Starting phenix.real_space_refine
on Fri Aug 22 14:55:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sqv_25396/08_2025/7sqv_25396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sqv_25396/08_2025/7sqv_25396.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sqv_25396/08_2025/7sqv_25396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sqv_25396/08_2025/7sqv_25396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sqv_25396/08_2025/7sqv_25396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sqv_25396/08_2025/7sqv_25396.cif"
  }
  resolution = 2.3
  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=   0.002 sd=   0.029
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      21      5.16       5
     C    2814      2.51       5
     N     776      2.21       5
     O     860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4471
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 4084
          Classifications: {'peptide': 523}
          Link IDs: {'PTRANS': 32, 'TRANS': 490}
    Chain: "C"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 180
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "B"
      Number of atoms: 153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 153
          Classifications: {'peptide': 19}
          Link IDs: {'TRANS': 18}
    Chain: "D"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 47
          Classifications: {'peptide': 6}
          Link IDs: {'TRANS': 5}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 1.48, per 1000 atoms: 0.33
  Number of scatterers: 4471
  At special positions: 0
  Unit cell: (78.225, 78.225, 91.0975, 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      21     16.00
     O     860      8.00
     N     776      7.00
     C    2814      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 191.7 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1060

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 5 sheets defined
      41.4% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 78
    Processing helix  chain 'A' and resid 82 through 86
      removed outlier: 4.288A  pdb=" N   PHE A  86 " --> pdb=" O   LYS A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 153
    Processing helix  chain 'A' and resid 154 through 170
    Processing helix  chain 'A' and resid 171 through 175
      removed outlier: 3.571A  pdb=" N   GLY A 175 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 221
      removed outlier: 6.321A  pdb=" N   ASP A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LYS A 219 " --> pdb=" O   ARG A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 3.603A  pdb=" N   ALA A 231 " --> pdb=" O   GLY A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 351
    Processing helix  chain 'A' and resid 356 through 364
      removed outlier: 4.253A  pdb=" N   LEU A 360 " --> pdb=" O   TRP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 374
      No H-bonds generated for 'chain 'A' and resid 372 through 374'
    Processing helix  chain 'A' and resid 375 through 381
      removed outlier: 4.090A  pdb=" N   VAL A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 403
    Processing helix  chain 'A' and resid 422 through 427
    Processing helix  chain 'A' and resid 427 through 432
      removed outlier: 3.591A  pdb=" N   ALA A 431 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 462
      removed outlier: 3.531A  pdb=" N   LYS A 452 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A 462 " --> pdb=" O   PHE A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 470
    Processing helix  chain 'A' and resid 500 through 502
      No H-bonds generated for 'chain 'A' and resid 500 through 502'
    Processing helix  chain 'A' and resid 503 through 511
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 529 through 546
    Processing helix  chain 'A' and resid 561 through 575
    Processing helix  chain 'C' and resid 598 through 602
      removed outlier: 3.582A  pdb=" N   GLY C 602 " --> pdb=" O   ARG C 599 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 607 through 611
      removed outlier: 3.900A  pdb=" N   ILE C 610 " --> pdb=" O   SER C 607 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TYR C 611 " --> pdb=" O   GLY C 608 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 607 through 611'
    Processing helix  chain 'B' and resid 48 through 53
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 91
      removed outlier: 6.958A  pdb=" N   ASN A 115 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   ARG A 178 " --> pdb=" O   ASN A 115 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   PHE A 117 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ALA A 180 " --> pdb=" O   PHE A 117 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   GLY A 119 " --> pdb=" O   ALA A 180 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   LEU A 182 " --> pdb=" O   GLY A 119 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   VAL A 121 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 137
    Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498
      removed outlier: 5.847A  pdb=" N   TYR A 478 " --> pdb=" O   PHE A 560 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   PHE A 560 " --> pdb=" O   TYR A 478 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   THR A 480 " --> pdb=" O   TYR A 558 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   TYR A 558 " --> pdb=" O   THR A 480 " (cutoff:3.500A)
      removed outlier: 7.565A  pdb=" N   ASN A 482 " --> pdb=" O   MET A 556 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   MET A 556 " --> pdb=" O   ASN A 482 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ILE A 484 " --> pdb=" O   TRP A 554 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   TRP A 554 " --> pdb=" O   ILE A 484 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU A 486 " --> pdb=" O   THR A 552 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   ILE A 412 " --> pdb=" O   PHE A 560 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   SER A 325 " --> pdb=" O   ASP A 415 " (cutoff:3.500A)
      removed outlier: 14.442A  pdb=" N   TYR A 327 " --> pdb=" O   PRO A 417 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   THR A 285 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   ALA A 326 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ALA A 283 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   LEU A 281 " --> pdb=" O   PRO A 328 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   GLN A 278 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ILE A 268 " --> pdb=" O   GLN A 278 " (cutoff:3.500A)
      removed outlier: 5.525A  pdb=" N   ARG A 280 " --> pdb=" O   ASN A 266 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ASN A 266 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A 282 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN A 234 " --> pdb=" O   ARG A 267 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 249
    Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 306

    194 hydrogen bonds defined for protein.
    531 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: 0.79

  Time building geometry restraints manager: 0.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1509
        1.34 -     1.46: 864
        1.46 -     1.58: 2145
        1.58 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 4559
  Sorted by residual:
  bond pdb=" CB  ASN A 296 "
       pdb=" CG  ASN A 296 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.32e+00
  bond pdb=" CA  VAL A 311 "
       pdb=" CB  VAL A 311 "
    ideal  model  delta    sigma   weight residual
    1.537  1.546 -0.009 1.29e-02 6.01e+03 4.97e-01
  bond pdb=" CA  ILE A 429 "
       pdb=" C   ILE A 429 "
    ideal  model  delta    sigma   weight residual
    1.523  1.529 -0.006 9.20e-03 1.18e+04 4.20e-01
  bond pdb=" CA  ASN A 296 "
       pdb=" CB  ASN A 296 "
    ideal  model  delta    sigma   weight residual
    1.530  1.537 -0.008 1.38e-02 5.25e+03 3.18e-01
  bond pdb=" CA  GLU A 443 "
       pdb=" C   GLU A 443 "
    ideal  model  delta    sigma   weight residual
    1.519  1.525 -0.006 1.01e-02 9.80e+03 3.00e-01
  ... (remaining 4554 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.97: 6048
        0.97 -     1.95: 117
        1.95 -     2.92: 34
        2.92 -     3.89: 4
        3.89 -     4.87: 1
  Bond angle restraints: 6204
  Sorted by residual:
  angle pdb=" C   MET A 428 "
        pdb=" N   ILE A 429 "
        pdb=" CA  ILE A 429 "
      ideal   model   delta    sigma   weight residual
     120.33  122.22   -1.89 8.00e-01 1.56e+00 5.57e+00
  angle pdb=" CA  ASN A 296 "
        pdb=" CB  ASN A 296 "
        pdb=" CG  ASN A 296 "
      ideal   model   delta    sigma   weight residual
     112.60  114.51   -1.91 1.00e+00 1.00e+00 3.67e+00
  angle pdb=" C   ILE A 429 "
        pdb=" CA  ILE A 429 "
        pdb=" CB  ILE A 429 "
      ideal   model   delta    sigma   weight residual
     114.00  111.69    2.31 1.31e+00 5.83e-01 3.11e+00
  angle pdb=" C   ASN A 296 "
        pdb=" CA  ASN A 296 "
        pdb=" CB  ASN A 296 "
      ideal   model   delta    sigma   weight residual
     110.17  111.69   -1.52 1.11e+00 8.12e-01 1.88e+00
  angle pdb=" C   ARG A 215 "
        pdb=" N   LEU A 216 "
        pdb=" CA  LEU A 216 "
      ideal   model   delta    sigma   weight residual
     121.81  119.15    2.66 1.94e+00 2.66e-01 1.88e+00
  ... (remaining 6199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.31: 2350
       16.31 -    32.61: 276
       32.61 -    48.92: 76
       48.92 -    65.22: 21
       65.22 -    81.53: 9
  Dihedral angle restraints: 2732
    sinusoidal: 1077
      harmonic: 1655
  Sorted by residual:
  dihedral pdb=" CA  ASP A 542 "
           pdb=" CB  ASP A 542 "
           pdb=" CG  ASP A 542 "
           pdb=" OD1 ASP A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.42   54.42     1      2.00e+01 2.50e-03 1.00e+01
  dihedral pdb=" N   GLU A 570 "
           pdb=" CA  GLU A 570 "
           pdb=" CB  GLU A 570 "
           pdb=" CG  GLU A 570 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.41  -57.59     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CB  MET B  46 "
           pdb=" CG  MET B  46 "
           pdb=" SD  MET B  46 "
           pdb=" CE  MET B  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.39   57.39     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 2729 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 432
       0.026 -    0.052: 155
       0.052 -    0.078: 53
       0.078 -    0.105: 35
       0.105 -    0.131: 20
  Chirality restraints: 695
  Sorted by residual:
  chirality pdb=" CA  ILE A 484 "
            pdb=" N   ILE A 484 "
            pdb=" C   ILE A 484 "
            pdb=" CB  ILE A 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.27e-01
  chirality pdb=" CA  VAL A 256 "
            pdb=" N   VAL A 256 "
            pdb=" C   VAL A 256 "
            pdb=" CB  VAL A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CA  ILE A  87 "
            pdb=" N   ILE A  87 "
            pdb=" C   ILE A  87 "
            pdb=" CB  ILE A  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 692 not shown)

  Planarity restraints: 817
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 335 "    0.032 5.00e-02 4.00e+02   4.88e-02 3.82e+00
        pdb=" N   PRO A 336 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 336 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 336 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  92 "   -0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO A  93 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 512 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 513 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 513 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 513 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 814 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1406
        2.83 -     3.35: 3660
        3.35 -     3.87: 6882
        3.87 -     4.38: 7919
        4.38 -     4.90: 13889
  Nonbonded interactions: 33756
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 525 "
            pdb=" NH2 ARG A 533 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" NE2 GLN A 137 "
            pdb=" OD1 ASN A 142 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OD1 ASP A 250 "
            pdb=" N   ASN A 254 "
     model   vdw
     2.429 3.120
  nonbonded pdb=" O   SER B  63 "
            pdb=" OG  SER B  63 "
     model   vdw
     2.433 3.040
  nonbonded pdb=" NZ  LYS A 439 "
            pdb=" O   VAL A 440 "
     model   vdw
     2.444 3.120
  ... (remaining 33751 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:             10.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.340
  Find NCS groups from input model:        0.030
  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:10.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
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      :  0.001   0.029   4559  Z= 0.077
  Angle     :  0.380   4.867   6204  Z= 0.208
  Chirality :  0.040   0.131    695
  Planarity :  0.004   0.049    817
  Dihedral  : 16.078  81.526   1672
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 18.79 %
    Favored  : 80.58 %
  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:  1.86 (0.36), residues: 565
  helix:  2.23 (0.39), residues: 191
  sheet:  1.75 (0.47), residues: 127
  loop :  0.20 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 366 
 TYR   0.004   0.001   TYR A 292 
 PHE   0.004   0.001   PHE D 631 
 TRP   0.010   0.001   TRP A 519 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00150 ( 4559)
  covalent geometry    : angle       0.38024 ( 6204)
  hydrogen bonds       : bond        0.18776 (  194)
  hydrogen bonds       : angle       5.71623 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  539 GLU cc_start: 0.7696 (tt0) cc_final: 0.7397 (tp30)
  outliers start: 3
  outliers final: 3
  residues processed: 53
  average time/residue: 0.7305
  time to fit residues: 40.1042
Evaluate side-chains
  49 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  542 ASP
Chi-restraints excluded: chain A residue  544 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0170
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.4018

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
A 492 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.087009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.064990 restraints weight = 7291.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2807 rms_B_bonded: 2.81
r_work: 0.2664 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2541 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.0768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4559  Z= 0.111
  Angle     :  0.441   4.797   6204  Z= 0.240
  Chirality :  0.042   0.135    695
  Planarity :  0.004   0.045    817
  Dihedral  :  4.214  42.661    634
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 17.95 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.36), residues: 565
  helix:  2.44 (0.40), residues: 193
  sheet:  1.41 (0.45), residues: 129
  loop :  0.41 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 366 
 TYR   0.007   0.001   TYR A 287 
 PHE   0.005   0.001   PHE A 577 
 TRP   0.008   0.001   TRP A 149 
 HIS   0.002   0.000   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 4559)
  covalent geometry    : angle       0.44079 ( 6204)
  hydrogen bonds       : bond        0.05383 (  194)
  hydrogen bonds       : angle       4.69598 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  172 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8104 (mppt)
REVERT: A  539 GLU cc_start: 0.8910 (tt0) cc_final: 0.8411 (tp30)
  outliers start: 5
  outliers final: 2
  residues processed: 49
  average time/residue: 0.6807
  time to fit residues: 34.4648
Evaluate side-chains
  45 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0870
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.4556

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.086297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.064359 restraints weight = 7226.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 2.79
r_work: 0.2654 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2529 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4559  Z= 0.113
  Angle     :  0.437   4.702   6204  Z= 0.238
  Chirality :  0.042   0.135    695
  Planarity :  0.004   0.044    817
  Dihedral  :  3.441  15.327    630
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 0.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 17.75 %
    Favored  : 80.79 %
  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:  1.85 (0.36), residues: 565
  helix:  2.38 (0.39), residues: 193
  sheet:  1.14 (0.45), residues: 131
  loop :  0.40 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 366 
 TYR   0.008   0.001   TYR A 455 
 PHE   0.005   0.001   PHE A 577 
 TRP   0.009   0.001   TRP A 519 
 HIS   0.002   0.001   HIS A 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4559)
  covalent geometry    : angle       0.43749 ( 6204)
  hydrogen bonds       : bond        0.05188 (  194)
  hydrogen bonds       : angle       4.53059 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  172 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8152 (mppt)
REVERT: A  539 GLU cc_start: 0.8915 (tt0) cc_final: 0.8421 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 48
  average time/residue: 0.6289
  time to fit residues: 31.2314
Evaluate side-chains
  48 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.084201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.062155 restraints weight = 7301.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.2763 rms_B_bonded: 2.81
r_work: 0.2615 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2489 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8925
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4559  Z= 0.157
  Angle     :  0.478   5.746   6204  Z= 0.261
  Chirality :  0.043   0.138    695
  Planarity :  0.005   0.047    817
  Dihedral  :  3.689  17.880    630
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 0.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.33 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.35), residues: 565
  helix:  2.36 (0.39), residues: 192
  sheet:  1.02 (0.43), residues: 137
  loop :  0.31 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.009   0.001   TYR A 455 
 PHE   0.007   0.001   PHE A 577 
 TRP   0.009   0.002   TRP A 519 
 HIS   0.003   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 4559)
  covalent geometry    : angle       0.47835 ( 6204)
  hydrogen bonds       : bond        0.06111 (  194)
  hydrogen bonds       : angle       4.58617 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  172 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8164 (mppt)
REVERT: A  539 GLU cc_start: 0.8931 (tt0) cc_final: 0.8488 (tp30)
  outliers start: 8
  outliers final: 5
  residues processed: 51
  average time/residue: 0.6787
  time to fit residues: 35.7020
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.083163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.061347 restraints weight = 7304.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2743 rms_B_bonded: 2.79
r_work: 0.2599 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2477 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8929
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4559  Z= 0.170
  Angle     :  0.486   4.777   6204  Z= 0.269
  Chirality :  0.044   0.139    695
  Planarity :  0.005   0.050    817
  Dihedral  :  3.845  19.703    630
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.12 %
    Favored  : 80.79 %
  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:  1.57 (0.35), residues: 565
  helix:  2.38 (0.39), residues: 190
  sheet:  0.88 (0.42), residues: 137
  loop :  0.11 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 533 
 TYR   0.010   0.001   TYR A 455 
 PHE   0.008   0.001   PHE A 577 
 TRP   0.010   0.002   TRP A 519 
 HIS   0.003   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 4559)
  covalent geometry    : angle       0.48641 ( 6204)
  hydrogen bonds       : bond        0.06340 (  194)
  hydrogen bonds       : angle       4.61942 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  172 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8174 (mppt)
REVERT: A  233 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7085 (p0)
  outliers start: 10
  outliers final: 5
  residues processed: 52
  average time/residue: 0.6905
  time to fit residues: 37.1103
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   chunk 52 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0870
   overall best weight:    0.4358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.084972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.063227 restraints weight = 7340.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 2.80
r_work: 0.2619 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2494 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4559  Z= 0.112
  Angle     :  0.451   5.476   6204  Z= 0.244
  Chirality :  0.042   0.137    695
  Planarity :  0.005   0.049    817
  Dihedral  :  3.652  18.954    630
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 0.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.16 %
    Favored  : 80.38 %
  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:  1.74 (0.35), residues: 565
  helix:  2.41 (0.39), residues: 192
  sheet:  0.94 (0.43), residues: 137
  loop :  0.32 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 366 
 TYR   0.008   0.001   TYR A 287 
 PHE   0.006   0.001   PHE A 577 
 TRP   0.011   0.001   TRP A 519 
 HIS   0.001   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4559)
  covalent geometry    : angle       0.45060 ( 6204)
  hydrogen bonds       : bond        0.04958 (  194)
  hydrogen bonds       : angle       4.46509 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  172 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8179 (mppt)
REVERT: A  539 GLU cc_start: 0.8883 (tt0) cc_final: 0.8361 (tp30)
  outliers start: 7
  outliers final: 5
  residues processed: 49
  average time/residue: 0.7779
  time to fit residues: 39.3890
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0770
   chunk 30 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.5138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.084515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.062667 restraints weight = 7313.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 2.81
r_work: 0.2611 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2486 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4559  Z= 0.122
  Angle     :  0.451   5.094   6204  Z= 0.246
  Chirality :  0.042   0.137    695
  Planarity :  0.005   0.049    817
  Dihedral  :  3.649  18.692    630
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 0.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.95 %
    Favored  : 80.17 %
  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:  1.75 (0.35), residues: 565
  helix:  2.43 (0.39), residues: 192
  sheet:  0.94 (0.43), residues: 135
  loop :  0.31 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 366 
 TYR   0.008   0.001   TYR A 455 
 PHE   0.007   0.001   PHE A 577 
 TRP   0.010   0.002   TRP A 519 
 HIS   0.002   0.001   HIS A 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4559)
  covalent geometry    : angle       0.45077 ( 6204)
  hydrogen bonds       : bond        0.05177 (  194)
  hydrogen bonds       : angle       4.44208 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  172 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8160 (mppt)
REVERT: A  233 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7328 (p0)
REVERT: A  539 GLU cc_start: 0.8898 (tt0) cc_final: 0.8374 (tp30)
  outliers start: 9
  outliers final: 6
  residues processed: 51
  average time/residue: 0.6825
  time to fit residues: 36.0374
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    0.1980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 492 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.084120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.062285 restraints weight = 7254.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.2754 rms_B_bonded: 2.79
r_work: 0.2604 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2478 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8880
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4559  Z= 0.134
  Angle     :  0.475   7.078   6204  Z= 0.256
  Chirality :  0.043   0.138    695
  Planarity :  0.005   0.049    817
  Dihedral  :  3.702  18.707    630
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 0.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 18.16 %
    Favored  : 80.17 %
  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:  1.71 (0.35), residues: 565
  helix:  2.48 (0.39), residues: 190
  sheet:  0.91 (0.44), residues: 135
  loop :  0.24 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 533 
 TYR   0.008   0.001   TYR A 455 
 PHE   0.007   0.001   PHE A 577 
 TRP   0.009   0.002   TRP A 519 
 HIS   0.003   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4559)
  covalent geometry    : angle       0.47455 ( 6204)
  hydrogen bonds       : bond        0.05464 (  194)
  hydrogen bonds       : angle       4.47004 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  172 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8163 (mppt)
REVERT: A  233 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7299 (p0)
REVERT: A  539 GLU cc_start: 0.8884 (tt0) cc_final: 0.8367 (tp30)
  outliers start: 8
  outliers final: 6
  residues processed: 49
  average time/residue: 0.6952
  time to fit residues: 35.2099
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.084030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.062297 restraints weight = 7346.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.2746 rms_B_bonded: 2.81
r_work: 0.2597 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2472 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4559  Z= 0.144
  Angle     :  0.479   6.435   6204  Z= 0.260
  Chirality :  0.043   0.139    695
  Planarity :  0.005   0.049    817
  Dihedral  :  3.743  19.014    630
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 0.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.37 %
    Favored  : 80.17 %
  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:  1.67 (0.35), residues: 565
  helix:  2.46 (0.39), residues: 190
  sheet:  0.88 (0.43), residues: 135
  loop :  0.21 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 537 
 TYR   0.009   0.001   TYR A 455 
 PHE   0.007   0.001   PHE A 577 
 TRP   0.009   0.002   TRP A 519 
 HIS   0.003   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 4559)
  covalent geometry    : angle       0.47947 ( 6204)
  hydrogen bonds       : bond        0.05658 (  194)
  hydrogen bonds       : angle       4.49086 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   78 GLU cc_start: 0.8650 (tt0) cc_final: 0.8368 (tm-30)
REVERT: A  172 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8152 (mppt)
REVERT: A  233 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7358 (p0)
REVERT: A  539 GLU cc_start: 0.8883 (tt0) cc_final: 0.8366 (tp30)
  outliers start: 7
  outliers final: 5
  residues processed: 48
  average time/residue: 0.7693
  time to fit residues: 38.0171
Evaluate side-chains
  50 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0970
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0000
   chunk 35 optimal weight:    0.0770
   chunk 28 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0870
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.1718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.087194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.065478 restraints weight = 7222.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 2.79
r_work: 0.2669 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2545 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4559  Z= 0.081
  Angle     :  0.401   4.581   6204  Z= 0.216
  Chirality :  0.041   0.133    695
  Planarity :  0.004   0.047    817
  Dihedral  :  3.401  16.074    630
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 1.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 18.79 %
    Favored  : 80.17 %
  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:  1.85 (0.36), residues: 565
  helix:  2.52 (0.39), residues: 193
  sheet:  1.06 (0.44), residues: 133
  loop :  0.32 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 366 
 TYR   0.009   0.001   TYR A 287 
 PHE   0.005   0.001   PHE A 157 
 TRP   0.013   0.001   TRP A 519 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 4559)
  covalent geometry    : angle       0.40128 ( 6204)
  hydrogen bonds       : bond        0.03583 (  194)
  hydrogen bonds       : angle       4.26589 (  531)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   78 GLU cc_start: 0.8577 (tt0) cc_final: 0.8310 (tm-30)
REVERT: A  172 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8182 (mppt)
REVERT: A  539 GLU cc_start: 0.8909 (tt0) cc_final: 0.8382 (tp30)
  outliers start: 5
  outliers final: 2
  residues processed: 49
  average time/residue: 0.6919
  time to fit residues: 34.9998
Evaluate side-chains
  49 residues out of total 479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  172 LYS
Chi-restraints excluded: chain C residue  592 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0570
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.4098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.085657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.063879 restraints weight = 7295.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 2.80
r_work: 0.2635 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2510 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4559  Z= 0.107
  Angle     :  0.452   8.091   6204  Z= 0.240
  Chirality :  0.042   0.142    695
  Planarity :  0.004   0.047    817
  Dihedral  :  3.476  15.974    630
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 0.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 19.21 %
    Favored  : 79.96 %
  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:  1.85 (0.36), residues: 565
  helix:  2.52 (0.39), residues: 193
  sheet:  0.98 (0.43), residues: 137
  loop :  0.37 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 366 
 TYR   0.009   0.001   TYR A 287 
 PHE   0.006   0.001   PHE A 577 
 TRP   0.009   0.001   TRP A 519 
 HIS   0.003   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 4559)
  covalent geometry    : angle       0.45177 ( 6204)
  hydrogen bonds       : bond        0.04541 (  194)
  hydrogen bonds       : angle       4.29102 (  531)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2266.29 seconds
wall clock time: 39 minutes 13.29 seconds (2353.29 seconds total)