3.106 closest distance to " OD1 ASP A 200 " =    1.365
peak=   -3.105 closest distance to " O   LYS A 117 " =    1.576
peak=   -3.095 closest distance to " CZ  ARG A 259 " =    0.824
peak=   -3.095 closest distance to " O   HOH Z  60 " =    1.965
peak=   -3.091 closest distance to " CE  MET A  93 " =    1.193
peak=   -3.090 closest distance to " CA  TRP A 274 " =    1.440
peak=   -3.089 closest distance to " O   HOH Z 389 " =    4.756
peak=   -3.087 closest distance to " CB  PHE A 208 " =    2.164
peak=   -3.080 closest distance to " O   ASN A 249 " =    1.476
peak=   -3.070 closest distance to " O   HOH Z 139 " =    2.896
peak=   -3.066 closest distance to " O   HOH Z 377 " =    0.822
peak=   -3.062 closest distance to " O   ALA A   8 " =    1.932
peak=   -3.056 closest distance to " O   HOH Z 361 " =    3.445

================= 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    :  0.3984 0.3978   6.177727e+00   6.168385e+00
   1_bss:  0.3877 0.3843   6.165035e+00   6.141897e+00
   1_xyz:  0.2469 0.2743   5.797617e+00   5.876018e+00
   1_adp:  0.2254 0.2809   5.744818e+00   5.908446e+00
   1_occ:  0.2250 0.2811   5.743846e+00   5.908689e+00
   2_bss:  0.2226 0.2792   5.740485e+00   5.905596e+00
   2_xyz:  0.1500 0.1977   5.378985e+00   5.592600e+00
   2_adp:  0.1345 0.1768   5.271350e+00   5.477619e+00
   2_occ:  0.1342 0.1768   5.269871e+00   5.476212e+00
   3_bss:  0.1344 0.1760   5.268018e+00   5.471730e+00
   3_xyz:  0.1171 0.1585   5.157192e+00   5.380544e+00
   3_adp:  0.1134 0.1568   5.135495e+00   5.367870e+00
   3_occ:  0.1133 0.1567   5.135178e+00   5.367739e+00
   4_bss:  0.1133 0.1566   5.134808e+00   5.367425e+00
   4_xyz:  0.1117 0.1545   5.123778e+00   5.354066e+00
   4_adp:  0.1111 0.1549   5.122360e+00   5.357182e+00
   4_occ:  0.1110 0.1549   5.122297e+00   5.357360e+00
   5_bss:  0.1108 0.1549   5.122205e+00   5.357569e+00
   5_xyz:  0.1045 0.1532   5.088343e+00   5.348684e+00
   5_adp:  0.1044 0.1527   5.085326e+00   5.345084e+00
   5_occ:  0.1043 0.1527   5.085444e+00   5.345416e+00
   5_bss:  0.1043 0.1527   5.085731e+00   5.345722e+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:  0.327  19.739  -1.296  -0.233   0.822  -0.000   0.000   0.000
   1_xyz:  0.327  19.739  -1.296  -0.233   0.822  -0.000   0.000   0.000
   1_adp:  0.327  19.739  -1.296  -0.233   0.822  -0.000   0.000   0.000
   1_occ:  0.327  19.739  -1.296  -0.233   0.822  -0.000   0.000   0.000
   2_bss:  0.311  32.089  -2.482  -1.714  -0.985  -0.000  -0.000  -0.000
   2_xyz:  0.311  32.089  -2.482  -1.714  -0.985  -0.000  -0.000  -0.000
   2_adp:  0.311  32.089  -2.482  -1.714  -0.985  -0.000  -0.000  -0.000
   2_occ:  0.311  32.089  -2.482  -1.714  -0.985  -0.000  -0.000  -0.000
   3_bss:  0.319  36.400  -2.810  -2.291  -1.462  -0.000  -0.000  -0.000
   3_xyz:  0.319  36.400  -2.810  -2.291  -1.462  -0.000  -0.000  -0.000
   3_adp:  0.319  36.400  -2.810  -2.291  -1.462  -0.000  -0.000  -0.000
   3_occ:  0.319  36.400  -2.810  -2.291  -1.462  -0.000  -0.000  -0.000
   4_bss:  0.319  37.843  -2.922  -2.435  -1.626  -0.000  -0.000  -0.000
   4_xyz:  0.319  37.843  -2.922  -2.435  -1.626  -0.000  -0.000  -0.000
   4_adp:  0.319  37.843  -2.922  -2.435  -1.626  -0.000  -0.000  -0.000
   4_occ:  0.319  37.843  -2.922  -2.435  -1.626  -0.000  -0.000  -0.000
   5_bss:  0.319  37.843  -2.821  -2.346  -1.526  -0.000  -0.000  -0.000
   5_xyz:  0.319  37.843  -2.821  -2.346  -1.526  -0.000  -0.000  -0.000
   5_adp:  0.319  37.843  -2.821  -2.346  -1.526  -0.000  -0.000  -0.000
   5_occ:  0.319  37.843  -2.821  -2.346  -1.526  -0.000  -0.000  -0.000
   5_bss:  0.323  37.795  -2.662  -2.200  -1.344  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.078 0.6208  0.8208    45313.450
   1_bss:  40.682 0.6356  0.8317    41138.516
   1_xyz:  26.367 0.7986  0.9915    18878.611
   1_adp:  27.693 0.7835  0.9776    20178.580
   1_occ:  27.684 0.7836  0.9773    20167.582
   2_bss:  27.458 0.7855  0.9297    19813.684
   2_xyz:  18.610 0.8741  0.9996     9530.136
   2_adp:  15.815 0.8998  1.0123     7656.591
   2_occ:  15.795 0.9000  1.0121     7627.415
   3_bss:  15.680 0.9009  0.9955     7517.430
   3_xyz:  13.836 0.9159  0.9992     6153.048
   3_adp:  13.545 0.9184  0.9960     6035.188
   3_occ:  13.543 0.9185  0.9959     6026.400
   4_bss:  13.534 0.9185  0.9909     6022.123
   4_xyz:  13.252 0.9209  0.9911     5841.996
   4_adp:  13.277 0.9208  0.9868     5882.755
   4_occ:  13.280 0.9208  0.9867     5883.205
   5_bss:  13.297 0.9207  0.9902     5902.679
   5_xyz:  13.105 0.9220  0.9909     5797.808
   5_adp:  13.021 0.9227  0.9868     5766.989
   5_occ:  13.026 0.9227  0.9867     5770.739
   5_bss:  13.031 0.9226  0.9909     5777.788
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8070e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8070e-01
   1_xyz:   1.202  0.009  0.075 14.764  0.005  4.105   8.2989e-02
   1_adp:   1.202  0.009  0.075 14.764  0.005  4.105   8.2989e-02
   1_occ:   1.202  0.009  0.075 14.764  0.005  4.105   8.2989e-02
   2_bss:   1.202  0.009  0.075 14.764  0.005  4.105   8.2989e-02
   2_xyz:   1.049  0.007  0.072 14.577  0.004  4.107   6.1699e-02
   2_adp:   1.049  0.007  0.072 14.577  0.004  4.107   6.1699e-02
   2_occ:   1.049  0.007  0.072 14.577  0.004  4.107   6.1699e-02
   3_bss:   1.049  0.007  0.072 14.577  0.004  4.107   6.1699e-02
   3_xyz:   0.943  0.005  0.068 14.604  0.004  4.109   5.3382e-02
   3_adp:   0.943  0.005  0.068 14.604  0.004  4.109   5.3382e-02
   3_occ:   0.943  0.005  0.068 14.604  0.004  4.109   5.3382e-02
   4_bss:   0.943  0.005  0.068 14.604  0.004  4.109   5.3382e-02
   4_xyz:   0.860  0.004  0.063 14.227  0.003  4.109   4.6394e-02
   4_adp:   0.860  0.004  0.063 14.227  0.003  4.109   4.6394e-02
   4_occ:   0.860  0.004  0.063 14.227  0.003  4.109   4.6394e-02
   5_bss:   0.860  0.004  0.063 14.227  0.003  4.109   4.6394e-02
   5_xyz:   1.061  0.007  0.076 14.887  0.004  4.106   6.4885e-02
   5_adp:   1.061  0.007  0.076 14.887  0.004  4.106   6.4885e-02
   5_occ:   1.061  0.007  0.076 14.887  0.004  4.106   6.4885e-02
   5_bss:   1.061  0.007  0.076 14.887  0.004  4.106   6.4885e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.328   2.3790e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.328   2.3790e-01
   1_xyz:   8.975  0.044  0.315 87.229  0.049  2.032   8.1326e-02
   1_adp:   8.975  0.044  0.315 87.229  0.049  2.032   8.1326e-02
   1_occ:   8.975  0.044  0.315 87.229  0.049  2.032   8.1326e-02
   2_bss:   8.975  0.044  0.315 87.229  0.049  2.032   8.1326e-02
   2_xyz:   7.027  0.037  0.234 84.394  0.041  2.313   5.4093e-02
   2_adp:   7.027  0.037  0.234 84.394  0.041  2.313   5.4093e-02
   2_occ:   7.027  0.037  0.234 84.394  0.041  2.313   5.4093e-02
   3_bss:   7.027  0.037  0.234 84.394  0.041  2.313   5.4093e-02
   3_xyz:   6.626  0.036  0.226 84.471  0.043  2.327   4.7521e-02
   3_adp:   6.626  0.036  0.226 84.471  0.043  2.327   4.7521e-02
   3_occ:   6.626  0.036  0.226 84.471  0.043  2.327   4.7521e-02
   4_bss:   6.626  0.036  0.226 84.471  0.043  2.327   4.7521e-02
   4_xyz:   6.151  0.036  0.196 83.891  0.039  2.358   2.8881e-02
   4_adp:   6.151  0.036  0.196 83.891  0.039  2.358   2.8881e-02
   4_occ:   6.151  0.036  0.196 83.891  0.039  2.358   2.8881e-02
   5_bss:   6.151  0.036  0.196 83.891  0.039  2.358   2.8881e-02
   5_xyz:   6.620  0.042  0.252 83.378  0.039  2.225   5.2101e-02
   5_adp:   6.620  0.042  0.252 83.378  0.039  2.225   5.2101e-02
   5_occ:   6.620  0.042  0.252 83.378  0.039  2.225   5.2101e-02
   5_bss:   6.620  0.042  0.252 83.378  0.039  2.225   5.2101e-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:  78.85   0.00  17.86  76.79   0.00  13.82  78.85   5.13  39.81
   1_occ:  78.85   0.00  17.86  76.79   0.00  13.82  78.85   5.13  39.81
   2_bss:  78.85   0.00  17.86  76.79   0.00  13.82  78.85   5.13  39.81
   2_xyz:  78.85   0.00  17.86  76.79   0.00  13.82  78.85   5.13  39.81
   2_adp:  76.99   1.30  17.11  76.99   1.30  13.14  70.80   6.35  38.70
   2_occ:  76.99   1.30  17.11  76.99   1.30  13.14  70.80   6.35  38.70
   3_bss:  76.99   1.30  17.11  76.99   1.30  13.14  70.80   6.35  38.70
   3_xyz:  76.99   1.30  17.11  76.99   1.30  13.14  70.80   6.35  38.70
   3_adp:  82.87   0.00  17.17  82.87   0.00  13.02  75.03   2.31  39.75
   3_occ:  82.87   0.00  17.17  82.87   0.00  13.02  75.03   2.31  39.75
   4_bss:  82.87   0.00  17.17  82.87   0.00  13.02  75.03   2.31  39.75
   4_xyz:  82.87   0.00  17.17  82.87   0.00  13.02  75.03   2.31  39.75
   4_adp:  85.91   1.12  17.06  85.91   1.12  12.95  77.10   3.61  39.45
   4_occ:  85.91   1.12  17.06  85.91   1.12  12.95  77.10   3.61  39.45
   5_bss:  85.91   1.12  17.06  85.91   1.12  12.95  77.10   3.61  39.45
   5_xyz:  85.91   1.12  17.06  85.91   1.12  12.95  77.10   3.61  39.45
   5_adp:  86.92   1.36  16.74  86.92   1.36  12.77  78.68   5.52  38.36
   5_occ:  86.92   1.36  16.74  86.92   1.36  12.77  78.68   5.52  38.36
   5_bss:  86.87   1.31  16.69  86.87   1.31  12.72  78.63   5.47  38.31
------------------------------------------------------------------------
 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:    1.924    0.016    0.296
   1_adp:    1.924    0.016    0.296
   1_occ:    1.924    0.016    0.296
   2_bss:    1.924    0.016    0.296
   2_xyz:    1.579    0.008    0.468
   2_adp:    1.579    0.008    0.468
   2_occ:    1.579    0.008    0.468
   3_bss:    1.579    0.008    0.468
   3_xyz:    1.254    0.056    0.501
   3_adp:    1.254    0.056    0.501
   3_occ:    1.254    0.056    0.501
   4_bss:    1.254    0.056    0.501
   4_xyz:    1.291    0.037    0.517
   4_adp:    1.291    0.037    0.517
   4_occ:    1.291    0.037    0.517
   5_bss:    1.291    0.037    0.517
   5_xyz:    1.191    0.046    0.530
   5_adp:    1.191    0.046    0.530
   5_occ:    1.191    0.046    0.530
   5_bss:    1.191    0.046    0.530
------------------------------------------------------------------------

CPU time actual refinement: 346.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_277/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_277/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_277/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_277/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_277/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.38 
  Macro-tasks:
    bulk solvent and scale       = 42.84  
    individual site refinement   = 147.69 
    weights calculation          = 30.52  
    collect and process          = 6.66   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 227.85 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 109.51 
    alpha_beta                      = 8.39   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 119.88 
    fmodel                         = 7.36   
    r_factors                      = 0.31   
    phase_errors                   = 10.63  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 259.37 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.808 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    659 calls, 109.16 s
gradients_fft:          604 calls, 105.61 s

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

# Date 2008-01-16 Time 04:26:52 PST -0800 (1200486412.22 s)
Start R-work = 0.3984, R-free = 0.3978 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1743 (no bulk solvent and anisotropic scale)

Start R-work = 0.3877, R-free = 0.3843
Final R-work = 0.1043, R-free = 0.1527