Starting phenix.real_space_refine
on Thu Mar  5 06:50:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tdd_25825/03_2026/7tdd_25825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tdd_25825/03_2026/7tdd_25825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tdd_25825/03_2026/7tdd_25825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tdd_25825/03_2026/7tdd_25825.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tdd_25825/03_2026/7tdd_25825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tdd_25825/03_2026/7tdd_25825.map"
  }
  resolution = 3.5
  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=   0.016
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: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    6690      2.51       5
     N    1549      2.21       5
     O    1721      1.98       5
     H   10025      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20031
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 605, 10006
          Classifications: {'peptide': 605}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 586}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 10025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 10025
          Classifications: {'peptide': 606}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 587}
          Chain breaks: 5
  Time building chain proxies: 3.86, per 1000 atoms: 0.19
  Number of scatterers: 20031
  At special positions: 0
  Unit cell: (125.25, 99.365, 105.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     O    1721      8.00
     N    1549      7.00
     C    6690      6.00
     H   10025      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  93 " - pdb=" SG  CYS B 101 " 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: 1.74
  Conformation dependent library (CDL) restraints added in 595.2 milliseconds
  

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2322

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      87.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 28
    Processing helix  chain 'A' and resid 29 through 43
    Processing helix  chain 'A' and resid 61 through 69
    Processing helix  chain 'A' and resid 70 through 84
    Processing helix  chain 'A' and resid 90 through 95
    Processing helix  chain 'A' and resid 116 through 137
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 143 through 150
    Processing helix  chain 'A' and resid 150 through 173
    Processing helix  chain 'A' and resid 186 through 199
      removed outlier: 3.722A  pdb=" N   VAL A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 238
      removed outlier: 4.955A  pdb=" N   GLY A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASN A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE A 219 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 250 through 263
      removed outlier: 3.688A  pdb=" N   THR A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 270
      No H-bonds generated for 'chain 'A' and resid 268 through 270'
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 4.070A  pdb=" N   PHE A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 333
      removed outlier: 3.782A  pdb=" N   GLY A 318 " --> pdb=" O   LYS A 314 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET A 319 " --> pdb=" O   GLN A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 355
    Processing helix  chain 'A' and resid 386 through 399
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 3.528A  pdb=" N   HIS A 416 " --> pdb=" O   PRO A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 428
      removed outlier: 3.823A  pdb=" N   GLN A 421 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 451
    Processing helix  chain 'A' and resid 462 through 493
      removed outlier: 3.960A  pdb=" N   VAL A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   PHE A 488 " --> pdb=" O   TYR A 484 " (cutoff:3.500A)
      removed outlier: 8.894A  pdb=" N   GLU A 489 " --> pdb=" O   THR A 485 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 515
    Processing helix  chain 'A' and resid 530 through 540
    Processing helix  chain 'A' and resid 541 through 547
      removed outlier: 4.233A  pdb=" N   LEU A 545 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 588
      removed outlier: 4.213A  pdb=" N   PHE A 554 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      Proline residue:  A 563  - end of helix
      Proline residue:  A 567  - end of helix
    Processing helix  chain 'A' and resid 597 through 600
    Processing helix  chain 'A' and resid 601 through 606
    Processing helix  chain 'A' and resid 615 through 629
    Processing helix  chain 'A' and resid 632 through 644
      removed outlier: 3.833A  pdb=" N   MET A 636 " --> pdb=" O   TRP A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 647
      No H-bonds generated for 'chain 'A' and resid 645 through 647'
    Processing helix  chain 'A' and resid 648 through 661
      removed outlier: 4.183A  pdb=" N   PHE A 652 " --> pdb=" O   SER A 648 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 661 " --> pdb=" O   VAL A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 690
    Processing helix  chain 'B' and resid 17 through 27
    Processing helix  chain 'B' and resid 29 through 43
    Processing helix  chain 'B' and resid 61 through 70
    Processing helix  chain 'B' and resid 70 through 88
      removed outlier: 4.614A  pdb=" N   ASN B  85 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   PHE B  86 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   PHE B  87 " --> pdb=" O   PHE B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 96
      removed outlier: 3.620A  pdb=" N   ASN B  96 " --> pdb=" O   CYS B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 137
    Processing helix  chain 'B' and resid 137 through 143
      removed outlier: 4.544A  pdb=" N   TYR B 141 " --> pdb=" O   PHE B 137 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY B 143 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 150
    Processing helix  chain 'B' and resid 150 through 173
    Processing helix  chain 'B' and resid 186 through 199
      removed outlier: 3.931A  pdb=" N   VAL B 192 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE B 199 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
      removed outlier: 3.656A  pdb=" N   GLY B 211 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   MET B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 238
      removed outlier: 4.008A  pdb=" N   ASN B 218 " --> pdb=" O   GLY B 214 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE B 219 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
    Processing helix  chain 'B' and resid 250 through 264
      removed outlier: 3.508A  pdb=" N   THR B 263 " --> pdb=" O   PHE B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 270
      No H-bonds generated for 'chain 'B' and resid 268 through 270'
    Processing helix  chain 'B' and resid 271 through 278
    Processing helix  chain 'B' and resid 280 through 295
      removed outlier: 4.313A  pdb=" N   PHE B 284 " --> pdb=" O   TRP B 280 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 333
    Processing helix  chain 'B' and resid 345 through 354
      removed outlier: 4.369A  pdb=" N   LEU B 350 " --> pdb=" O   GLN B 346 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   GLN B 353 " --> pdb=" O   LYS B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 398
      removed outlier: 3.612A  pdb=" N   LEU B 397 " --> pdb=" O   GLN B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
      removed outlier: 3.657A  pdb=" N   HIS B 410 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 417 through 428
      removed outlier: 3.984A  pdb=" N   GLN B 421 " --> pdb=" O   SER B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 455
    Processing helix  chain 'B' and resid 461 through 487
      removed outlier: 3.793A  pdb=" N   PHE B 469 " --> pdb=" O   GLN B 465 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL B 470 " --> pdb=" O   VAL B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 493
    Processing helix  chain 'B' and resid 494 through 515
      removed outlier: 3.677A  pdb=" N   TRP B 505 " --> pdb=" O   PHE B 501 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   VAL B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 540
    Processing helix  chain 'B' and resid 542 through 547
      removed outlier: 3.754A  pdb=" N   MET B 546 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 550 through 565
      removed outlier: 4.270A  pdb=" N   PHE B 554 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      Proline residue:  B 563  - end of helix
    Processing helix  chain 'B' and resid 565 through 588
    Processing helix  chain 'B' and resid 597 through 600
    Processing helix  chain 'B' and resid 601 through 606
    Processing helix  chain 'B' and resid 615 through 629
    Processing helix  chain 'B' and resid 632 through 644
      removed outlier: 3.801A  pdb=" N   MET B 636 " --> pdb=" O   TRP B 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 645 through 647
      No H-bonds generated for 'chain 'B' and resid 645 through 647'
    Processing helix  chain 'B' and resid 648 through 660
      removed outlier: 4.097A  pdb=" N   PHE B 652 " --> pdb=" O   SER B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 690

    717 hydrogen bonds defined for protein.
    2124 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: 3.84

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 6804
        1.02 -     1.22: 3234
        1.22 -     1.42: 4881
        1.42 -     1.61: 5312
        1.61 -     1.81: 74
  Bond restraints: 20305
  Sorted by residual:
  bond pdb=" CB  THR B 264 "
       pdb=" OG1 THR B 264 "
    ideal  model  delta    sigma   weight residual
    1.433  1.269  0.164 1.60e-02 3.91e+03 1.05e+02
  bond pdb=" CA  ALA A 187 "
       pdb=" CB  ALA A 187 "
    ideal  model  delta    sigma   weight residual
    1.534  1.427  0.107 1.18e-02 7.18e+03 8.30e+01
  bond pdb=" CA  ALA B 187 "
       pdb=" CB  ALA B 187 "
    ideal  model  delta    sigma   weight residual
    1.534  1.427  0.107 1.18e-02 7.18e+03 8.27e+01
  bond pdb=" CZ  ARG B 191 "
       pdb=" NH2 ARG B 191 "
    ideal  model  delta    sigma   weight residual
    1.330  1.227  0.103 1.30e-02 5.92e+03 6.23e+01
  bond pdb=" CZ  ARG A 191 "
       pdb=" NH2 ARG A 191 "
    ideal  model  delta    sigma   weight residual
    1.330  1.228  0.102 1.30e-02 5.92e+03 6.21e+01
  ... (remaining 20300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 29979
        2.37 -     4.74: 4138
        4.74 -     7.10: 2017
        7.10 -     9.47: 414
        9.47 -    11.84: 42
  Bond angle restraints: 36590
  Sorted by residual:
  angle pdb=" N   ILE A 272 "
        pdb=" CA  ILE A 272 "
        pdb=" CB  ILE A 272 "
      ideal   model   delta    sigma   weight residual
     110.52  115.79   -5.27 6.70e-01 2.23e+00 6.19e+01
  angle pdb=" CA  PHE A  86 "
        pdb=" CB  PHE A  86 "
        pdb=" CG  PHE A  86 "
      ideal   model   delta    sigma   weight residual
     113.80  121.62   -7.82 1.00e+00 1.00e+00 6.11e+01
  angle pdb=" CA  ASN B 618 "
        pdb=" CB  ASN B 618 "
        pdb=" CG  ASN B 618 "
      ideal   model   delta    sigma   weight residual
     112.60  120.14   -7.54 1.00e+00 1.00e+00 5.69e+01
  angle pdb=" CA  ASN A  85 "
        pdb=" CB  ASN A  85 "
        pdb=" CG  ASN A  85 "
      ideal   model   delta    sigma   weight residual
     112.60  120.13   -7.53 1.00e+00 1.00e+00 5.67e+01
  angle pdb=" CA  ASP B 166 "
        pdb=" CB  ASP B 166 "
        pdb=" CG  ASP B 166 "
      ideal   model   delta    sigma   weight residual
     112.60  120.01   -7.41 1.00e+00 1.00e+00 5.50e+01
  ... (remaining 36585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 8826
       17.77 -    35.54: 444
       35.54 -    53.31: 133
       53.31 -    71.08: 160
       71.08 -    88.85: 9
  Dihedral angle restraints: 9572
    sinusoidal: 4945
      harmonic: 4627
  Sorted by residual:
  dihedral pdb=" C   MET A 629 "
           pdb=" N   MET A 629 "
           pdb=" CA  MET A 629 "
           pdb=" CB  MET A 629 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.24   17.64     0      2.50e+00 1.60e-01 4.98e+01
  dihedral pdb=" N   MET A 629 "
           pdb=" C   MET A 629 "
           pdb=" CA  MET A 629 "
           pdb=" CB  MET A 629 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.06  -15.26     0      2.50e+00 1.60e-01 3.73e+01
  dihedral pdb=" CA  MET A 629 "
           pdb=" C   MET A 629 "
           pdb=" N   GLY A 630 "
           pdb=" CA  GLY A 630 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.07   27.93     0      5.00e+00 4.00e-02 3.12e+01
  ... (remaining 9569 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 1160
       0.148 -    0.297: 28
       0.297 -    0.445: 33
       0.445 -    0.593: 218
       0.593 -    0.742: 147
  Chirality restraints: 1586
  Sorted by residual:
  chirality pdb=" CG  LEU B 623 "
            pdb=" CB  LEU B 623 "
            pdb=" CD1 LEU B 623 "
            pdb=" CD2 LEU B 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.38e+01
  chirality pdb=" CG  LEU A  84 "
            pdb=" CB  LEU A  84 "
            pdb=" CD1 LEU A  84 "
            pdb=" CD2 LEU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CG  LEU A 623 "
            pdb=" CB  LEU A 623 "
            pdb=" CD1 LEU A 623 "
            pdb=" CD2 LEU A 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.37e+01
  ... (remaining 1583 not shown)

  Planarity restraints: 2868
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  92 "   -0.183 2.00e-02 2.50e+03   6.12e-02 1.50e+02
        pdb=" CG  TRP A  92 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  92 "    0.049 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  92 "    0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  92 "    0.039 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  92 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  92 "    0.044 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  92 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  92 "    0.033 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  92 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD1 TRP A  92 "    0.054 2.00e-02 2.50e+03
        pdb=" HE1 TRP A  92 "    0.031 2.00e-02 2.50e+03
        pdb=" HE3 TRP A  92 "    0.058 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A  92 "   -0.085 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A  92 "    0.033 2.00e-02 2.50e+03
        pdb=" HH2 TRP A  92 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  92 "    0.153 2.00e-02 2.50e+03   5.03e-02 1.01e+02
        pdb=" CG  TRP B  92 "    0.008 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  92 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  92 "   -0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  92 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  92 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  92 "   -0.039 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  92 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  92 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  92 "    0.005 2.00e-02 2.50e+03
        pdb=" HD1 TRP B  92 "   -0.032 2.00e-02 2.50e+03
        pdb=" HE1 TRP B  92 "   -0.011 2.00e-02 2.50e+03
        pdb=" HE3 TRP B  92 "   -0.043 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B  92 "    0.070 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B  92 "   -0.018 2.00e-02 2.50e+03
        pdb=" HH2 TRP B  92 "    0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 185 "   -0.153 9.50e-02 1.11e+02   7.50e-02 7.08e+01
        pdb=" NE  ARG B 185 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 185 "   -0.037 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 185 "   -0.060 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 185 "   -0.014 2.00e-02 2.50e+03
        pdb="HH11 ARG B 185 "    0.122 2.00e-02 2.50e+03
        pdb="HH12 ARG B 185 "   -0.055 2.00e-02 2.50e+03
        pdb="HH21 ARG B 185 "    0.049 2.00e-02 2.50e+03
        pdb="HH22 ARG B 185 "    0.031 2.00e-02 2.50e+03
  ... (remaining 2865 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 704
        2.15 -     2.77: 37286
        2.77 -     3.38: 56753
        3.38 -     3.99: 70376
        3.99 -     4.60: 110325
  Nonbonded interactions: 275444
  Sorted by model distance:
  nonbonded pdb=" O   THR A 263 "
            pdb=" HG1 THR A 264 "
     model   vdw
     1.543 2.450
  nonbonded pdb=" O   VAL A 449 "
            pdb=" HG1 THR A 452 "
     model   vdw
     1.547 2.450
  nonbonded pdb=" O   GLU A 352 "
            pdb=" HG1 THR A 355 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" O   SER B 278 "
            pdb=" HG  SER B 281 "
     model   vdw
     1.583 2.450
  nonbonded pdb=" HH  TYR A 305 "
            pdb=" OE2 GLU A 673 "
     model   vdw
     1.591 2.450
  ... (remaining 275439 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 16 through 454 or resid 459 through 690))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.580
  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:             0.110
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     18.300
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  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:1.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6454
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      :  0.029   0.164  10282  Z= 1.418
  Angle     :  2.072  11.838  13983  Z= 1.394
  Chirality :  0.294   0.742   1586
  Planarity :  0.010   0.104   1709
  Dihedral  : 12.649  88.847   3595
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.52 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  3.23 %
    Favored  : 96.21 %
  Cbeta Deviations : 15.76 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.23), residues: 1187
  helix: -0.32 (0.15), residues: 926
  sheet:  None (None), residues: 0
  loop :  0.24 (0.42), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG B 540 
 TYR   0.097   0.011   TYR A 106 
 PHE   0.080   0.008   PHE A 599 
 TRP   0.109   0.011   TRP A  92 
 HIS   0.013   0.004   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.02881 (10280)
  covalent geometry    : angle       2.07216 (13979)
  SS BOND              : bond        0.00456 (    2)
  SS BOND              : angle       0.80965 (    4)
  hydrogen bonds       : bond        0.11888 (  717)
  hydrogen bonds       : angle       5.84845 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 262
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7049 (t0)
REVERT: A  260 ILE cc_start: 0.7258 (mt) cc_final: 0.7034 (mt)
REVERT: A  465 GLN cc_start: 0.7415 (mt0) cc_final: 0.6683 (mt0)
REVERT: A  468 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7131 (mt-10)
REVERT: A  490 ASN cc_start: 0.7660 (m-40) cc_final: 0.7250 (m110)
REVERT: A  563 PRO cc_start: 0.7130 (Cg_endo) cc_final: 0.6902 (Cg_exo)
REVERT: B  322 MET cc_start: 0.7012 (tpp) cc_final: 0.6627 (tpp)
REVERT: B  438 PHE cc_start: 0.7489 (t80) cc_final: 0.7216 (t80)
REVERT: B  671 VAL cc_start: 0.7748 (t) cc_final: 0.7463 (p)
REVERT: B  679 LEU cc_start: 0.8030 (mt) cc_final: 0.7808 (mt)
  outliers start: 6
  outliers final: 2
  residues processed: 268
  average time/residue: 0.2341
  time to fit residues: 85.1771
Evaluate side-chains
  237 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 234
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  690 GLN
Chi-restraints excluded: chain B residue  160 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 117 optimal weight:    0.5980
   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 497 ASN
A 665 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.188623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.152948 restraints weight = 45075.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.158875 restraints weight = 18921.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.162265 restraints weight = 11023.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.164378 restraints weight = 8185.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.165149 restraints weight = 6916.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10282  Z= 0.210
  Angle     :  0.594   5.337  13983  Z= 0.328
  Chirality :  0.040   0.175   1586
  Planarity :  0.004   0.045   1709
  Dihedral  :  5.646  87.144   1323
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  0.51 %
    Favored  : 99.41 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  8.96 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.24), residues: 1187
  helix:  1.18 (0.16), residues: 921
  sheet:  None (None), residues: 0
  loop :  0.72 (0.44), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 145 
 TYR   0.023   0.002   TYR B 294 
 PHE   0.022   0.002   PHE B 624 
 TRP   0.016   0.001   TRP B 271 
 HIS   0.010   0.002   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (10280)
  covalent geometry    : angle       0.59391 (13979)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       1.32230 (    4)
  hydrogen bonds       : bond        0.04916 (  717)
  hydrogen bonds       : angle       4.98984 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 249
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7230 (t0)
REVERT: A  251 TYR cc_start: 0.7620 (t80) cc_final: 0.6642 (t80)
REVERT: A  451 THR cc_start: 0.7627 (t) cc_final: 0.7402 (m)
REVERT: A  465 GLN cc_start: 0.7241 (mt0) cc_final: 0.6677 (mt0)
REVERT: A  490 ASN cc_start: 0.7613 (m-40) cc_final: 0.7385 (m-40)
REVERT: A  631 ASN cc_start: 0.7883 (m-40) cc_final: 0.7388 (m-40)
REVERT: B  136 PHE cc_start: 0.7680 (m-10) cc_final: 0.7479 (m-80)
REVERT: B  212 MET cc_start: 0.6973 (ptm) cc_final: 0.6633 (ptp)
REVERT: B  294 TYR cc_start: 0.7107 (m-80) cc_final: 0.6848 (m-80)
REVERT: B  300 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.6338 (tt)
REVERT: B  438 PHE cc_start: 0.7494 (t80) cc_final: 0.7212 (t80)
REVERT: B  621 VAL cc_start: 0.7016 (t) cc_final: 0.6598 (m)
REVERT: B  648 SER cc_start: 0.8192 (p) cc_final: 0.7990 (t)
REVERT: B  649 ILE cc_start: 0.8282 (mt) cc_final: 0.8030 (mm)
REVERT: B  656 TYR cc_start: 0.7648 (t80) cc_final: 0.7340 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 257
  average time/residue: 0.2170
  time to fit residues: 76.7695
Evaluate side-chains
  259 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 244
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  601 THR
Chi-restraints excluded: chain A residue  622 THR
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain A residue  690 GLN
Chi-restraints excluded: chain B residue  141 TYR
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  622 THR
Chi-restraints excluded: chain B residue  677 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 113 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 153 ASN
B 353 GLN
B 625 ASN
B 665 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.183131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.147555 restraints weight = 44958.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.153472 restraints weight = 18228.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.156983 restraints weight = 10468.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.158767 restraints weight = 7682.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.159765 restraints weight = 6567.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10282  Z= 0.257
  Angle     :  0.622   9.577  13983  Z= 0.340
  Chirality :  0.040   0.172   1586
  Planarity :  0.005   0.065   1709
  Dihedral  :  5.493  89.750   1322
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.19 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.79 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1187
  helix:  1.13 (0.16), residues: 930
  sheet:  None (None), residues: 0
  loop :  0.41 (0.43), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 203 
 TYR   0.025   0.002   TYR B 651 
 PHE   0.069   0.002   PHE B  31 
 TRP   0.016   0.002   TRP B 223 
 HIS   0.008   0.002   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 (10280)
  covalent geometry    : angle       0.62223 (13979)
  SS BOND              : bond        0.00392 (    2)
  SS BOND              : angle       0.68704 (    4)
  hydrogen bonds       : bond        0.05195 (  717)
  hydrogen bonds       : angle       4.87103 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 248
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 GLN cc_start: 0.7246 (mt0) cc_final: 0.6981 (mt0)
REVERT: A  490 ASN cc_start: 0.7754 (m-40) cc_final: 0.7505 (m-40)
REVERT: A  597 LYS cc_start: 0.8086 (mttt) cc_final: 0.7785 (tttt)
REVERT: A  606 ASP cc_start: 0.7360 (m-30) cc_final: 0.7029 (m-30)
REVERT: A  631 ASN cc_start: 0.7963 (m-40) cc_final: 0.7368 (m-40)
REVERT: B  126 ILE cc_start: 0.8122 (mm) cc_final: 0.7796 (mt)
REVERT: B  212 MET cc_start: 0.7262 (ptm) cc_final: 0.6978 (ptp)
REVERT: B  319 MET cc_start: 0.5774 (tmm) cc_final: 0.5503 (tmm)
REVERT: B  326 MET cc_start: 0.6403 (ttm) cc_final: 0.6050 (ttm)
REVERT: B  438 PHE cc_start: 0.7550 (t80) cc_final: 0.7283 (t80)
REVERT: B  534 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6780 (tt)
REVERT: B  607 ASP cc_start: 0.7813 (t0) cc_final: 0.7510 (t0)
REVERT: B  648 SER cc_start: 0.8227 (p) cc_final: 0.7953 (t)
REVERT: B  673 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7227 (mm-30)
  outliers start: 22
  outliers final: 10
  residues processed: 258
  average time/residue: 0.2117
  time to fit residues: 75.6662
Evaluate side-chains
  251 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 240
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  690 GLN
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  534 LEU
Chi-restraints excluded: chain B residue  535 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 6 optimal weight:    0.1980
   chunk 79 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 497 ASN
B 665 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.182697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.147354 restraints weight = 44503.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.153226 restraints weight = 17823.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.156720 restraints weight = 10185.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.158572 restraints weight = 7470.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.159293 restraints weight = 6368.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.4088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10282  Z= 0.200
  Angle     :  0.539   5.787  13983  Z= 0.296
  Chirality :  0.037   0.171   1586
  Planarity :  0.004   0.039   1709
  Dihedral  :  5.190  87.381   1320
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.77 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.73 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.24), residues: 1187
  helix:  1.47 (0.16), residues: 936
  sheet:  None (None), residues: 0
  loop :  0.46 (0.43), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 203 
 TYR   0.017   0.002   TYR B 256 
 PHE   0.025   0.001   PHE B 624 
 TRP   0.014   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (10280)
  covalent geometry    : angle       0.53864 (13979)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       0.63006 (    4)
  hydrogen bonds       : bond        0.04621 (  717)
  hydrogen bonds       : angle       4.65436 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 240
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7709 (t0)
REVERT: A  204 ASP cc_start: 0.6639 (m-30) cc_final: 0.6254 (m-30)
REVERT: A  465 GLN cc_start: 0.7224 (mt0) cc_final: 0.6919 (mt0)
REVERT: A  490 ASN cc_start: 0.7766 (m-40) cc_final: 0.7524 (m-40)
REVERT: A  606 ASP cc_start: 0.7381 (m-30) cc_final: 0.7086 (m-30)
REVERT: A  658 ILE cc_start: 0.8328 (mm) cc_final: 0.7969 (mt)
REVERT: B  126 ILE cc_start: 0.8133 (mm) cc_final: 0.7843 (mt)
REVERT: B  189 TYR cc_start: 0.8334 (m-80) cc_final: 0.8132 (m-80)
REVERT: B  212 MET cc_start: 0.7200 (ptm) cc_final: 0.7000 (ptp)
REVERT: B  264 THR cc_start: 0.8136 (p) cc_final: 0.7069 (m)
REVERT: B  294 TYR cc_start: 0.7355 (m-80) cc_final: 0.7109 (m-80)
REVERT: B  319 MET cc_start: 0.5779 (tmm) cc_final: 0.5517 (tmm)
REVERT: B  326 MET cc_start: 0.6325 (ttm) cc_final: 0.5989 (ttm)
REVERT: B  438 PHE cc_start: 0.7560 (t80) cc_final: 0.7304 (t80)
REVERT: B  584 VAL cc_start: 0.8017 (p) cc_final: 0.7679 (t)
REVERT: B  607 ASP cc_start: 0.7838 (t0) cc_final: 0.7550 (t0)
REVERT: B  629 MET cc_start: 0.7438 (mmm) cc_final: 0.7118 (mmt)
REVERT: B  648 SER cc_start: 0.8273 (p) cc_final: 0.7980 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 246
  average time/residue: 0.2219
  time to fit residues: 75.0032
Evaluate side-chains
  243 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 232
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  242 GLN
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  690 GLN
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  664 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN
B 454 ASN
B 625 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.177787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.142543 restraints weight = 44171.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.148143 restraints weight = 17667.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.151455 restraints weight = 10178.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.153423 restraints weight = 7555.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.154065 restraints weight = 6416.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.089  10282  Z= 0.381
  Angle     :  0.662   7.507  13983  Z= 0.368
  Chirality :  0.044   0.182   1586
  Planarity :  0.005   0.071   1709
  Dihedral  :  5.459  84.460   1320
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.86 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.65 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.24), residues: 1187
  helix:  0.97 (0.16), residues: 927
  sheet:  None (None), residues: 0
  loop : -0.16 (0.42), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 200 
 TYR   0.025   0.002   TYR B 294 
 PHE   0.030   0.002   PHE A 675 
 TRP   0.015   0.002   TRP B 223 
 HIS   0.006   0.002   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00842 (10280)
  covalent geometry    : angle       0.66177 (13979)
  SS BOND              : bond        0.00578 (    2)
  SS BOND              : angle       1.06138 (    4)
  hydrogen bonds       : bond        0.05684 (  717)
  hydrogen bonds       : angle       5.11214 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 244
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TYR cc_start: 0.4926 (m-80) cc_final: 0.4557 (m-80)
REVERT: A  278 SER cc_start: 0.8595 (t) cc_final: 0.8246 (p)
REVERT: A  326 MET cc_start: 0.7532 (ttm) cc_final: 0.7295 (ttm)
REVERT: A  465 GLN cc_start: 0.7255 (mt0) cc_final: 0.7014 (mt0)
REVERT: A  490 ASN cc_start: 0.7942 (m-40) cc_final: 0.7614 (m-40)
REVERT: A  606 ASP cc_start: 0.7430 (m-30) cc_final: 0.7180 (m-30)
REVERT: A  634 VAL cc_start: 0.8276 (t) cc_final: 0.7967 (p)
REVERT: B  126 ILE cc_start: 0.8112 (mm) cc_final: 0.7796 (mm)
REVERT: B  168 LEU cc_start: 0.8044 (tp) cc_final: 0.7785 (tp)
REVERT: B  319 MET cc_start: 0.5923 (tmm) cc_final: 0.5675 (tmm)
REVERT: B  320 ASP cc_start: 0.6630 (m-30) cc_final: 0.5874 (m-30)
REVERT: B  607 ASP cc_start: 0.7817 (t0) cc_final: 0.7593 (t0)
REVERT: B  637 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6772 (mm-30)
REVERT: B  648 SER cc_start: 0.8247 (p) cc_final: 0.7844 (t)
REVERT: B  673 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7221 (mm-30)
  outliers start: 19
  outliers final: 12
  residues processed: 250
  average time/residue: 0.2273
  time to fit residues: 78.6442
Evaluate side-chains
  245 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 233
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  497 ASN
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  659 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0980
   chunk 49 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 321 GLN
A 690 GLN
B 665 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.180031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.145035 restraints weight = 44003.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.150842 restraints weight = 17440.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.154263 restraints weight = 9902.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.155834 restraints weight = 7261.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.156962 restraints weight = 6277.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10282  Z= 0.164
  Angle     :  0.524   6.411  13983  Z= 0.286
  Chirality :  0.036   0.152   1586
  Planarity :  0.004   0.048   1709
  Dihedral  :  4.413  23.092   1317
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.68 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.40 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.24), residues: 1187
  helix:  1.47 (0.16), residues: 935
  sheet:  None (None), residues: 0
  loop :  0.12 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 203 
 TYR   0.018   0.001   TYR B  78 
 PHE   0.021   0.001   PHE A 675 
 TRP   0.013   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10280)
  covalent geometry    : angle       0.52368 (13979)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       0.39885 (    4)
  hydrogen bonds       : bond        0.04597 (  717)
  hydrogen bonds       : angle       4.64254 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 230
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TYR cc_start: 0.4794 (m-80) cc_final: 0.4371 (m-80)
REVERT: A  229 PHE cc_start: 0.7382 (t80) cc_final: 0.7169 (t80)
REVERT: A  326 MET cc_start: 0.7474 (ttm) cc_final: 0.7242 (ttm)
REVERT: A  465 GLN cc_start: 0.7139 (mt0) cc_final: 0.6918 (mt0)
REVERT: A  490 ASN cc_start: 0.7877 (m-40) cc_final: 0.7544 (m-40)
REVERT: A  606 ASP cc_start: 0.7401 (m-30) cc_final: 0.7144 (m-30)
REVERT: A  634 VAL cc_start: 0.8215 (t) cc_final: 0.7989 (p)
REVERT: B  168 LEU cc_start: 0.7905 (tp) cc_final: 0.7682 (tp)
REVERT: B  189 TYR cc_start: 0.8226 (m-80) cc_final: 0.7496 (m-80)
REVERT: B  320 ASP cc_start: 0.6599 (m-30) cc_final: 0.5866 (m-30)
REVERT: B  584 VAL cc_start: 0.8041 (p) cc_final: 0.7722 (t)
REVERT: B  607 ASP cc_start: 0.7803 (t0) cc_final: 0.7558 (t0)
REVERT: B  648 SER cc_start: 0.8256 (p) cc_final: 0.7895 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 234
  average time/residue: 0.2189
  time to fit residues: 70.9446
Evaluate side-chains
  236 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 226
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  659 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  664 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN
B 665 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.178566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.143514 restraints weight = 44210.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.149139 restraints weight = 17560.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152618 restraints weight = 10086.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.154367 restraints weight = 7401.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.155047 restraints weight = 6342.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.5208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  10282  Z= 0.277
  Angle     :  0.584   8.014  13983  Z= 0.320
  Chirality :  0.038   0.165   1586
  Planarity :  0.004   0.071   1709
  Dihedral  :  4.517  23.291   1317
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.70 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.77 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.24), residues: 1187
  helix:  1.38 (0.16), residues: 931
  sheet:  None (None), residues: 0
  loop : -0.14 (0.42), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 203 
 TYR   0.020   0.002   TYR B  78 
 PHE   0.018   0.001   PHE A 675 
 TRP   0.013   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 (10280)
  covalent geometry    : angle       0.58425 (13979)
  SS BOND              : bond        0.00457 (    2)
  SS BOND              : angle       0.62473 (    4)
  hydrogen bonds       : bond        0.05048 (  717)
  hydrogen bonds       : angle       4.79307 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 230
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TYR cc_start: 0.4913 (m-80) cc_final: 0.4366 (m-80)
REVERT: A  326 MET cc_start: 0.7522 (ttm) cc_final: 0.7289 (ttm)
REVERT: A  465 GLN cc_start: 0.7243 (mt0) cc_final: 0.6994 (mt0)
REVERT: A  490 ASN cc_start: 0.7961 (m-40) cc_final: 0.7615 (m-40)
REVERT: A  606 ASP cc_start: 0.7434 (m-30) cc_final: 0.7177 (m-30)
REVERT: B  126 ILE cc_start: 0.8069 (tp) cc_final: 0.7818 (tt)
REVERT: B  168 LEU cc_start: 0.7956 (tp) cc_final: 0.7723 (tp)
REVERT: B  320 ASP cc_start: 0.6608 (m-30) cc_final: 0.6359 (m-30)
REVERT: B  584 VAL cc_start: 0.8071 (p) cc_final: 0.7740 (t)
REVERT: B  607 ASP cc_start: 0.7796 (t0) cc_final: 0.7579 (t0)
REVERT: B  648 SER cc_start: 0.8247 (p) cc_final: 0.7873 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 234
  average time/residue: 0.2301
  time to fit residues: 74.1259
Evaluate side-chains
  239 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 228
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  497 ASN
Chi-restraints excluded: chain A residue  600 GLU
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  659 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  310 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 56 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9980
   chunk 57 optimal weight:    0.4980
   chunk 68 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   chunk 6 optimal weight:    0.0980
   chunk 35 optimal weight:    0.1980
   chunk 3 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 115 optimal weight:    0.1980
   overall best weight:    0.1780

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS
B 625 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.182150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.147356 restraints weight = 43990.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.153127 restraints weight = 17306.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.156538 restraints weight = 9836.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.158300 restraints weight = 7220.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.158847 restraints weight = 6165.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10282  Z= 0.116
  Angle     :  0.502   8.252  13983  Z= 0.268
  Chirality :  0.035   0.142   1586
  Planarity :  0.003   0.038   1709
  Dihedral  :  4.189  18.589   1317
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.35 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 15.51 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.24), residues: 1187
  helix:  1.79 (0.16), residues: 934
  sheet:  None (None), residues: 0
  loop :  0.30 (0.44), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 203 
 TYR   0.022   0.001   TYR B  78 
 PHE   0.015   0.001   PHE A 501 
 TRP   0.012   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (10280)
  covalent geometry    : angle       0.50184 (13979)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       0.18368 (    4)
  hydrogen bonds       : bond        0.04186 (  717)
  hydrogen bonds       : angle       4.42250 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 228
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TYR cc_start: 0.4794 (m-80) cc_final: 0.4281 (m-80)
REVERT: A  326 MET cc_start: 0.7503 (ttm) cc_final: 0.7256 (ttm)
REVERT: A  465 GLN cc_start: 0.7185 (mt0) cc_final: 0.6952 (mt0)
REVERT: A  490 ASN cc_start: 0.7946 (m-40) cc_final: 0.7597 (m-40)
REVERT: A  606 ASP cc_start: 0.7430 (m-30) cc_final: 0.7149 (m-30)
REVERT: A  637 GLU cc_start: 0.7534 (tp30) cc_final: 0.7324 (tp30)
REVERT: B  126 ILE cc_start: 0.8046 (tp) cc_final: 0.7821 (tt)
REVERT: B  168 LEU cc_start: 0.7904 (tp) cc_final: 0.7669 (tp)
REVERT: B  320 ASP cc_start: 0.6602 (m-30) cc_final: 0.6183 (m-30)
REVERT: B  584 VAL cc_start: 0.7920 (p) cc_final: 0.7612 (t)
REVERT: B  607 ASP cc_start: 0.7792 (t0) cc_final: 0.7576 (t0)
REVERT: B  648 SER cc_start: 0.8266 (p) cc_final: 0.7878 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 229
  average time/residue: 0.2293
  time to fit residues: 72.2072
Evaluate side-chains
  235 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 227
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 99 optimal weight:    0.1980
   chunk 111 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   chunk 98 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN
B 665 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.180453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.145516 restraints weight = 43866.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.151164 restraints weight = 17319.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.154580 restraints weight = 9919.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.156048 restraints weight = 7302.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.157135 restraints weight = 6361.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.5396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10282  Z= 0.168
  Angle     :  0.514   8.960  13983  Z= 0.278
  Chirality :  0.035   0.146   1586
  Planarity :  0.004   0.038   1709
  Dihedral  :  4.166  19.268   1317
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.11 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 15.51 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.31 (0.24), residues: 1187
  helix:  1.89 (0.16), residues: 935
  sheet:  None (None), residues: 0
  loop :  0.31 (0.44), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 324 
 TYR   0.016   0.001   TYR B  78 
 PHE   0.013   0.001   PHE A 501 
 TRP   0.012   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (10280)
  covalent geometry    : angle       0.51405 (13979)
  SS BOND              : bond        0.00330 (    2)
  SS BOND              : angle       0.38552 (    4)
  hydrogen bonds       : bond        0.04312 (  717)
  hydrogen bonds       : angle       4.45910 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 227
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TYR cc_start: 0.4911 (m-80) cc_final: 0.4361 (m-80)
REVERT: A  326 MET cc_start: 0.7486 (ttm) cc_final: 0.7239 (ttm)
REVERT: A  465 GLN cc_start: 0.7191 (mt0) cc_final: 0.6974 (mt0)
REVERT: A  490 ASN cc_start: 0.7932 (m-40) cc_final: 0.7602 (m-40)
REVERT: A  606 ASP cc_start: 0.7438 (m-30) cc_final: 0.7167 (m-30)
REVERT: A  637 GLU cc_start: 0.7540 (tp30) cc_final: 0.7241 (tp30)
REVERT: B  126 ILE cc_start: 0.8081 (tp) cc_final: 0.7853 (tt)
REVERT: B  168 LEU cc_start: 0.7883 (tp) cc_final: 0.7650 (tp)
REVERT: B  320 ASP cc_start: 0.6612 (m-30) cc_final: 0.6273 (m-30)
REVERT: B  584 VAL cc_start: 0.7911 (p) cc_final: 0.7592 (t)
REVERT: B  607 ASP cc_start: 0.7770 (t0) cc_final: 0.7559 (t0)
REVERT: B  648 SER cc_start: 0.8231 (p) cc_final: 0.7874 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 228
  average time/residue: 0.2314
  time to fit residues: 72.7581
Evaluate side-chains
  233 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 225
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   chunk 112 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 109 optimal weight:    0.2980
   chunk 62 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0050
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN
B 665 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.181349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.146561 restraints weight = 44133.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.152186 restraints weight = 17466.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.155609 restraints weight = 10039.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.157449 restraints weight = 7382.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.158107 restraints weight = 6314.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6758
moved from start:          0.5511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10282  Z= 0.162
  Angle     :  0.518   9.653  13983  Z= 0.278
  Chirality :  0.035   0.144   1586
  Planarity :  0.004   0.057   1709
  Dihedral  :  4.109  18.300   1317
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.27 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 15.60 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.24), residues: 1187
  helix:  1.94 (0.16), residues: 935
  sheet:  None (None), residues: 0
  loop :  0.30 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 324 
 TYR   0.015   0.001   TYR B  78 
 PHE   0.013   0.001   PHE A 501 
 TRP   0.013   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10280)
  covalent geometry    : angle       0.51773 (13979)
  SS BOND              : bond        0.00291 (    2)
  SS BOND              : angle       0.35188 (    4)
  hydrogen bonds       : bond        0.04228 (  717)
  hydrogen bonds       : angle       4.40647 ( 2124)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 226
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TYR cc_start: 0.4906 (m-80) cc_final: 0.4328 (m-80)
REVERT: A  326 MET cc_start: 0.7501 (ttm) cc_final: 0.7248 (ttm)
REVERT: A  465 GLN cc_start: 0.7202 (mt0) cc_final: 0.6983 (mt0)
REVERT: A  490 ASN cc_start: 0.7964 (m-40) cc_final: 0.7645 (m-40)
REVERT: A  606 ASP cc_start: 0.7451 (m-30) cc_final: 0.7190 (m-30)
REVERT: B  320 ASP cc_start: 0.6592 (m-30) cc_final: 0.6301 (m-30)
REVERT: B  648 SER cc_start: 0.8223 (p) cc_final: 0.7870 (t)
  outliers start: 11
  outliers final: 10
  residues processed: 227
  average time/residue: 0.2406
  time to fit residues: 74.7060
Evaluate side-chains
  236 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 226
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  328 GLU
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 93 optimal weight:    0.2980
   chunk 83 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 77 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN
B 665 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.180420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.145540 restraints weight = 44182.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.151229 restraints weight = 17341.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.154637 restraints weight = 9890.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.156330 restraints weight = 7263.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.157419 restraints weight = 6243.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.5620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10282  Z= 0.184
  Angle     :  0.520   6.395  13983  Z= 0.283
  Chirality :  0.036   0.144   1586
  Planarity :  0.004   0.041   1709
  Dihedral  :  4.126  18.937   1317
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.27 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 15.51 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.35 (0.24), residues: 1187
  helix:  1.93 (0.16), residues: 938
  sheet:  None (None), residues: 0
  loop :  0.28 (0.43), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 428 
 TYR   0.014   0.001   TYR B 256 
 PHE   0.013   0.001   PHE B 469 
 TRP   0.019   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10280)
  covalent geometry    : angle       0.51960 (13979)
  SS BOND              : bond        0.00340 (    2)
  SS BOND              : angle       0.43827 (    4)
  hydrogen bonds       : bond        0.04337 (  717)
  hydrogen bonds       : angle       4.42355 ( 2124)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3497.77 seconds
wall clock time: 60 minutes 9.28 seconds (3609.28 seconds total)