Starting phenix.real_space_refine
on Fri Oct 10 11:32:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jtz_36657/10_2025/8jtz_36657.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jtz_36657/10_2025/8jtz_36657.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jtz_36657/10_2025/8jtz_36657.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jtz_36657/10_2025/8jtz_36657.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jtz_36657/10_2025/8jtz_36657.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jtz_36657/10_2025/8jtz_36657.map"
  }
  resolution = 3.27
  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=   0.086
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      34      5.16       5
     C    2620      2.51       5
     N     650      2.21       5
     O     695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3999
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 530, 3970
          Classifications: {'peptide': 530}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 27, 'TRANS': 502}
          Unresolved non-hydrogen bonds: 146
          Unresolved non-hydrogen angles: 190
          Unresolved non-hydrogen dihedrals: 123
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 92
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'SNL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.41, per 1000 atoms: 0.35
  Number of scatterers: 3999
  At special positions: 0
  Unit cell: (111.498, 55.2075, 66.0325, 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      34     16.00
     O     695      8.00
     N     650      7.00
     C    2620      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 142 " distance=2.03

  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: 0.35
  Conformation dependent library (CDL) restraints added in 183.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  974

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      74.3% alpha, 1.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 12
    Processing helix  chain 'A' and resid 15 through 31
      removed outlier: 4.391A  pdb=" N   LEU A  28 " --> pdb=" O   ILE A  24 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   SER A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 52 through 63
      removed outlier: 3.824A  pdb=" N   ALA A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU A  57 " --> pdb=" O   PRO A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 74
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 144 through 147
    Processing helix  chain 'A' and resid 148 through 194
      removed outlier: 4.351A  pdb=" N   GLN A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ARG A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   LYS A 176 " --> pdb=" O   ARG A 172 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LEU A 177 " --> pdb=" O   PHE A 173 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   CYS A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 228
      removed outlier: 3.518A  pdb=" N   MET A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   LYS A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL A 228 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 258
      removed outlier: 3.696A  pdb=" N   MET A 239 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLN A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   MET A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA A 243 " --> pdb=" O   MET A 239 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 269
    Processing helix  chain 'A' and resid 269 through 278
      removed outlier: 3.866A  pdb=" N   PHE A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 291
    Processing helix  chain 'A' and resid 294 through 310
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 4.087A  pdb=" N   LYS A 318 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 368
      removed outlier: 4.022A  pdb=" N   MET A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 384
    Processing helix  chain 'A' and resid 385 through 397
      removed outlier: 4.437A  pdb=" N   GLY A 389 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 420
    Processing helix  chain 'A' and resid 427 through 456
      removed outlier: 3.766A  pdb=" N   ASN A 431 " --> pdb=" O   LEU A 427 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA A 454 " --> pdb=" O   CYS A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 470
    Processing helix  chain 'A' and resid 470 through 491
      removed outlier: 4.337A  pdb=" N   ASP A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ILE A 475 " --> pdb=" O   SER A 471 " (cutoff:3.500A)
      Proline residue:  A 481  - end of helix
    Processing helix  chain 'A' and resid 493 through 510
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 524 through 530
      removed outlier: 3.872A  pdb=" N   ALA A 528 " --> pdb=" O   THR A 524 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLU A 529 " --> pdb=" O   MET A 525 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50
      removed outlier: 3.723A  pdb=" N   HIS A  49 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A 126 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91

    260 hydrogen bonds defined for protein.
    771 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: 0.64

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 625
        1.31 -     1.44: 1085
        1.44 -     1.57: 2338
        1.57 -     1.69: 2
        1.69 -     1.82: 50
  Bond restraints: 4100
  Sorted by residual:
  bond pdb=" C15 SNL A 601 "
       pdb=" O58 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.553 -0.221 2.00e-02 2.50e+03 1.22e+02
  bond pdb=" C22 SNL A 601 "
       pdb=" S61 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.829  1.676  0.153 2.00e-02 2.50e+03 5.86e+01
  bond pdb=" C16 SNL A 601 "
       pdb=" S61 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.767  1.677  0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" C9  SNL A 601 "
       pdb=" O58 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.443  1.527 -0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" C18 SNL A 601 "
       pdb=" C19 SNL A 601 "
    ideal  model  delta    sigma   weight residual
    1.463  1.536 -0.073 2.00e-02 2.50e+03 1.34e+01
  ... (remaining 4095 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.24: 5521
        3.24 -     6.49: 68
        6.49 -     9.73: 11
        9.73 -    12.98: 1
       12.98 -    16.22: 2
  Bond angle restraints: 5603
  Sorted by residual:
  angle pdb=" C13 SNL A 601 "
        pdb=" C9  SNL A 601 "
        pdb=" C5  SNL A 601 "
      ideal   model   delta    sigma   weight residual
     116.85  133.07  -16.22 3.00e+00 1.11e-01 2.92e+01
  angle pdb=" C8  SNL A 601 "
        pdb=" C9  SNL A 601 "
        pdb=" O58 SNL A 601 "
      ideal   model   delta    sigma   weight residual
     111.01   97.51   13.50 3.00e+00 1.11e-01 2.03e+01
  angle pdb=" N   CYS A  26 "
        pdb=" CA  CYS A  26 "
        pdb=" C   CYS A  26 "
      ideal   model   delta    sigma   weight residual
     113.01  108.27    4.74 1.20e+00 6.94e-01 1.56e+01
  angle pdb=" N   GLU A 529 "
        pdb=" CA  GLU A 529 "
        pdb=" C   GLU A 529 "
      ideal   model   delta    sigma   weight residual
     112.54  107.82    4.72 1.22e+00 6.72e-01 1.50e+01
  angle pdb=" CB  MET A 448 "
        pdb=" CG  MET A 448 "
        pdb=" SD  MET A 448 "
      ideal   model   delta    sigma   weight residual
     112.70  123.89  -11.19 3.00e+00 1.11e-01 1.39e+01
  ... (remaining 5598 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 2152
       17.28 -    34.57: 229
       34.57 -    51.85: 66
       51.85 -    69.13: 13
       69.13 -    86.42: 2
  Dihedral angle restraints: 2462
    sinusoidal: 944
      harmonic: 1518
  Sorted by residual:
  dihedral pdb=" CB  CYS A  50 "
           pdb=" SG  CYS A  50 "
           pdb=" SG  CYS A 121 "
           pdb=" CB  CYS A 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -137.58   51.58     1      1.00e+01 1.00e-02 3.63e+01
  dihedral pdb=" CA  VAL A 461 "
           pdb=" C   VAL A 461 "
           pdb=" N   ARG A 462 "
           pdb=" CA  ARG A 462 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.37  -21.63     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CB  CYS A  88 "
           pdb=" SG  CYS A  88 "
           pdb=" SG  CYS A 142 "
           pdb=" CB  CYS A 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  126.86  -33.86     1      1.00e+01 1.00e-02 1.63e+01
  ... (remaining 2459 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.140: 650
       0.140 -    0.280: 7
       0.280 -    0.420: 0
       0.420 -    0.560: 0
       0.560 -    0.700: 2
  Chirality restraints: 659
  Sorted by residual:
  chirality pdb=" C9  SNL A 601 "
            pdb=" C13 SNL A 601 "
            pdb=" C5  SNL A 601 "
            pdb=" C8  SNL A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.67   -1.97   -0.70 2.00e-01 2.50e+01 1.22e+01
  chirality pdb=" C2  SNL A 601 "
            pdb=" C1  SNL A 601 "
            pdb=" C20 SNL A 601 "
            pdb=" C24 SNL A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.82   -2.22   -0.59 2.00e-01 2.50e+01 8.84e+00
  chirality pdb=" CG  LEU A 192 "
            pdb=" CB  LEU A 192 "
            pdb=" CD1 LEU A 192 "
            pdb=" CD2 LEU A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 656 not shown)

  Planarity restraints: 699
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 340 "   -0.035 5.00e-02 4.00e+02   5.25e-02 4.41e+00
        pdb=" N   PRO A 341 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 279 "   -0.008 2.00e-02 2.50e+03   1.37e-02 3.76e+00
        pdb=" CG  TYR A 279 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 279 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 279 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 279 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 279 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 279 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 279 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 393 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.09e+00
        pdb=" C   ALA A 393 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ALA A 393 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 394 "    0.010 2.00e-02 2.50e+03
  ... (remaining 696 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 777
        2.77 -     3.30: 3806
        3.30 -     3.84: 6889
        3.84 -     4.37: 7472
        4.37 -     4.90: 13237
  Nonbonded interactions: 32181
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 476 "
            pdb=" OG1 THR A 480 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" NH1 ARG A 486 "
            pdb=" OE1 GLU A 489 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" O   THR A 516 "
            pdb=" OG1 THR A 516 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" OD1 ASN A 186 "
            pdb=" OG  SER A 213 "
     model   vdw
     2.384 3.040
  nonbonded pdb=" NH2 ARG A 233 "
            pdb=" O   VAL A 519 "
     model   vdw
     2.412 3.120
  ... (remaining 32176 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 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:             0.800
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.320
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
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      :  0.006   0.221   4103  Z= 0.317
  Angle     :  0.904  16.225   5609  Z= 0.433
  Chirality :  0.057   0.700    659
  Planarity :  0.005   0.052    699
  Dihedral  : 15.420  86.417   1479
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 22.17 %
    Favored  : 77.59 %
  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 aren not related in a simple way.
  whole: -1.05 (0.34), residues: 528
  helix: -0.20 (0.25), residues: 374
  sheet:  None (None), residues: 0
  loop : -1.69 (0.47), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 339 
 TYR   0.033   0.002   TYR A 279 
 PHE   0.009   0.001   PHE A  44 
 TRP   0.012   0.001   TRP A 354 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 ( 4100)
  covalent geometry    : angle       0.90413 ( 5603)
  SS BOND              : bond        0.00126 (    3)
  SS BOND              : angle       0.39981 (    6)
  hydrogen bonds       : bond        0.11979 (  260)
  hydrogen bonds       : angle       6.55258 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  173 PHE cc_start: 0.8210 (m-80) cc_final: 0.7963 (m-80)
REVERT: A  368 MET cc_start: 0.7095 (tpp) cc_final: 0.6661 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 68
  average time/residue: 0.0715
  time to fit residues: 6.1571
Evaluate side-chains
  63 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.1980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.165877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.130971 restraints weight = 4646.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.54
r_work: 0.3466 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4103  Z= 0.131
  Angle     :  0.535   5.663   5609  Z= 0.264
  Chirality :  0.036   0.138    659
  Planarity :  0.004   0.044    699
  Dihedral  :  4.762  57.448    638
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.67 %
    Favored  : 76.11 %
  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 aren not related in a simple way.
  whole:  0.16 (0.37), residues: 528
  helix:  0.73 (0.27), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.43 (0.52), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 486 
 TYR   0.009   0.001   TYR A 168 
 PHE   0.009   0.001   PHE A 159 
 TRP   0.010   0.001   TRP A 261 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4100)
  covalent geometry    : angle       0.53504 ( 5603)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.54162 (    6)
  hydrogen bonds       : bond        0.04310 (  260)
  hydrogen bonds       : angle       4.72076 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  193 MET cc_start: 0.7514 (tpp) cc_final: 0.7306 (ttm)
REVERT: A  368 MET cc_start: 0.7246 (tpp) cc_final: 0.6784 (tpp)
REVERT: A  408 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.5024 (ttt)
  outliers start: 9
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0637
  time to fit residues: 6.3286
Evaluate side-chains
  78 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 PHE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 23 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 453 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 = 0.3939 r_free = 0.3939 target = 0.161641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.126343 restraints weight = 4635.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.61
r_work: 0.3418 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4103  Z= 0.137
  Angle     :  0.525   5.858   5609  Z= 0.261
  Chirality :  0.036   0.138    659
  Planarity :  0.004   0.044    699
  Dihedral  :  4.586  56.909    638
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.92 %
    Favored  : 74.63 %
  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 aren not related in a simple way.
  whole:  0.61 (0.38), residues: 528
  helix:  1.07 (0.28), residues: 385
  sheet:  None (None), residues: 0
  loop : -1.37 (0.54), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  61 
 TYR   0.007   0.001   TYR A 279 
 PHE   0.009   0.001   PHE A 227 
 TRP   0.009   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4100)
  covalent geometry    : angle       0.52410 ( 5603)
  SS BOND              : bond        0.00481 (    3)
  SS BOND              : angle       0.97480 (    6)
  hydrogen bonds       : bond        0.04398 (  260)
  hydrogen bonds       : angle       4.55787 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7606 (m-30) cc_final: 0.6650 (t0)
REVERT: A  192 LEU cc_start: 0.8159 (mm) cc_final: 0.7836 (mt)
REVERT: A  234 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7546 (ttp-110)
REVERT: A  368 MET cc_start: 0.7250 (tpp) cc_final: 0.6762 (tpp)
  outliers start: 14
  outliers final: 6
  residues processed: 80
  average time/residue: 0.0723
  time to fit residues: 7.2412
Evaluate side-chains
  75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 ARG
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  450 CYS
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.161069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.125400 restraints weight = 4591.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.60
r_work: 0.3405 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4103  Z= 0.129
  Angle     :  0.521   5.722   5609  Z= 0.257
  Chirality :  0.036   0.130    659
  Planarity :  0.004   0.045    699
  Dihedral  :  3.915  34.597    636
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.67 %
    Favored  : 74.38 %
  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 aren not related in a simple way.
  whole:  0.89 (0.39), residues: 528
  helix:  1.28 (0.28), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.21 (0.54), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 486 
 TYR   0.007   0.001   TYR A 352 
 PHE   0.009   0.001   PHE A  32 
 TRP   0.005   0.001   TRP A 288 
 HIS   0.001   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4100)
  covalent geometry    : angle       0.52030 ( 5603)
  SS BOND              : bond        0.00170 (    3)
  SS BOND              : angle       0.93294 (    6)
  hydrogen bonds       : bond        0.04279 (  260)
  hydrogen bonds       : angle       4.46540 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7668 (m-30) cc_final: 0.6711 (t0)
REVERT: A  192 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7902 (mt)
REVERT: A  234 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7606 (ttp-110)
REVERT: A  239 MET cc_start: 0.8037 (ttp) cc_final: 0.7609 (ttp)
REVERT: A  368 MET cc_start: 0.7311 (tpp) cc_final: 0.6849 (tpp)
  outliers start: 16
  outliers final: 9
  residues processed: 80
  average time/residue: 0.0673
  time to fit residues: 6.7952
Evaluate side-chains
  80 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  234 ARG
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  450 CYS
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    0.4980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 453 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 = 0.3919 r_free = 0.3919 target = 0.159389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.123621 restraints weight = 4636.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.58
r_work: 0.3393 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4103  Z= 0.139
  Angle     :  0.530   5.764   5609  Z= 0.260
  Chirality :  0.037   0.132    659
  Planarity :  0.004   0.044    699
  Dihedral  :  3.907  33.643    636
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 21.43 %
    Favored  : 73.40 %
  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 aren not related in a simple way.
  whole:  1.01 (0.39), residues: 528
  helix:  1.34 (0.28), residues: 381
  sheet:  None (None), residues: 0
  loop : -1.05 (0.56), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 439 
 TYR   0.007   0.001   TYR A 352 
 PHE   0.008   0.001   PHE A 227 
 TRP   0.006   0.001   TRP A 261 
 HIS   0.001   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4100)
  covalent geometry    : angle       0.53016 ( 5603)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.71577 (    6)
  hydrogen bonds       : bond        0.04352 (  260)
  hydrogen bonds       : angle       4.45201 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7722 (mt)
REVERT: A  234 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7651 (ttp-110)
REVERT: A  368 MET cc_start: 0.7344 (tpp) cc_final: 0.6910 (tpp)
  outliers start: 21
  outliers final: 12
  residues processed: 86
  average time/residue: 0.0711
  time to fit residues: 7.6090
Evaluate side-chains
  84 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  234 ARG
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  450 CYS
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0070
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 11 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 453 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 = 0.3939 r_free = 0.3939 target = 0.161577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.125966 restraints weight = 4668.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.61
r_work: 0.3404 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4103  Z= 0.119
  Angle     :  0.524   8.422   5609  Z= 0.255
  Chirality :  0.036   0.129    659
  Planarity :  0.004   0.044    699
  Dihedral  :  3.867  32.035    636
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 22.17 %
    Favored  : 73.40 %
  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 aren not related in a simple way.
  whole:  1.11 (0.39), residues: 528
  helix:  1.46 (0.28), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.17 (0.54), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 486 
 TYR   0.007   0.001   TYR A 352 
 PHE   0.009   0.001   PHE A 227 
 TRP   0.005   0.001   TRP A 288 
 HIS   0.001   0.000   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4100)
  covalent geometry    : angle       0.52412 ( 5603)
  SS BOND              : bond        0.00190 (    3)
  SS BOND              : angle       0.66519 (    6)
  hydrogen bonds       : bond        0.04199 (  260)
  hydrogen bonds       : angle       4.43564 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  192 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7695 (mm)
REVERT: A  234 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7834 (ttp-110)
REVERT: A  368 MET cc_start: 0.7392 (tpp) cc_final: 0.7039 (tpp)
  outliers start: 18
  outliers final: 12
  residues processed: 83
  average time/residue: 0.0649
  time to fit residues: 6.8822
Evaluate side-chains
  88 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  234 ARG
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  450 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.159924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.124749 restraints weight = 4727.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.54
r_work: 0.3386 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4103  Z= 0.145
  Angle     :  0.551   8.185   5609  Z= 0.267
  Chirality :  0.037   0.132    659
  Planarity :  0.004   0.044    699
  Dihedral  :  3.935  32.245    636
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 21.67 %
    Favored  : 73.65 %
  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 aren not related in a simple way.
  whole:  1.13 (0.39), residues: 528
  helix:  1.44 (0.28), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.99 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 233 
 TYR   0.007   0.001   TYR A 352 
 PHE   0.010   0.001   PHE A 227 
 TRP   0.006   0.001   TRP A 261 
 HIS   0.001   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4100)
  covalent geometry    : angle       0.55072 ( 5603)
  SS BOND              : bond        0.00219 (    3)
  SS BOND              : angle       0.66079 (    6)
  hydrogen bonds       : bond        0.04388 (  260)
  hydrogen bonds       : angle       4.46157 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A  151 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7354 (t80)
REVERT: A  239 MET cc_start: 0.7977 (ttp) cc_final: 0.7620 (ttp)
REVERT: A  368 MET cc_start: 0.7310 (tpp) cc_final: 0.6949 (tpp)
  outliers start: 19
  outliers final: 13
  residues processed: 83
  average time/residue: 0.0661
  time to fit residues: 6.8587
Evaluate side-chains
  81 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  450 CYS
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0570
   chunk 41 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0010
   chunk 51 optimal weight:    0.4980
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.3904

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.162622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.127149 restraints weight = 4644.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.59
r_work: 0.3419 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4103  Z= 0.112
  Angle     :  0.520   8.233   5609  Z= 0.252
  Chirality :  0.036   0.127    659
  Planarity :  0.004   0.044    699
  Dihedral  :  3.824  30.047    636
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.40 %
    Favored  : 73.15 %
  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 aren not related in a simple way.
  whole:  1.23 (0.39), residues: 528
  helix:  1.53 (0.28), residues: 383
  sheet:  None (None), residues: 0
  loop : -1.08 (0.54), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 233 
 TYR   0.006   0.001   TYR A 352 
 PHE   0.007   0.001   PHE A 275 
 TRP   0.005   0.001   TRP A 491 
 HIS   0.002   0.000   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 4100)
  covalent geometry    : angle       0.51978 ( 5603)
  SS BOND              : bond        0.00099 (    3)
  SS BOND              : angle       0.59317 (    6)
  hydrogen bonds       : bond        0.04039 (  260)
  hydrogen bonds       : angle       4.39173 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  368 MET cc_start: 0.7324 (tpp) cc_final: 0.7050 (tpp)
  outliers start: 14
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0658
  time to fit residues: 6.8970
Evaluate side-chains
  81 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  450 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 31 optimal weight:    0.3980
   chunk 9 optimal weight:    9.9990
   chunk 46 optimal weight:    0.7980
   chunk 42 optimal weight:    0.2980
   chunk 3 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 453 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 = 0.3939 r_free = 0.3939 target = 0.161516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.125918 restraints weight = 4744.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 2.64
r_work: 0.3404 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4103  Z= 0.126
  Angle     :  0.552   8.185   5609  Z= 0.263
  Chirality :  0.037   0.193    659
  Planarity :  0.004   0.044    699
  Dihedral  :  3.840  30.516    636
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.17 %
    Favored  : 74.38 %
  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 aren not related in a simple way.
  whole:  1.25 (0.39), residues: 528
  helix:  1.53 (0.28), residues: 383
  sheet:  None (None), residues: 0
  loop : -1.04 (0.54), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 233 
 TYR   0.007   0.001   TYR A 279 
 PHE   0.009   0.001   PHE A 275 
 TRP   0.006   0.001   TRP A 491 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4100)
  covalent geometry    : angle       0.55200 ( 5603)
  SS BOND              : bond        0.00191 (    3)
  SS BOND              : angle       0.61490 (    6)
  hydrogen bonds       : bond        0.04176 (  260)
  hydrogen bonds       : angle       4.36592 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  340 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7940 (t)
REVERT: A  368 MET cc_start: 0.7277 (tpp) cc_final: 0.7018 (tpp)
  outliers start: 14
  outliers final: 11
  residues processed: 78
  average time/residue: 0.0532
  time to fit residues: 5.4819
Evaluate side-chains
  82 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  450 CYS
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.159793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.124077 restraints weight = 4700.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.64
r_work: 0.3382 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4103  Z= 0.149
  Angle     :  0.563   8.388   5609  Z= 0.272
  Chirality :  0.038   0.194    659
  Planarity :  0.004   0.044    699
  Dihedral  :  3.925  30.610    636
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.41 %
    Favored  : 74.14 %
  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 aren not related in a simple way.
  whole:  1.22 (0.39), residues: 528
  helix:  1.49 (0.28), residues: 380
  sheet:  None (None), residues: 0
  loop : -0.92 (0.55), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 233 
 TYR   0.007   0.001   TYR A 352 
 PHE   0.010   0.001   PHE A 227 
 TRP   0.007   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4100)
  covalent geometry    : angle       0.56272 ( 5603)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       0.62703 (    6)
  hydrogen bonds       : bond        0.04404 (  260)
  hydrogen bonds       : angle       4.44628 (  771)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  340 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7975 (t)
REVERT: A  368 MET cc_start: 0.7269 (tpp) cc_final: 0.7014 (tpp)
REVERT: A  467 MET cc_start: 0.7841 (mmt) cc_final: 0.7640 (mmp)
  outliers start: 14
  outliers final: 12
  residues processed: 77
  average time/residue: 0.0525
  time to fit residues: 5.3791
Evaluate side-chains
  82 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  442 ILE
Chi-restraints excluded: chain A residue  450 CYS
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  509 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0980
   chunk 3 optimal weight:    0.1980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 453 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 = 0.3947 r_free = 0.3947 target = 0.162597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.127286 restraints weight = 4703.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.61
r_work: 0.3419 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4103  Z= 0.117
  Angle     :  0.533   8.330   5609  Z= 0.258
  Chirality :  0.036   0.184    659
  Planarity :  0.004   0.044    699
  Dihedral  :  3.821  29.058    636
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 22.41 %
    Favored  : 74.38 %
  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 aren not related in a simple way.
  whole:  1.25 (0.39), residues: 528
  helix:  1.54 (0.28), residues: 381
  sheet:  None (None), residues: 0
  loop : -1.03 (0.54), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 233 
 TYR   0.006   0.001   TYR A 352 
 PHE   0.008   0.001   PHE A 275 
 TRP   0.007   0.001   TRP A 217 
 HIS   0.002   0.000   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4100)
  covalent geometry    : angle       0.53340 ( 5603)
  SS BOND              : bond        0.00164 (    3)
  SS BOND              : angle       0.58114 (    6)
  hydrogen bonds       : bond        0.04104 (  260)
  hydrogen bonds       : angle       4.39720 (  771)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1008.24 seconds
wall clock time: 18 minutes 5.80 seconds (1085.80 seconds total)