Starting phenix.real_space_refine
on Tue Aug  4 13:41:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qw4_18680/08_2026/8qw4_18680.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qw4_18680/08_2026/8qw4_18680.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qw4_18680/08_2026/8qw4_18680.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qw4_18680/08_2026/8qw4_18680.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qw4_18680/08_2026/8qw4_18680.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qw4_18680/08_2026/8qw4_18680.cif"
  }
  resolution = 2.9
  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=  -0.001 sd=   0.019
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      27      5.16       5
     C    2286      2.51       5
     N     564      2.21       5
     O     602      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3479
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 320, 2591
          Classifications: {'peptide': 320}
          Link IDs: {'PTRANS': 13, 'TRANS': 306}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 888
          Classifications: {'peptide': 114}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 111}
          Chain breaks: 1
  Time building chain proxies: 1.01, per 1000 atoms: 0.29
  Number of scatterers: 3479
  At special positions: 0
  Unit cell: (93.072, 57.339, 101.382, 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      27     16.00
     O     602      8.00
     N     564      7.00
     C    2286      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 264 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 286 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  98 " distance=2.02

  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: 0.27
  Conformation dependent library (CDL) restraints added in 127.5 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  808

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 4 sheets defined
      52.5% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 195 through 225
      removed outlier: 3.885A  pdb=" N   LEU A 199 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   GLY A 207 " --> pdb=" O   ARG A 203 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ILE A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   THR A 220 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A 221 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 253
      removed outlier: 3.963A  pdb=" N   PHE A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 283 through 313
      removed outlier: 3.615A  pdb=" N   THR A 287 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   MET A 288 " --> pdb=" O   LYS A 284 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LEU A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE A 290 " --> pdb=" O   CYS A 286 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET A 291 " --> pdb=" O   THR A 287 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   ILE A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE A 295 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 326
    Processing helix  chain 'A' and resid 327 through 345
      Proline residue:  A 339  - end of helix
    Processing helix  chain 'A' and resid 367 through 375
      removed outlier: 3.625A  pdb=" N   LEU A 371 " --> pdb=" O   ASP A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 402
      removed outlier: 4.147A  pdb=" N   SER A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ARG A 399 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   VAL A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   ILE A 402 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 411
    Processing helix  chain 'A' and resid 413 through 443
      removed outlier: 4.077A  pdb=" N   PHE A 417 " --> pdb=" O   LYS A 413 " (cutoff:3.500A)
      Proline residue:  A 431  - end of helix
    Processing helix  chain 'A' and resid 445 through 452
      removed outlier: 3.647A  pdb=" N   TRP A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLU A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   THR A 451 " --> pdb=" O   GLY A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.533A  pdb=" N   LEU A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 489
      removed outlier: 3.598A  pdb=" N   TYR A 484 " --> pdb=" O   PHE A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 493
      Proline residue:  A 493  - end of helix
      No H-bonds generated for 'chain 'A' and resid 490 through 493'
    Processing helix  chain 'A' and resid 494 through 499
    Processing helix  chain 'B' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178
      removed outlier: 6.357A  pdb=" N   TYR A 177 " --> pdb=" O   CYS A 185 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 27
      removed outlier: 4.382A  pdb=" N   ASP B  79 " --> pdb=" O   ALA B  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62
      removed outlier: 6.821A  pdb=" N   TRP B  39 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   ASP B  53 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   MET B  37 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL B  36 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 94 through 95

    156 hydrogen bonds defined for protein.
    438 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: 0.51

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1034
        1.34 -     1.46: 921
        1.46 -     1.59: 1564
        1.59 -     1.71: 0
        1.71 -     1.83: 41
  Bond restraints: 3560
  Sorted by residual:
  bond pdb=" N   GLU A 407 "
       pdb=" CA  GLU A 407 "
    ideal  model  delta    sigma   weight residual
    1.460  1.486 -0.026 1.50e-02 4.44e+03 2.99e+00
  bond pdb=" C   ASP A 476 "
       pdb=" N   LEU A 477 "
    ideal  model  delta    sigma   weight residual
    1.331  1.307  0.024 1.40e-02 5.10e+03 2.97e+00
  bond pdb=" C   LEU A 406 "
       pdb=" N   GLU A 407 "
    ideal  model  delta    sigma   weight residual
    1.330  1.351 -0.021 1.28e-02 6.10e+03 2.77e+00
  bond pdb=" CB  THR A 276 "
       pdb=" CG2 THR A 276 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.63e+00
  bond pdb=" CB  TYR A 177 "
       pdb=" CG  TYR A 177 "
    ideal  model  delta    sigma   weight residual
    1.512  1.477  0.035 2.20e-02 2.07e+03 2.48e+00
  ... (remaining 3555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 4614
        2.38 -     4.76: 169
        4.76 -     7.14: 31
        7.14 -     9.52: 5
        9.52 -    11.91: 3
  Bond angle restraints: 4822
  Sorted by residual:
  angle pdb=" C   GLU A 235 "
        pdb=" N   ARG A 236 "
        pdb=" CA  ARG A 236 "
      ideal   model   delta    sigma   weight residual
     120.09  125.89   -5.80 1.25e+00 6.40e-01 2.15e+01
  angle pdb=" N   ARG A 459 "
        pdb=" CA  ARG A 459 "
        pdb=" C   ARG A 459 "
      ideal   model   delta    sigma   weight residual
     110.80  101.02    9.78 2.13e+00 2.20e-01 2.11e+01
  angle pdb=" N   GLY A 354 "
        pdb=" CA  GLY A 354 "
        pdb=" C   GLY A 354 "
      ideal   model   delta    sigma   weight residual
     112.13  118.02   -5.89 1.34e+00 5.57e-01 1.93e+01
  angle pdb=" C   ALA B  43 "
        pdb=" N   PRO B  44 "
        pdb=" CA  PRO B  44 "
      ideal   model   delta    sigma   weight residual
     127.00  136.73   -9.73 2.40e+00 1.74e-01 1.64e+01
  angle pdb=" C   CYS A 458 "
        pdb=" N   ARG A 459 "
        pdb=" CA  ARG A 459 "
      ideal   model   delta    sigma   weight residual
     121.54  129.22   -7.68 1.91e+00 2.74e-01 1.62e+01
  ... (remaining 4817 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 1877
       16.29 -    32.57: 177
       32.57 -    48.86: 30
       48.86 -    65.14: 4
       65.14 -    81.43: 6
  Dihedral angle restraints: 2094
    sinusoidal: 837
      harmonic: 1257
  Sorted by residual:
  dihedral pdb=" CB  CYS A 189 "
           pdb=" SG  CYS A 189 "
           pdb=" SG  CYS A 264 "
           pdb=" CB  CYS A 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.10   71.10     1      1.00e+01 1.00e-02 6.49e+01
  dihedral pdb=" CA  TYR A 177 "
           pdb=" C   TYR A 177 "
           pdb=" N   SER A 178 "
           pdb=" CA  SER A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.73  -34.27     0      5.00e+00 4.00e-02 4.70e+01
  dihedral pdb=" CA  SER A 178 "
           pdb=" C   SER A 178 "
           pdb=" N   PHE A 179 "
           pdb=" CA  PHE A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.92  -33.08     0      5.00e+00 4.00e-02 4.38e+01
  ... (remaining 2091 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 361
       0.048 -    0.096: 136
       0.096 -    0.144: 34
       0.144 -    0.192: 17
       0.192 -    0.241: 2
  Chirality restraints: 550
  Sorted by residual:
  chirality pdb=" CA  VAL A 316 "
            pdb=" N   VAL A 316 "
            pdb=" C   VAL A 316 "
            pdb=" CB  VAL A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.20    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CA  PRO B  90 "
            pdb=" N   PRO B  90 "
            pdb=" C   PRO B  90 "
            pdb=" CB  PRO B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  PRO A 405 "
            pdb=" N   PRO A 405 "
            pdb=" C   PRO A 405 "
            pdb=" CB  PRO A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 9.11e-01
  ... (remaining 547 not shown)

  Planarity restraints: 587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 316 "   -0.077 5.00e-02 4.00e+02   1.16e-01 2.14e+01
        pdb=" N   PRO A 317 "    0.200 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 474 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.47e+00
        pdb=" N   PRO A 475 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 475 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 475 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 428 "    0.010 2.00e-02 2.50e+03   1.41e-02 3.99e+00
        pdb=" CG  TYR A 428 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 428 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 428 "    0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 428 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 428 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 428 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 428 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 584 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 75
        2.65 -     3.21: 3457
        3.21 -     3.78: 5258
        3.78 -     4.34: 7053
        4.34 -     4.90: 11275
  Nonbonded interactions: 27118
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 455 "
            pdb=" NH2 ARG A 459 "
     model   vdw
     2.091 3.120
  nonbonded pdb=" OH  TYR A 241 "
            pdb=" O   VAL A 490 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ASN A 410 "
            pdb=" N   LYS A 413 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   ASP A 260 "
            pdb=" NH1 ARG A 261 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   THR A 217 "
            pdb=" OG1 THR A 220 "
     model   vdw
     2.300 3.040
  ... (remaining 27113 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
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:             7.080
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.470
  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:6.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6381
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      :  0.007   0.057   3564  Z= 0.338
  Angle     :  1.104  11.906   4830  Z= 0.610
  Chirality :  0.058   0.241    550
  Planarity :  0.008   0.116    587
  Dihedral  : 13.197  81.429   1274
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.05 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.00 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

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: -3.29 (0.39), residues: 420
  helix: -0.99 (0.37), residues: 189
  sheet: -1.69 (0.86), residues: 38
  loop : -3.62 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  41 
 TYR   0.034   0.003   TYR A 428 
 PHE   0.020   0.003   PHE A 201 
 TRP   0.013   0.002   TRP B 104 
 HIS   0.003   0.001   HIS A 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00748 /  0.34 ( 3560)
  covalent geometry    : angle       1.09835 /  0.61 ( 4822)
  SS BOND              : bond        0.00704 /  0.35 (    4)
  SS BOND              : angle       3.02074 /  1.62 (    8)
  hydrogen bonds       : bond        0.16799 / 11.22 (  156)
  hydrogen bonds       : angle       6.60400 /  4.67 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6980 (tpt90) cc_final: 0.5436 (mtp180)
REVERT: A  336 TRP cc_start: 0.7890 (m100) cc_final: 0.7653 (m-10)
REVERT: A  349 MET cc_start: 0.4417 (mmt) cc_final: 0.3585 (ptt)
REVERT: A  442 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6693 (mp0)
REVERT: B   35 ASP cc_start: 0.7720 (m-30) cc_final: 0.7504 (m-30)
REVERT: B   55 THR cc_start: 0.7761 (p) cc_final: 0.7497 (m)
  outliers start: 1
  outliers final: 2
  residues processed: 119
  average time/residue: 0.5611
  time to fit residues: 68.6880
Evaluate side-chains
  67 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  352 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.2980
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.3380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 GLN ** 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 = 0.4526 r_free = 0.4526 target = 0.186725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.171095 restraints weight = 8096.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.4373 rms_B_bonded: 3.58
r_work: 0.4278 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3564  Z= 0.173
  Angle     :  0.862   8.097   4830  Z= 0.438
  Chirality :  0.049   0.188    550
  Planarity :  0.007   0.069    587
  Dihedral  :  7.291  36.516    478
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 17.94 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.79 (0.39), residues: 420
  helix: -0.69 (0.38), residues: 188
  sheet: -1.03 (0.85), residues: 38
  loop : -3.31 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 372 
 TYR   0.016   0.002   TYR A 445 
 PHE   0.025   0.002   PHE B  32 
 TRP   0.014   0.002   TRP A 449 
 HIS   0.001   0.001   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.17 ( 3560)
  covalent geometry    : angle       0.86171 /  0.44 ( 4822)
  SS BOND              : bond        0.00230 /  0.11 (    4)
  SS BOND              : angle       1.16149 /  0.60 (    8)
  hydrogen bonds       : bond        0.05012 /  3.13 (  156)
  hydrogen bonds       : angle       5.33947 /  3.78 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.081 
Fit side-chains
REVERT: A  203 ARG cc_start: 0.6683 (tpt90) cc_final: 0.5183 (mtp180)
REVERT: A  291 MET cc_start: 0.6511 (ptt) cc_final: 0.6225 (pmm)
REVERT: A  336 TRP cc_start: 0.8470 (m100) cc_final: 0.7681 (m-10)
REVERT: A  349 MET cc_start: 0.4920 (mmt) cc_final: 0.3455 (ptt)
REVERT: A  367 ASP cc_start: 0.7844 (t0) cc_final: 0.7539 (t0)
REVERT: A  415 VAL cc_start: 0.5976 (OUTLIER) cc_final: 0.4867 (t)
REVERT: A  445 TYR cc_start: 0.6674 (t80) cc_final: 0.6394 (t80)
REVERT: B   35 ASP cc_start: 0.8701 (m-30) cc_final: 0.8437 (m-30)
REVERT: B  109 TYR cc_start: 0.7746 (m-80) cc_final: 0.7360 (m-80)
  outliers start: 18
  outliers final: 5
  residues processed: 83
  average time/residue: 0.4178
  time to fit residues: 35.9459
Evaluate side-chains
  73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  213 CYS
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    0.1980
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 24 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 37 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0270
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.3038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 265 ASN
A 279 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.187631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.171893 restraints weight = 8071.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.4381 rms_B_bonded: 3.71
r_work: 0.4284 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3564  Z= 0.156
  Angle     :  0.797   8.294   4830  Z= 0.405
  Chirality :  0.048   0.284    550
  Planarity :  0.006   0.059    587
  Dihedral  :  6.731  34.580    476
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.43 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.60 (0.40), residues: 420
  helix: -0.46 (0.38), residues: 189
  sheet: -1.05 (0.82), residues: 36
  loop : -3.26 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 183 
 TYR   0.019   0.002   TYR A 428 
 PHE   0.021   0.002   PHE B  32 
 TRP   0.022   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 3560)
  covalent geometry    : angle       0.79687 /  0.41 ( 4822)
  SS BOND              : bond        0.00200 /  0.10 (    4)
  SS BOND              : angle       0.83268 /  0.39 (    8)
  hydrogen bonds       : bond        0.04489 /  2.80 (  156)
  hydrogen bonds       : angle       5.11736 /  3.59 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6640 (tpt90) cc_final: 0.5214 (tpt-90)
REVERT: A  243 VAL cc_start: 0.8885 (m) cc_final: 0.8684 (p)
REVERT: A  336 TRP cc_start: 0.8359 (m100) cc_final: 0.7572 (m-10)
REVERT: A  349 MET cc_start: 0.4820 (mmt) cc_final: 0.3420 (ptt)
REVERT: A  367 ASP cc_start: 0.7697 (t0) cc_final: 0.7222 (t0)
REVERT: A  415 VAL cc_start: 0.5817 (OUTLIER) cc_final: 0.4639 (t)
REVERT: A  433 LEU cc_start: 0.8154 (tm) cc_final: 0.7648 (pp)
REVERT: A  480 PHE cc_start: 0.7968 (m-10) cc_final: 0.7656 (m-80)
REVERT: B   35 ASP cc_start: 0.8856 (m-30) cc_final: 0.8550 (m-30)
REVERT: B  109 TYR cc_start: 0.7784 (m-80) cc_final: 0.7470 (m-80)
  outliers start: 14
  outliers final: 4
  residues processed: 86
  average time/residue: 0.4090
  time to fit residues: 36.5669
Evaluate side-chains
  66 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 6 optimal weight:    0.1980
   chunk 27 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0470
   chunk 38 optimal weight:    0.0980
   overall best weight:    0.3278

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.187784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.172852 restraints weight = 8175.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.4386 rms_B_bonded: 3.53
r_work: 0.4294 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3564  Z= 0.149
  Angle     :  0.789   9.541   4830  Z= 0.391
  Chirality :  0.046   0.179    550
  Planarity :  0.005   0.059    587
  Dihedral  :  6.236  24.730    473
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 25.59 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.34 (0.40), residues: 420
  helix: -0.28 (0.38), residues: 189
  sheet: -0.82 (0.85), residues: 36
  loop : -3.09 (0.42), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 183 
 TYR   0.022   0.002   TYR A 428 
 PHE   0.016   0.002   PHE B  32 
 TRP   0.012   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 ( 3560)
  covalent geometry    : angle       0.78927 /  0.39 ( 4822)
  SS BOND              : bond        0.00182 /  0.09 (    4)
  SS BOND              : angle       0.61060 /  0.28 (    8)
  hydrogen bonds       : bond        0.04267 /  2.70 (  156)
  hydrogen bonds       : angle       4.97917 /  3.50 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6638 (tpt90) cc_final: 0.5198 (tpt-90)
REVERT: A  349 MET cc_start: 0.4796 (mmt) cc_final: 0.3735 (ptt)
REVERT: A  415 VAL cc_start: 0.5727 (OUTLIER) cc_final: 0.4443 (t)
REVERT: A  433 LEU cc_start: 0.8331 (tm) cc_final: 0.7779 (pp)
REVERT: A  445 TYR cc_start: 0.6448 (t80) cc_final: 0.6183 (t80)
REVERT: A  482 MET cc_start: 0.7152 (pp-130) cc_final: 0.6940 (mtt)
REVERT: B   35 ASP cc_start: 0.8806 (m-30) cc_final: 0.8510 (m-30)
REVERT: B  109 TYR cc_start: 0.7775 (m-80) cc_final: 0.7477 (m-80)
  outliers start: 20
  outliers final: 7
  residues processed: 85
  average time/residue: 0.4073
  time to fit residues: 36.1170
Evaluate side-chains
  72 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 40 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.7495 > 50:)
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.183455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.167797 restraints weight = 8021.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.4349 rms_B_bonded: 3.66
r_work: 0.4253 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6716
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3564  Z= 0.188
  Angle     :  0.856  10.362   4830  Z= 0.419
  Chirality :  0.048   0.171    550
  Planarity :  0.005   0.059    587
  Dihedral  :  6.420  27.727    473
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 26.65 %
    Favored  : 66.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.26 (0.41), residues: 420
  helix: -0.30 (0.38), residues: 189
  sheet: -0.62 (0.88), residues: 36
  loop : -2.98 (0.44), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 183 
 TYR   0.020   0.002   TYR A 204 
 PHE   0.022   0.002   PHE A 224 
 TRP   0.013   0.002   TRP A 449 
 HIS   0.002   0.001   HIS A 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.19 ( 3560)
  covalent geometry    : angle       0.85663 /  0.42 ( 4822)
  SS BOND              : bond        0.00270 /  0.14 (    4)
  SS BOND              : angle       0.71861 /  0.33 (    8)
  hydrogen bonds       : bond        0.04351 /  2.75 (  156)
  hydrogen bonds       : angle       5.01497 /  3.49 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5246 (tpt-90)
REVERT: A  336 TRP cc_start: 0.8369 (m100) cc_final: 0.7549 (m-10)
REVERT: A  349 MET cc_start: 0.5068 (mmt) cc_final: 0.3601 (ptt)
REVERT: A  367 ASP cc_start: 0.8022 (t0) cc_final: 0.7809 (t0)
REVERT: A  415 VAL cc_start: 0.6154 (OUTLIER) cc_final: 0.4948 (t)
REVERT: A  433 LEU cc_start: 0.8387 (tm) cc_final: 0.7827 (pp)
REVERT: A  445 TYR cc_start: 0.6594 (t80) cc_final: 0.6361 (t80)
REVERT: A  482 MET cc_start: 0.7303 (pp-130) cc_final: 0.6990 (mtt)
REVERT: A  501 LYS cc_start: 0.8799 (tppp) cc_final: 0.8389 (mmmt)
REVERT: B   35 ASP cc_start: 0.8885 (m-30) cc_final: 0.8592 (m-30)
REVERT: B  103 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8034 (tp30)
REVERT: B  109 TYR cc_start: 0.7832 (m-80) cc_final: 0.7487 (m-80)
  outliers start: 27
  outliers final: 13
  residues processed: 85
  average time/residue: 0.4349
  time to fit residues: 38.2242
Evaluate side-chains
  78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 16 optimal weight:    0.0980
   chunk 17 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.184698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.169047 restraints weight = 7901.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.4353 rms_B_bonded: 3.60
r_work: 0.4258 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.4258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3564  Z= 0.160
  Angle     :  0.843   9.924   4830  Z= 0.413
  Chirality :  0.047   0.174    550
  Planarity :  0.005   0.060    587
  Dihedral  :  6.265  27.618    473
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 26.91 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.21 (0.41), residues: 420
  helix: -0.27 (0.39), residues: 189
  sheet: -0.53 (0.86), residues: 35
  loop : -2.95 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 183 
 TYR   0.021   0.002   TYR A 428 
 PHE   0.013   0.002   PHE A 253 
 TRP   0.008   0.001   TRP A 449 
 HIS   0.002   0.001   HIS A 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 ( 3560)
  covalent geometry    : angle       0.84381 /  0.41 ( 4822)
  SS BOND              : bond        0.00254 /  0.13 (    4)
  SS BOND              : angle       0.60910 /  0.28 (    8)
  hydrogen bonds       : bond        0.04280 /  2.70 (  156)
  hydrogen bonds       : angle       5.02178 /  3.50 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7773 (mm)
REVERT: A  203 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5245 (tpt-90)
REVERT: A  250 LEU cc_start: 0.8108 (tt) cc_final: 0.7903 (tt)
REVERT: A  349 MET cc_start: 0.5006 (mmt) cc_final: 0.3593 (ptt)
REVERT: A  367 ASP cc_start: 0.7990 (t0) cc_final: 0.7727 (t0)
REVERT: A  415 VAL cc_start: 0.6129 (OUTLIER) cc_final: 0.4826 (t)
REVERT: A  433 LEU cc_start: 0.8382 (tm) cc_final: 0.7823 (pp)
REVERT: A  445 TYR cc_start: 0.6620 (t80) cc_final: 0.6360 (t80)
REVERT: A  482 MET cc_start: 0.7357 (pp-130) cc_final: 0.7072 (mtt)
REVERT: A  501 LYS cc_start: 0.8780 (tppp) cc_final: 0.8422 (mmmt)
REVERT: B   35 ASP cc_start: 0.8838 (m-30) cc_final: 0.8552 (m-30)
REVERT: B  103 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7992 (tp30)
REVERT: B  109 TYR cc_start: 0.7829 (m-80) cc_final: 0.7468 (m-80)
  outliers start: 21
  outliers final: 10
  residues processed: 80
  average time/residue: 0.4093
  time to fit residues: 34.1177
Evaluate side-chains
  75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0370
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    0.1980
   chunk 1 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0670
   chunk 3 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.2996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.185398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.169832 restraints weight = 8013.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.4360 rms_B_bonded: 3.65
r_work: 0.4264 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.4618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3564  Z= 0.148
  Angle     :  0.835  10.629   4830  Z= 0.409
  Chirality :  0.046   0.175    550
  Planarity :  0.005   0.061    587
  Dihedral  :  6.086  27.796    473
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 27.18 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.12 (0.42), residues: 420
  helix: -0.16 (0.39), residues: 189
  sheet: -0.48 (0.86), residues: 35
  loop : -2.96 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 183 
 TYR   0.029   0.002   TYR A 428 
 PHE   0.015   0.002   PHE A 240 
 TRP   0.007   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 3560)
  covalent geometry    : angle       0.83574 /  0.41 ( 4822)
  SS BOND              : bond        0.00264 /  0.13 (    4)
  SS BOND              : angle       0.59995 /  0.28 (    8)
  hydrogen bonds       : bond        0.04215 /  2.67 (  156)
  hydrogen bonds       : angle       4.99917 /  3.47 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7757 (mm)
REVERT: A  203 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5216 (tpt-90)
REVERT: A  250 LEU cc_start: 0.8054 (tt) cc_final: 0.7743 (tt)
REVERT: A  349 MET cc_start: 0.4983 (mmt) cc_final: 0.3617 (ptt)
REVERT: A  367 ASP cc_start: 0.7880 (t0) cc_final: 0.7670 (t0)
REVERT: A  415 VAL cc_start: 0.6029 (OUTLIER) cc_final: 0.4702 (t)
REVERT: A  433 LEU cc_start: 0.8340 (tm) cc_final: 0.7809 (pp)
REVERT: A  445 TYR cc_start: 0.6682 (t80) cc_final: 0.6412 (t80)
REVERT: A  482 MET cc_start: 0.7327 (pp-130) cc_final: 0.7090 (mtt)
REVERT: A  501 LYS cc_start: 0.8709 (tppp) cc_final: 0.8404 (mmmt)
REVERT: B   35 ASP cc_start: 0.8844 (m-30) cc_final: 0.8555 (m-30)
REVERT: B  103 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7990 (tp30)
REVERT: B  109 TYR cc_start: 0.7809 (m-80) cc_final: 0.7519 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 81
  average time/residue: 0.4331
  time to fit residues: 36.4135
Evaluate side-chains
  76 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0870
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0050
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.3572

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.184539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.169160 restraints weight = 8103.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.4358 rms_B_bonded: 3.69
r_work: 0.4260 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3564  Z= 0.158
  Angle     :  0.863  11.423   4830  Z= 0.417
  Chirality :  0.047   0.173    550
  Planarity :  0.005   0.061    587
  Dihedral  :  6.023  27.394    473
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 27.18 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.10 (0.42), residues: 420
  helix: -0.11 (0.39), residues: 189
  sheet: -0.58 (0.83), residues: 35
  loop : -2.96 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 183 
 TYR   0.032   0.002   TYR A 428 
 PHE   0.022   0.002   PHE A 240 
 TRP   0.006   0.001   TRP A 311 
 HIS   0.001   0.000   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 ( 3560)
  covalent geometry    : angle       0.86327 /  0.42 ( 4822)
  SS BOND              : bond        0.00206 /  0.10 (    4)
  SS BOND              : angle       0.60929 /  0.28 (    8)
  hydrogen bonds       : bond        0.04095 /  2.60 (  156)
  hydrogen bonds       : angle       4.96327 /  3.45 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7696 (mm)
REVERT: A  203 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5207 (tpt-90)
REVERT: A  250 LEU cc_start: 0.8027 (tt) cc_final: 0.7701 (tt)
REVERT: A  325 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8127 (mt-10)
REVERT: A  349 MET cc_start: 0.4900 (mmt) cc_final: 0.3678 (ptt)
REVERT: A  367 ASP cc_start: 0.7859 (t0) cc_final: 0.7614 (t0)
REVERT: A  433 LEU cc_start: 0.8263 (tm) cc_final: 0.7739 (pp)
REVERT: A  445 TYR cc_start: 0.6629 (t80) cc_final: 0.6383 (t80)
REVERT: A  482 MET cc_start: 0.7288 (pp-130) cc_final: 0.7041 (mtt)
REVERT: B   35 ASP cc_start: 0.8840 (m-30) cc_final: 0.8564 (m-30)
REVERT: B  103 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8049 (tp30)
REVERT: B  109 TYR cc_start: 0.7817 (m-80) cc_final: 0.7469 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 78
  average time/residue: 0.4433
  time to fit residues: 35.8565
Evaluate side-chains
  74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue   37 MET
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    0.0870
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.3758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.184830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.169917 restraints weight = 7890.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.4362 rms_B_bonded: 3.62
r_work: 0.4265 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.4265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.4962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3564  Z= 0.160
  Angle     :  0.890  12.069   4830  Z= 0.430
  Chirality :  0.046   0.173    550
  Planarity :  0.005   0.061    587
  Dihedral  :  5.985  27.884    473
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 27.70 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.06 (0.42), residues: 420
  helix: -0.07 (0.39), residues: 189
  sheet: -0.47 (0.84), residues: 35
  loop : -2.95 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 183 
 TYR   0.032   0.002   TYR A 428 
 PHE   0.021   0.002   PHE A 240 
 TRP   0.014   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.16 ( 3560)
  covalent geometry    : angle       0.89085 /  0.43 ( 4822)
  SS BOND              : bond        0.00208 /  0.10 (    4)
  SS BOND              : angle       0.64216 /  0.31 (    8)
  hydrogen bonds       : bond        0.03960 /  2.51 (  156)
  hydrogen bonds       : angle       4.99896 /  3.46 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 LEU cc_start: 0.7507 (mt) cc_final: 0.7226 (mt)
REVERT: A  199 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7696 (mm)
REVERT: A  203 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5209 (tpt-90)
REVERT: A  325 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8158 (mt-10)
REVERT: A  349 MET cc_start: 0.4906 (mmt) cc_final: 0.3456 (ptt)
REVERT: A  433 LEU cc_start: 0.8262 (tm) cc_final: 0.7745 (pp)
REVERT: A  445 TYR cc_start: 0.6753 (t80) cc_final: 0.6543 (t80)
REVERT: B  103 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8124 (tp30)
REVERT: B  109 TYR cc_start: 0.7776 (m-80) cc_final: 0.7438 (m-80)
  outliers start: 20
  outliers final: 10
  residues processed: 75
  average time/residue: 0.4150
  time to fit residues: 32.2777
Evaluate side-chains
  74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  286 CYS
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 2 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   overall best weight:    0.5980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.182149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.167233 restraints weight = 8151.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.4338 rms_B_bonded: 3.64
r_work: 0.4240 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.5082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3564  Z= 0.187
  Angle     :  0.978  12.744   4830  Z= 0.468
  Chirality :  0.048   0.170    550
  Planarity :  0.005   0.063    587
  Dihedral  :  6.185  28.650    473
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 30.61 %
    Favored  : 65.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.12 (0.41), residues: 420
  helix: -0.12 (0.39), residues: 190
  sheet: -0.53 (0.84), residues: 35
  loop : -3.00 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 183 
 TYR   0.032   0.002   TYR A 428 
 PHE   0.010   0.002   PHE A 240 
 TRP   0.015   0.002   TRP A 449 
 HIS   0.001   0.000   HIS A 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.19 ( 3560)
  covalent geometry    : angle       0.97840 /  0.47 ( 4822)
  SS BOND              : bond        0.00277 /  0.14 (    4)
  SS BOND              : angle       0.64781 /  0.29 (    8)
  hydrogen bonds       : bond        0.04021 /  2.53 (  156)
  hydrogen bonds       : angle       5.05428 /  3.49 (  438)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7633 (mm)
REVERT: A  203 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5204 (tpt-90)
REVERT: A  279 GLN cc_start: 0.6317 (tm-30) cc_final: 0.5841 (tm-30)
REVERT: A  325 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8202 (mt-10)
REVERT: A  336 TRP cc_start: 0.8321 (m100) cc_final: 0.7419 (m-10)
REVERT: A  349 MET cc_start: 0.4945 (mmt) cc_final: 0.3567 (ptt)
REVERT: A  433 LEU cc_start: 0.8301 (tm) cc_final: 0.7767 (pp)
REVERT: A  482 MET cc_start: 0.5994 (mtt) cc_final: 0.5518 (pp-130)
REVERT: B   35 ASP cc_start: 0.8800 (m-30) cc_final: 0.8534 (m-30)
REVERT: B  103 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8099 (tp30)
REVERT: B  109 TYR cc_start: 0.7843 (m-80) cc_final: 0.7525 (m-80)
  outliers start: 15
  outliers final: 8
  residues processed: 73
  average time/residue: 0.4280
  time to fit residues: 32.4718
Evaluate side-chains
  74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  108 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0770
   chunk 16 optimal weight:    0.0270
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.3996

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.183476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.168496 restraints weight = 8093.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.4349 rms_B_bonded: 3.65
r_work: 0.4251 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.5206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3564  Z= 0.168
  Angle     :  0.959  14.272   4830  Z= 0.458
  Chirality :  0.048   0.180    550
  Planarity :  0.005   0.062    587
  Dihedral  :  6.057  28.585    473
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 31.13 %
    Favored  : 65.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -2.14 (0.41), residues: 420
  helix: -0.09 (0.39), residues: 186
  sheet: -0.64 (0.86), residues: 35
  loop : -3.00 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 183 
 TYR   0.029   0.002   TYR A 428 
 PHE   0.013   0.002   PHE A 296 
 TRP   0.014   0.001   TRP A 449 
 HIS   0.001   0.000   HIS A 181 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.17 ( 3560)
  covalent geometry    : angle       0.95933 /  0.46 ( 4822)
  SS BOND              : bond        0.00207 /  0.10 (    4)
  SS BOND              : angle       0.76323 /  0.38 (    8)
  hydrogen bonds       : bond        0.04007 /  2.51 (  156)
  hydrogen bonds       : angle       5.07925 /  3.49 (  438)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1746.96 seconds
wall clock time: 30 minutes 30.24 seconds (1830.24 seconds total)