Starting phenix.real_space_refine
on Tue Mar  3 12:37:48 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7ryq_24745/03_2026/7ryq_24745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ryq_24745/03_2026/7ryq_24745.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ryq_24745/03_2026/7ryq_24745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ryq_24745/03_2026/7ryq_24745.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ryq_24745/03_2026/7ryq_24745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ryq_24745/03_2026/7ryq_24745.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    2773      2.51       5
     N     744      2.21       5
     O     790      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4332
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 4332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4332
          Classifications: {'peptide': 527}
          Link IDs: {'PTRANS': 15, 'TRANS': 511}
          Chain breaks: 5
  Time building chain proxies: 0.96, per 1000 atoms: 0.22
  Number of scatterers: 4332
  At special positions: 0
  Unit cell: (75.46, 74.48, 142.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O     790      8.00
     N     744      7.00
     C    2773      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 98.6 milliseconds
  

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1028

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 21
      removed outlier: 3.993A  pdb=" N   ALA B  18 " --> pdb=" O   GLN B  14 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LEU B  19 " --> pdb=" O   ALA B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 51
      removed outlier: 3.725A  pdb=" N   LEU B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 95
      removed outlier: 3.730A  pdb=" N   ALA B  95 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 105
    Processing helix  chain 'B' and resid 112 through 128
    Processing helix  chain 'B' and resid 136 through 152
      removed outlier: 3.599A  pdb=" N   ASN B 143 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ASN B 144 " --> pdb=" O   GLN B 140 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU B 148 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   TRP B 149 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU B 151 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 173
      removed outlier: 3.761A  pdb=" N   ALA B 160 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TYR B 161 " --> pdb=" O   THR B 157 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   MET B 173 " --> pdb=" O   TYR B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 206
    Processing helix  chain 'B' and resid 206 through 219
      removed outlier: 3.856A  pdb=" N   ASN B 210 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN B 216 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B 217 " --> pdb=" O   TYR B 213 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   TYR B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLN B 219 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 239
      removed outlier: 3.507A  pdb=" N   LYS B 236 " --> pdb=" O   HIS B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 264
      removed outlier: 4.241A  pdb=" N   ASN B 252 " --> pdb=" O   GLU B 248 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR B 255 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   GLN B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   PHE B 259 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   TYR B 260 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 280
      removed outlier: 5.374A  pdb=" N   HIS B 271 " --> pdb=" O   MET B 267 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   CYS B 272 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LEU B 273 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ASN B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   VAL B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ILE B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   PHE B 280 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 306
    Processing helix  chain 'B' and resid 306 through 325
      removed outlier: 3.670A  pdb=" N   ILE B 310 " --> pdb=" O   ARG B 306 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TRP B 314 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE B 315 " --> pdb=" O   ALA B 311 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LYS B 316 " --> pdb=" O   ARG B 312 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU B 321 " --> pdb=" O   TYR B 317 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA B 325 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 328
      No H-bonds generated for 'chain 'B' and resid 326 through 328'
    Processing helix  chain 'B' and resid 346 through 364
      removed outlier: 3.568A  pdb=" N   LYS B 350 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLU B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   LEU B 352 " --> pdb=" O   ARG B 348 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLU B 355 " --> pdb=" O   GLU B 351 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU B 356 " --> pdb=" O   LEU B 352 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG B 359 " --> pdb=" O   GLU B 355 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLN B 364 " --> pdb=" O   LYS B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 381
    Processing helix  chain 'B' and resid 389 through 410
      removed outlier: 4.989A  pdb=" N   VAL B 403 " --> pdb=" O   GLY B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 434
      removed outlier: 3.628A  pdb=" N   HIS B 419 " --> pdb=" O   TYR B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 460
      Proline residue:  B 456  - end of helix
    Processing helix  chain 'B' and resid 464 through 492
    Processing helix  chain 'B' and resid 500 through 525
    Processing helix  chain 'B' and resid 539 through 555
    Processing helix  chain 'B' and resid 560 through 584
      removed outlier: 3.923A  pdb=" N   GLU B 565 " --> pdb=" O   ASP B 561 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU B 566 " --> pdb=" O   PRO B 562 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU B 584 " --> pdb=" O   VAL B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 621
      Proline residue:  B 608  - end of helix

    274 hydrogen bonds defined for protein.
    822 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.57

  Time building geometry restraints manager: 0.32 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 1400
        1.34 -     1.46: 788
        1.46 -     1.58: 2192
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 4419
  Sorted by residual:
  bond pdb=" CA  ARG B 385 "
       pdb=" CB  ARG B 385 "
    ideal  model  delta    sigma   weight residual
    1.526  1.545 -0.019 9.30e-03 1.16e+04 4.16e+00
  bond pdb=" N   GLU B 109 "
       pdb=" CA  GLU B 109 "
    ideal  model  delta    sigma   weight residual
    1.459  1.481 -0.022 1.32e-02 5.74e+03 2.75e+00
  bond pdb=" CA  PRO B 527 "
       pdb=" C   PRO B 527 "
    ideal  model  delta    sigma   weight residual
    1.517  1.538 -0.021 1.46e-02 4.69e+03 2.10e+00
  bond pdb=" CA  PHE B 203 "
       pdb=" CB  PHE B 203 "
    ideal  model  delta    sigma   weight residual
    1.528  1.550 -0.022 1.56e-02 4.11e+03 1.90e+00
  bond pdb=" CA  LEU B 111 "
       pdb=" C   LEU B 111 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.015 1.12e-02 7.97e+03 1.88e+00
  ... (remaining 4414 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 5786
        2.87 -     5.74: 148
        5.74 -     8.62: 14
        8.62 -    11.49: 1
       11.49 -    14.36: 2
  Bond angle restraints: 5951
  Sorted by residual:
  angle pdb=" N   ASN B 528 "
        pdb=" CA  ASN B 528 "
        pdb=" C   ASN B 528 "
      ideal   model   delta    sigma   weight residual
     109.41  123.29  -13.88 1.52e+00 4.33e-01 8.34e+01
  angle pdb=" N   LYS B 205 "
        pdb=" CA  LYS B 205 "
        pdb=" C   LYS B 205 "
      ideal   model   delta    sigma   weight residual
     110.80  125.16  -14.36 2.13e+00 2.20e-01 4.55e+01
  angle pdb=" N   VAL B 381 "
        pdb=" CA  VAL B 381 "
        pdb=" C   VAL B 381 "
      ideal   model   delta    sigma   weight residual
     112.98  106.45    6.53 1.25e+00 6.40e-01 2.73e+01
  angle pdb=" N   PRO B 527 "
        pdb=" CA  PRO B 527 "
        pdb=" C   PRO B 527 "
      ideal   model   delta    sigma   weight residual
     113.53  120.63   -7.10 1.39e+00 5.18e-01 2.61e+01
  angle pdb=" N   LYS B 350 "
        pdb=" CA  LYS B 350 "
        pdb=" C   LYS B 350 "
      ideal   model   delta    sigma   weight residual
     111.28  116.24   -4.96 1.09e+00 8.42e-01 2.07e+01
  ... (remaining 5946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2406
       17.34 -    34.69: 216
       34.69 -    52.03: 61
       52.03 -    69.37: 13
       69.37 -    86.71: 6
  Dihedral angle restraints: 2702
    sinusoidal: 1126
      harmonic: 1576
  Sorted by residual:
  dihedral pdb=" CA  LEU B  94 "
           pdb=" C   LEU B  94 "
           pdb=" N   ALA B  95 "
           pdb=" CA  ALA B  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.28  -28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  GLU B 437 "
           pdb=" C   GLU B 437 "
           pdb=" N   THR B 438 "
           pdb=" CA  THR B 438 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.71  -25.29     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  ASP B 388 "
           pdb=" C   ASP B 388 "
           pdb=" N   PHE B 389 "
           pdb=" CA  PHE B 389 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.25  -23.75     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 2699 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 535
       0.068 -    0.135: 96
       0.135 -    0.202: 14
       0.202 -    0.270: 4
       0.270 -    0.337: 3
  Chirality restraints: 652
  Sorted by residual:
  chirality pdb=" CA  LYS B 205 "
            pdb=" N   LYS B 205 "
            pdb=" C   LYS B 205 "
            pdb=" CB  LYS B 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.84e+00
  chirality pdb=" CA  GLU B 109 "
            pdb=" N   GLU B 109 "
            pdb=" C   GLU B 109 "
            pdb=" CB  GLU B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  PRO B 527 "
            pdb=" N   PRO B 527 "
            pdb=" C   PRO B 527 "
            pdb=" CB  PRO B 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 649 not shown)

  Planarity restraints: 758
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  51 "   -0.052 5.00e-02 4.00e+02   7.87e-02 9.92e+00
        pdb=" N   PRO B  52 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO B  52 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B  52 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 578 "    0.026 2.00e-02 2.50e+03   2.18e-02 8.28e+00
        pdb=" CG  PHE B 578 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 578 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 578 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 578 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 578 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 578 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 526 "    0.042 5.00e-02 4.00e+02   6.38e-02 6.51e+00
        pdb=" N   PRO B 527 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 527 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 527 "    0.036 5.00e-02 4.00e+02
  ... (remaining 755 not shown)

  Histogram of nonbonded interaction distances:
        1.25 -     1.98: 7
        1.98 -     2.71: 275
        2.71 -     3.44: 7338
        3.44 -     4.17: 10282
        4.17 -     4.90: 17111
  Nonbonded interactions: 35013
  Sorted by model distance:
  nonbonded pdb=" CA  SER B 523 "
            pdb=" CG  PRO B 527 "
     model   vdw
     1.251 3.870
  nonbonded pdb=" N   SER B 523 "
            pdb=" CG  PRO B 527 "
     model   vdw
     1.404 3.520
  nonbonded pdb=" O   ASP B 522 "
            pdb=" CD  PRO B 527 "
     model   vdw
     1.613 3.440
  nonbonded pdb=" NE  ARG B 525 "
            pdb=" OE1 GLU B 533 "
     model   vdw
     1.718 3.120
  nonbonded pdb=" CD  ARG B 525 "
            pdb=" OE1 GLU B 533 "
     model   vdw
     1.721 3.440
  ... (remaining 35008 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.320
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4419  Z= 0.287
  Angle     :  1.083  14.362   5951  Z= 0.668
  Chirality :  0.058   0.337    652
  Planarity :  0.007   0.079    758
  Dihedral  : 15.485  86.712   1674
  Min Nonbonded Distance : 1.251

Molprobity Statistics.
  All-atom Clashscore : 39.14
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 10.68 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  :  3.23 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.36), residues: 515
  helix: -0.47 (0.25), residues: 383
  sheet:  None (None), residues: 0
  loop : -2.28 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 270 
 TYR   0.026   0.003   TYR B 516 
 PHE   0.050   0.004   PHE B 578 
 TRP   0.013   0.002   TRP B 314 
 HIS   0.008   0.002   HIS B 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 4419)
  covalent geometry    : angle       1.08340 ( 5951)
  hydrogen bonds       : bond        0.16314 (  274)
  hydrogen bonds       : angle       6.57436 (  822)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  335 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9039 (mm-30)
REVERT: B  397 LEU cc_start: 0.9336 (tt) cc_final: 0.9103 (mt)
REVERT: B  486 ASP cc_start: 0.8766 (m-30) cc_final: 0.8517 (m-30)
  outliers start: 29
  outliers final: 11
  residues processed: 82
  average time/residue: 0.0939
  time to fit residues: 9.2346
Evaluate side-chains
  50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.0770
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 216 GLN
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 508 ASN
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.068486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.058712 restraints weight = 46439.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.059819 restraints weight = 29761.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.060638 restraints weight = 21216.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.061162 restraints weight = 16375.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.061575 restraints weight = 13609.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4419  Z= 0.170
  Angle     :  0.826  14.559   5951  Z= 0.426
  Chirality :  0.047   0.365    652
  Planarity :  0.006   0.063    758
  Dihedral  :  6.384  27.640    579
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.96 %
    Favored  : 94.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.36), residues: 515
  helix: -0.06 (0.25), residues: 387
  sheet:  None (None), residues: 0
  loop : -2.53 (0.54), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 270 
 TYR   0.025   0.002   TYR B 317 
 PHE   0.027   0.003   PHE B 578 
 TRP   0.019   0.002   TRP B 314 
 HIS   0.006   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4419)
  covalent geometry    : angle       0.82648 ( 5951)
  hydrogen bonds       : bond        0.06236 (  274)
  hydrogen bonds       : angle       5.44230 (  822)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 LEU cc_start: 0.9341 (mm) cc_final: 0.9023 (mm)
REVERT: B  210 ASN cc_start: 0.9149 (m110) cc_final: 0.8856 (t0)
REVERT: B  486 ASP cc_start: 0.8695 (m-30) cc_final: 0.8490 (m-30)
REVERT: B  548 PHE cc_start: 0.8858 (m-80) cc_final: 0.8588 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1067
  time to fit residues: 7.5793
Evaluate side-chains
  40 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 49 optimal weight:    0.0030
   chunk 45 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.1980
   chunk 23 optimal weight:    0.0030
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.3200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 209 HIS
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.061155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.049362 restraints weight = 45163.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.050464 restraints weight = 33027.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.051062 restraints weight = 26236.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.051690 restraints weight = 22600.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.052186 restraints weight = 19657.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4419  Z= 0.159
  Angle     :  0.743  11.402   5951  Z= 0.382
  Chirality :  0.045   0.312    652
  Planarity :  0.005   0.050    758
  Dihedral  :  6.015  25.063    579
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  2.80 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.36), residues: 515
  helix:  0.19 (0.25), residues: 387
  sheet:  None (None), residues: 0
  loop : -2.47 (0.52), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 270 
 TYR   0.014   0.002   TYR B 516 
 PHE   0.026   0.002   PHE B 409 
 TRP   0.009   0.001   TRP B 314 
 HIS   0.008   0.001   HIS B 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4419)
  covalent geometry    : angle       0.74273 ( 5951)
  hydrogen bonds       : bond        0.05663 (  274)
  hydrogen bonds       : angle       5.18821 (  822)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 LEU cc_start: 0.9351 (mm) cc_final: 0.8990 (mm)
REVERT: B  204 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6911 (pm20)
REVERT: B  210 ASN cc_start: 0.9186 (m110) cc_final: 0.8897 (t0)
REVERT: B  486 ASP cc_start: 0.8875 (m-30) cc_final: 0.8635 (m-30)
REVERT: B  548 PHE cc_start: 0.8810 (m-10) cc_final: 0.8540 (m-80)
REVERT: B  549 ARG cc_start: 0.8954 (ptm-80) cc_final: 0.8643 (ptt90)
  outliers start: 2
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0961
  time to fit residues: 7.0523
Evaluate side-chains
  43 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 46 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0020
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    0.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 426 HIS
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.070094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.060177 restraints weight = 45139.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.061353 restraints weight = 29097.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.062167 restraints weight = 20854.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.062697 restraints weight = 16132.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.062976 restraints weight = 13303.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4419  Z= 0.140
  Angle     :  0.702  11.369   5951  Z= 0.361
  Chirality :  0.043   0.313    652
  Planarity :  0.005   0.053    758
  Dihedral  :  5.753  24.116    579
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.88 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.36), residues: 515
  helix:  0.28 (0.25), residues: 389
  sheet:  None (None), residues: 0
  loop : -2.74 (0.50), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 359 
 TYR   0.022   0.001   TYR B 482 
 PHE   0.044   0.002   PHE B  13 
 TRP   0.007   0.001   TRP B 314 
 HIS   0.004   0.001   HIS B 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 4419)
  covalent geometry    : angle       0.70250 ( 5951)
  hydrogen bonds       : bond        0.05060 (  274)
  hydrogen bonds       : angle       4.94820 (  822)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 LEU cc_start: 0.9360 (mm) cc_final: 0.9003 (mm)
REVERT: B  210 ASN cc_start: 0.9134 (m110) cc_final: 0.8760 (t0)
REVERT: B  267 MET cc_start: 0.6106 (mmt) cc_final: 0.5430 (mmt)
REVERT: B  486 ASP cc_start: 0.8828 (m-30) cc_final: 0.8564 (m-30)
REVERT: B  548 PHE cc_start: 0.8779 (m-10) cc_final: 0.8489 (m-80)
REVERT: B  549 ARG cc_start: 0.8964 (ptm-80) cc_final: 0.8697 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0749
  time to fit residues: 5.4051
Evaluate side-chains
  41 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 216 GLN
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.066662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.056935 restraints weight = 46070.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.057983 restraints weight = 29940.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.058746 restraints weight = 21822.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.059262 restraints weight = 17089.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.059638 restraints weight = 14172.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4419  Z= 0.186
  Angle     :  0.757  13.167   5951  Z= 0.400
  Chirality :  0.046   0.373    652
  Planarity :  0.005   0.065    758
  Dihedral  :  5.886  25.709    579
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.36), residues: 515
  helix:  0.36 (0.26), residues: 389
  sheet:  None (None), residues: 0
  loop : -2.68 (0.51), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 393 
 TYR   0.019   0.002   TYR B  33 
 PHE   0.025   0.003   PHE B 409 
 TRP   0.009   0.001   TRP B 314 
 HIS   0.006   0.001   HIS B 271 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4419)
  covalent geometry    : angle       0.75683 ( 5951)
  hydrogen bonds       : bond        0.05330 (  274)
  hydrogen bonds       : angle       5.14727 (  822)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  210 ASN cc_start: 0.9155 (m110) cc_final: 0.8806 (t0)
REVERT: B  419 HIS cc_start: 0.8650 (m-70) cc_final: 0.8138 (m90)
REVERT: B  484 MET cc_start: 0.9451 (mmp) cc_final: 0.9223 (ptt)
REVERT: B  486 ASP cc_start: 0.8907 (m-30) cc_final: 0.8652 (m-30)
REVERT: B  548 PHE cc_start: 0.8785 (m-10) cc_final: 0.8480 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0936
  time to fit residues: 5.7600
Evaluate side-chains
  41 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   chunk 39 optimal weight:    0.0010
   chunk 24 optimal weight:    0.0070
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.4404

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.069818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.059885 restraints weight = 45634.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.060946 restraints weight = 28713.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.061706 restraints weight = 20549.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.062251 restraints weight = 15956.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.062647 restraints weight = 13162.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4419  Z= 0.139
  Angle     :  0.683  10.689   5951  Z= 0.354
  Chirality :  0.044   0.296    652
  Planarity :  0.005   0.057    758
  Dihedral  :  5.642  27.024    579
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.36), residues: 515
  helix:  0.54 (0.26), residues: 391
  sheet:  None (None), residues: 0
  loop : -2.58 (0.51), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 393 
 TYR   0.025   0.002   TYR B 402 
 PHE   0.017   0.002   PHE B 203 
 TRP   0.010   0.001   TRP B 314 
 HIS   0.001   0.000   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4419)
  covalent geometry    : angle       0.68338 ( 5951)
  hydrogen bonds       : bond        0.04754 (  274)
  hydrogen bonds       : angle       4.90741 (  822)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 MET cc_start: 0.6138 (mmt) cc_final: 0.5565 (mmt)
REVERT: B  419 HIS cc_start: 0.8757 (m-70) cc_final: 0.8230 (m90)
REVERT: B  450 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7608 (mtp180)
REVERT: B  453 MET cc_start: 0.8182 (ppp) cc_final: 0.7758 (ppp)
REVERT: B  484 MET cc_start: 0.9483 (mmp) cc_final: 0.9219 (ptt)
REVERT: B  486 ASP cc_start: 0.8795 (m-30) cc_final: 0.8524 (m-30)
REVERT: B  548 PHE cc_start: 0.8780 (m-10) cc_final: 0.8480 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0684
  time to fit residues: 4.2988
Evaluate side-chains
  38 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0370
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.7660

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.069384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.059483 restraints weight = 45342.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.060545 restraints weight = 28824.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.061303 restraints weight = 20806.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.061832 restraints weight = 16336.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.062179 restraints weight = 13551.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4419  Z= 0.138
  Angle     :  0.688  12.580   5951  Z= 0.355
  Chirality :  0.045   0.410    652
  Planarity :  0.005   0.065    758
  Dihedral  :  5.526  27.588    579
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.36), residues: 515
  helix:  0.50 (0.25), residues: 391
  sheet:  None (None), residues: 0
  loop : -2.54 (0.51), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 270 
 TYR   0.023   0.001   TYR B 402 
 PHE   0.022   0.002   PHE B 409 
 TRP   0.008   0.001   TRP B 314 
 HIS   0.023   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4419)
  covalent geometry    : angle       0.68820 ( 5951)
  hydrogen bonds       : bond        0.04799 (  274)
  hydrogen bonds       : angle       4.91051 (  822)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 MET cc_start: 0.6112 (mmt) cc_final: 0.5491 (mmt)
REVERT: B  419 HIS cc_start: 0.8811 (m-70) cc_final: 0.8269 (m90)
REVERT: B  453 MET cc_start: 0.8404 (ppp) cc_final: 0.7974 (ppp)
REVERT: B  486 ASP cc_start: 0.8908 (m-30) cc_final: 0.8620 (m-30)
REVERT: B  548 PHE cc_start: 0.8799 (m-10) cc_final: 0.8502 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0805
  time to fit residues: 4.5729
Evaluate side-chains
  38 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.069279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.059207 restraints weight = 46043.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.060325 restraints weight = 29644.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.061091 restraints weight = 21364.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.061670 restraints weight = 16671.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.062025 restraints weight = 13725.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4419  Z= 0.132
  Angle     :  0.679  11.964   5951  Z= 0.350
  Chirality :  0.044   0.347    652
  Planarity :  0.005   0.068    758
  Dihedral  :  5.422  27.685    579
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.36), residues: 515
  helix:  0.53 (0.25), residues: 391
  sheet:  None (None), residues: 0
  loop : -2.49 (0.52), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 393 
 TYR   0.023   0.002   TYR B 402 
 PHE   0.015   0.001   PHE B 203 
 TRP   0.008   0.001   TRP B 314 
 HIS   0.016   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4419)
  covalent geometry    : angle       0.67906 ( 5951)
  hydrogen bonds       : bond        0.04621 (  274)
  hydrogen bonds       : angle       4.92592 (  822)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 MET cc_start: 0.6224 (mmt) cc_final: 0.5627 (mmt)
REVERT: B  415 TYR cc_start: 0.9014 (m-80) cc_final: 0.8792 (m-80)
REVERT: B  419 HIS cc_start: 0.8834 (m-70) cc_final: 0.8301 (m90)
REVERT: B  453 MET cc_start: 0.8392 (ppp) cc_final: 0.8007 (ppp)
REVERT: B  486 ASP cc_start: 0.8933 (m-30) cc_final: 0.8664 (m-30)
REVERT: B  548 PHE cc_start: 0.8786 (m-10) cc_final: 0.8522 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0716
  time to fit residues: 4.1553
Evaluate side-chains
  38 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
B 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.068246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.058250 restraints weight = 46287.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.059385 restraints weight = 29978.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.060162 restraints weight = 21527.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.060727 restraints weight = 16783.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.061122 restraints weight = 13861.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4419  Z= 0.141
  Angle     :  0.681  11.570   5951  Z= 0.351
  Chirality :  0.044   0.324    652
  Planarity :  0.005   0.069    758
  Dihedral  :  5.463  27.369    579
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.36), residues: 515
  helix:  0.59 (0.25), residues: 391
  sheet:  None (None), residues: 0
  loop : -2.52 (0.52), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 442 
 TYR   0.022   0.002   TYR B 402 
 PHE   0.019   0.002   PHE B 409 
 TRP   0.009   0.001   TRP B 314 
 HIS   0.014   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4419)
  covalent geometry    : angle       0.68138 ( 5951)
  hydrogen bonds       : bond        0.04652 (  274)
  hydrogen bonds       : angle       4.94309 (  822)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: B  267 MET cc_start: 0.6261 (mmt) cc_final: 0.5660 (mmt)
REVERT: B  415 TYR cc_start: 0.9044 (m-80) cc_final: 0.8803 (m-80)
REVERT: B  419 HIS cc_start: 0.8776 (m-70) cc_final: 0.8279 (m90)
REVERT: B  453 MET cc_start: 0.8383 (ppp) cc_final: 0.7996 (ppp)
REVERT: B  486 ASP cc_start: 0.8967 (m-30) cc_final: 0.8716 (m-30)
REVERT: B  548 PHE cc_start: 0.8798 (m-10) cc_final: 0.8558 (m-80)
REVERT: B  549 ARG cc_start: 0.8945 (ptm-80) cc_final: 0.8692 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0745
  time to fit residues: 4.4322
Evaluate side-chains
  39 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.067883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.057948 restraints weight = 46151.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.059019 restraints weight = 30080.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.059783 restraints weight = 21528.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.060344 restraints weight = 16754.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.060729 restraints weight = 13871.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4419  Z= 0.147
  Angle     :  0.688  11.355   5951  Z= 0.356
  Chirality :  0.044   0.310    652
  Planarity :  0.005   0.071    758
  Dihedral  :  5.485  27.427    579
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.36), residues: 515
  helix:  0.61 (0.25), residues: 393
  sheet:  None (None), residues: 0
  loop : -2.63 (0.53), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 442 
 TYR   0.022   0.002   TYR B 402 
 PHE   0.012   0.002   PHE B 203 
 TRP   0.010   0.001   TRP B 314 
 HIS   0.013   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4419)
  covalent geometry    : angle       0.68768 ( 5951)
  hydrogen bonds       : bond        0.04742 (  274)
  hydrogen bonds       : angle       4.94791 (  822)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1030 Ramachandran restraints generated.
    515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: B  415 TYR cc_start: 0.9056 (m-80) cc_final: 0.8825 (m-80)
REVERT: B  419 HIS cc_start: 0.8798 (m-70) cc_final: 0.8274 (m90)
REVERT: B  453 MET cc_start: 0.8387 (ppp) cc_final: 0.8001 (ppp)
REVERT: B  486 ASP cc_start: 0.9001 (m-30) cc_final: 0.8766 (m-30)
REVERT: B  548 PHE cc_start: 0.8802 (m-10) cc_final: 0.8525 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0620
  time to fit residues: 3.6850
Evaluate side-chains
  36 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 HIS
B 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.068890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.058660 restraints weight = 46246.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.059704 restraints weight = 30141.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.060504 restraints weight = 21845.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.061066 restraints weight = 16941.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.061460 restraints weight = 14108.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4419  Z= 0.133
  Angle     :  0.683  11.114   5951  Z= 0.352
  Chirality :  0.044   0.303    652
  Planarity :  0.005   0.071    758
  Dihedral  :  5.427  27.010    579
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.36), residues: 515
  helix:  0.71 (0.26), residues: 393
  sheet:  None (None), residues: 0
  loop : -2.61 (0.53), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 450 
 TYR   0.018   0.002   TYR B 402 
 PHE   0.024   0.002   PHE B 396 
 TRP   0.013   0.001   TRP B 314 
 HIS   0.013   0.001   HIS B 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4419)
  covalent geometry    : angle       0.68303 ( 5951)
  hydrogen bonds       : bond        0.04625 (  274)
  hydrogen bonds       : angle       4.92766 (  822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 864.72 seconds
wall clock time: 15 minutes 38.19 seconds (938.19 seconds total)