Starting phenix.real_space_refine
on Wed Sep 17 21:22:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yo3_39434/09_2025/8yo3_39434.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yo3_39434/09_2025/8yo3_39434.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yo3_39434/09_2025/8yo3_39434.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yo3_39434/09_2025/8yo3_39434.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yo3_39434/09_2025/8yo3_39434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yo3_39434/09_2025/8yo3_39434.map"
  }
  resolution = 3.62
  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=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    7360      2.51       5
     N    1948      2.21       5
     O    2164      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11514
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3563
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 13, 'TRANS': 428}
    Chain: "C"
      Number of atoms: 2194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2194
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 7, 'TRANS': 265}
    Chain: "B"
      Number of atoms: 3563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3563
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 13, 'TRANS': 428}
    Chain: "D"
      Number of atoms: 2194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2194
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 7, 'TRANS': 265}
  Time building chain proxies: 2.89, per 1000 atoms: 0.25
  Number of scatterers: 11514
  At special positions: 0
  Unit cell: (108, 147, 113, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    2164      8.00
     N    1948      7.00
     C    7360      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 569.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2672

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 20 sheets defined
      46.4% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 16
      removed outlier: 3.631A  pdb=" N   SER A  10 " --> pdb=" O   ARG A   6 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE A  11 " --> pdb=" O   ASP A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 26
      removed outlier: 3.505A  pdb=" N   ASN A  26 " --> pdb=" O   TYR A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 51
    Processing helix  chain 'A' and resid 61 through 72
      removed outlier: 3.611A  pdb=" N   VAL A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ALA A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   ASP A  70 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A  71 " --> pdb=" O   GLY A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 89
      removed outlier: 3.690A  pdb=" N   ASN A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
      removed outlier: 3.594A  pdb=" N   TYR A 127 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 136
    Processing helix  chain 'A' and resid 156 through 161
      removed outlier: 3.856A  pdb=" N   GLY A 161 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 190
    Processing helix  chain 'A' and resid 239 through 254
      removed outlier: 4.205A  pdb=" N   ASP A 249 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      Proline residue:  A 250  - end of helix
    Processing helix  chain 'A' and resid 283 through 295
    Processing helix  chain 'A' and resid 319 through 366
      removed outlier: 3.608A  pdb=" N   LEU A 323 " --> pdb=" O   ASN A 319 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR A 333 " --> pdb=" O   GLU A 329 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TYR A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY A 366 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 384
    Processing helix  chain 'A' and resid 391 through 397
    Processing helix  chain 'A' and resid 399 through 403
    Processing helix  chain 'A' and resid 404 through 427
    Processing helix  chain 'A' and resid 429 through 438
      removed outlier: 3.588A  pdb=" N   ASP A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 419 through 427
      removed outlier: 4.118A  pdb=" N   LEU C 423 " --> pdb=" O   ALA C 419 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ASP C 425 " --> pdb=" O   GLY C 421 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 452
    Processing helix  chain 'C' and resid 455 through 466
    Processing helix  chain 'C' and resid 509 through 514
      removed outlier: 3.500A  pdb=" N   LYS C 514 " --> pdb=" O   GLY C 510 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 523 through 527
    Processing helix  chain 'C' and resid 528 through 534
    Processing helix  chain 'C' and resid 559 through 564
    Processing helix  chain 'C' and resid 565 through 575
      removed outlier: 4.060A  pdb=" N   SER C 569 " --> pdb=" O   SER C 565 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU C 571 " --> pdb=" O   TYR C 567 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 578 through 583
      removed outlier: 3.757A  pdb=" N   GLU C 582 " --> pdb=" O   PRO C 578 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 607 through 616
      removed outlier: 4.588A  pdb=" N   ASP C 616 " --> pdb=" O   GLU C 612 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 628 through 632
      removed outlier: 3.561A  pdb=" N   SER C 631 " --> pdb=" O   GLY C 628 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU C 632 " --> pdb=" O   LEU C 629 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 628 through 632'
    Processing helix  chain 'C' and resid 633 through 643
    Processing helix  chain 'C' and resid 654 through 662
      removed outlier: 3.594A  pdb=" N   LEU C 658 " --> pdb=" O   ASN C 654 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE C 659 " --> pdb=" O   TRP C 655 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   GLU C 660 " --> pdb=" O   LYS C 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 16
    Processing helix  chain 'B' and resid 18 through 25
    Processing helix  chain 'B' and resid 37 through 51
      removed outlier: 3.516A  pdb=" N   PHE B  42 " --> pdb=" O   PRO B  38 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL B  43 " --> pdb=" O   VAL B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 67
    Processing helix  chain 'B' and resid 67 through 72
    Processing helix  chain 'B' and resid 75 through 89
      removed outlier: 4.302A  pdb=" N   SER B  79 " --> pdb=" O   HIS B  75 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA B  80 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ASN B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 130
      removed outlier: 3.702A  pdb=" N   TYR B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 136
    Processing helix  chain 'B' and resid 156 through 161
      removed outlier: 3.859A  pdb=" N   GLY B 161 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 191
    Processing helix  chain 'B' and resid 239 through 247
    Processing helix  chain 'B' and resid 247 through 254
      removed outlier: 3.511A  pdb=" N   LEU B 251 " --> pdb=" O   ILE B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 295
    Processing helix  chain 'B' and resid 319 through 366
      removed outlier: 3.532A  pdb=" N   LEU B 323 " --> pdb=" O   ASN B 319 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU B 329 " --> pdb=" O   LYS B 325 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR B 333 " --> pdb=" O   GLU B 329 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TYR B 334 " --> pdb=" O   VAL B 330 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ILE B 360 " --> pdb=" O   LYS B 356 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS B 361 " --> pdb=" O   ALA B 357 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER B 365 " --> pdb=" O   LYS B 361 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY B 366 " --> pdb=" O   LYS B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 384
    Processing helix  chain 'B' and resid 385 through 390
      removed outlier: 3.940A  pdb=" N   SER B 390 " --> pdb=" O   ASP B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 397
    Processing helix  chain 'B' and resid 399 through 403
    Processing helix  chain 'B' and resid 404 through 427
    Processing helix  chain 'B' and resid 429 through 437
      removed outlier: 3.569A  pdb=" N   ASP B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 440
      No H-bonds generated for 'chain 'B' and resid 438 through 440'
    Processing helix  chain 'D' and resid 420 through 427
      removed outlier: 4.075A  pdb=" N   ASP D 425 " --> pdb=" O   GLY D 421 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 455 through 466
      removed outlier: 3.563A  pdb=" N   CYS D 462 " --> pdb=" O   LEU D 458 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 509 through 514
      removed outlier: 3.525A  pdb=" N   LYS D 514 " --> pdb=" O   GLY D 510 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 523 through 527
    Processing helix  chain 'D' and resid 528 through 534
    Processing helix  chain 'D' and resid 559 through 564
      removed outlier: 3.620A  pdb=" N   GLY D 564 " --> pdb=" O   HIS D 560 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
      removed outlier: 4.064A  pdb=" N   SER D 569 " --> pdb=" O   SER D 565 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   LEU D 571 " --> pdb=" O   TYR D 567 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 578 through 584
      removed outlier: 3.627A  pdb=" N   GLU D 582 " --> pdb=" O   PRO D 578 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 607 through 616
      removed outlier: 4.659A  pdb=" N   ASP D 616 " --> pdb=" O   GLU D 612 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 628 through 632
      removed outlier: 3.591A  pdb=" N   SER D 631 " --> pdb=" O   GLY D 628 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 633 through 643
    Processing helix  chain 'D' and resid 654 through 662
      removed outlier: 3.534A  pdb=" N   PHE D 659 " --> pdb=" O   TRP D 655 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLU D 660 " --> pdb=" O   LYS D 656 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4
      removed outlier: 6.404A  pdb=" N   LEU C 411 " --> pdb=" O   ALA C 553 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   MET C 555 " --> pdb=" O   LEU C 411 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   LEU C 413 " --> pdb=" O   MET C 555 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60
    Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 166
    Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 211
    Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 223
    Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 308
      removed outlier: 4.384A  pdb=" N   ILE A 305 " --> pdb=" O   TYR A 317 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 474 through 476
      removed outlier: 6.847A  pdb=" N   GLU C 475 " --> pdb=" O   LYS C 543 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 490 through 495
    Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 508
    Processing sheet with id=AB1, first strand: chain 'C' and resid 604 through 605
      removed outlier: 3.712A  pdb=" N   ILE C 595 " --> pdb=" O   ARG C 624 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ARG C 624 " --> pdb=" O   ILE C 595 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 3
      removed outlier: 6.613A  pdb=" N   GLN B   2 " --> pdb=" O   TYR D 646 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 60
    Processing sheet with id=AB4, first strand: chain 'B' and resid 162 through 165
    Processing sheet with id=AB5, first strand: chain 'B' and resid 207 through 211
    Processing sheet with id=AB6, first strand: chain 'B' and resid 221 through 223
    Processing sheet with id=AB7, first strand: chain 'B' and resid 305 through 308
      removed outlier: 4.315A  pdb=" N   ILE B 305 " --> pdb=" O   TYR B 317 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 411 through 414
      removed outlier: 6.246A  pdb=" N   LEU D 411 " --> pdb=" O   ALA D 553 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   MET D 555 " --> pdb=" O   LEU D 411 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   LEU D 413 " --> pdb=" O   MET D 555 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 490 through 495
    Processing sheet with id=AC1, first strand: chain 'D' and resid 505 through 508
    Processing sheet with id=AC2, first strand: chain 'D' and resid 594 through 595

    473 hydrogen bonds defined for protein.
    1305 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: 1.93

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3724
        1.34 -     1.46: 1766
        1.46 -     1.57: 6182
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 11750
  Sorted by residual:
  bond pdb=" C   TYR D 567 "
       pdb=" N   PRO D 568 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 9.80e-03 1.04e+04 2.05e+00
  bond pdb=" CB  ASP A  70 "
       pdb=" CG  ASP A  70 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.29e+00
  bond pdb=" CA  ASP A  70 "
       pdb=" CB  ASP A  70 "
    ideal  model  delta    sigma   weight residual
    1.528  1.546 -0.017 1.56e-02 4.11e+03 1.23e+00
  bond pdb=" C   TYR C 567 "
       pdb=" N   PRO C 568 "
    ideal  model  delta    sigma   weight residual
    1.337  1.348 -0.012 1.06e-02 8.90e+03 1.19e+00
  bond pdb=" CB  LYS A   9 "
       pdb=" CG  LYS A   9 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.19e+00
  ... (remaining 11745 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 15675
        2.43 -     4.86: 124
        4.86 -     7.29: 22
        7.29 -     9.72: 4
        9.72 -    12.15: 1
  Bond angle restraints: 15826
  Sorted by residual:
  angle pdb=" CB  LYS A   9 "
        pdb=" CG  LYS A   9 "
        pdb=" CD  LYS A   9 "
      ideal   model   delta    sigma   weight residual
     111.30  119.79   -8.49 2.30e+00 1.89e-01 1.36e+01
  angle pdb=" CA  LEU B 395 "
        pdb=" CB  LEU B 395 "
        pdb=" CG  LEU B 395 "
      ideal   model   delta    sigma   weight residual
     116.30  128.45  -12.15 3.50e+00 8.16e-02 1.21e+01
  angle pdb=" N   ILE C 420 "
        pdb=" CA  ILE C 420 "
        pdb=" C   ILE C 420 "
      ideal   model   delta    sigma   weight residual
     113.07  108.43    4.64 1.36e+00 5.41e-01 1.16e+01
  angle pdb=" CA  MET C 447 "
        pdb=" CB  MET C 447 "
        pdb=" CG  MET C 447 "
      ideal   model   delta    sigma   weight residual
     114.10  119.51   -5.41 2.00e+00 2.50e-01 7.32e+00
  angle pdb=" C   SER D 565 "
        pdb=" N   ILE D 566 "
        pdb=" CA  ILE D 566 "
      ideal   model   delta    sigma   weight residual
     121.97  126.78   -4.81 1.80e+00 3.09e-01 7.14e+00
  ... (remaining 15821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 6046
       17.85 -    35.70: 803
       35.70 -    53.56: 195
       53.56 -    71.41: 32
       71.41 -    89.26: 16
  Dihedral angle restraints: 7092
    sinusoidal: 2928
      harmonic: 4164
  Sorted by residual:
  dihedral pdb=" CA  GLY A 366 "
           pdb=" C   GLY A 366 "
           pdb=" N   GLU A 367 "
           pdb=" CA  GLU A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.07  -23.93     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  GLY B 366 "
           pdb=" C   GLY B 366 "
           pdb=" N   GLU B 367 "
           pdb=" CA  GLU B 367 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.10  -22.90     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  TYR B 238 "
           pdb=" C   TYR B 238 "
           pdb=" N   ASP B 239 "
           pdb=" CA  ASP B 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.40   22.60     0      5.00e+00 4.00e-02 2.04e+01
  ... (remaining 7089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1273
       0.040 -    0.080: 308
       0.080 -    0.120: 121
       0.120 -    0.159: 8
       0.159 -    0.199: 2
  Chirality restraints: 1712
  Sorted by residual:
  chirality pdb=" CG  LEU D 431 "
            pdb=" CB  LEU D 431 "
            pdb=" CD1 LEU D 431 "
            pdb=" CD2 LEU D 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CG  LEU C 431 "
            pdb=" CB  LEU C 431 "
            pdb=" CD1 LEU C 431 "
            pdb=" CD2 LEU C 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.48e-01
  chirality pdb=" CA  ILE A  29 "
            pdb=" N   ILE A  29 "
            pdb=" C   ILE A  29 "
            pdb=" CB  ILE A  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 1709 not shown)

  Planarity restraints: 2026
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  17 "    0.012 2.00e-02 2.50e+03   2.35e-02 5.54e+00
        pdb=" C   LEU A  17 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   LEU A  17 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA A  18 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 359 "   -0.009 2.00e-02 2.50e+03   1.37e-02 3.26e+00
        pdb=" CG  PHE B 359 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 359 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 359 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 359 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 359 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 359 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 360 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   ILE B 360 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE B 360 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS B 361 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2023 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 477
        2.72 -     3.27: 11771
        3.27 -     3.81: 19018
        3.81 -     4.36: 23177
        4.36 -     4.90: 39116
  Nonbonded interactions: 93559
  Sorted by model distance:
  nonbonded pdb=" O   ASN D 654 "
            pdb=" ND2 ASN D 654 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" O   ASN C 654 "
            pdb=" ND2 ASN C 654 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" O   GLY D 572 "
            pdb=" OG  SER D 575 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   ILE B 153 "
            pdb=" OH  TYR B 434 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   TRP B  91 "
            pdb=" OH  TYR B 236 "
     model   vdw
     2.218 3.040
  ... (remaining 93554 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     12.280
  Find NCS groups from input model:        0.170
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
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      :  0.002   0.033  11750  Z= 0.111
  Angle     :  0.570  12.152  15826  Z= 0.298
  Chirality :  0.040   0.199   1712
  Planarity :  0.003   0.035   2026
  Dihedral  : 16.911  89.260   4420
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 24.11 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.23), residues: 1422
  helix:  0.54 (0.23), residues: 564
  sheet: -0.61 (0.41), residues: 190
  loop : -0.04 (0.26), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 107 
 TYR   0.016   0.001   TYR C 422 
 PHE   0.031   0.001   PHE B 359 
 TRP   0.025   0.001   TRP C 655 
 HIS   0.008   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (11750)
  covalent geometry    : angle       0.56973 (15826)
  hydrogen bonds       : bond        0.22547 (  473)
  hydrogen bonds       : angle       8.03280 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 179
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  297 LEU cc_start: 0.7715 (mm) cc_final: 0.7463 (tp)
REVERT: A  398 MET cc_start: 0.7872 (mtm) cc_final: 0.7666 (mtp)
  outliers start: 9
  outliers final: 4
  residues processed: 179
  average time/residue: 0.0907
  time to fit residues: 24.8045
Evaluate side-chains
  170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 166
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain B residue   21 MET
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0970
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  26 ASN
A 176 HIS
C 654 ASN
B 176 HIS
D 536 ASN
D 642 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.166242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.116742 restraints weight = 16755.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120234 restraints weight = 9782.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.122501 restraints weight = 7167.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.123647 restraints weight = 5983.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.124574 restraints weight = 5440.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11750  Z= 0.142
  Angle     :  0.559   7.846  15826  Z= 0.298
  Chirality :  0.042   0.165   1712
  Planarity :  0.003   0.044   2026
  Dihedral  :  5.154  58.261   1560
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.85 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.23), residues: 1422
  helix:  0.53 (0.22), residues: 582
  sheet: -1.19 (0.40), residues: 170
  loop : -0.03 (0.26), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 107 
 TYR   0.017   0.001   TYR C 422 
 PHE   0.023   0.001   PHE B 350 
 TRP   0.016   0.001   TRP C 655 
 HIS   0.007   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (11750)
  covalent geometry    : angle       0.55897 (15826)
  hydrogen bonds       : bond        0.04044 (  473)
  hydrogen bonds       : angle       5.54202 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 183
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8005 (mp10) cc_final: 0.7734 (mp10)
REVERT: C  431 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8247 (pp)
REVERT: C  447 MET cc_start: 0.4916 (tmm) cc_final: 0.4589 (tmm)
REVERT: C  517 MET cc_start: 0.1024 (ppp) cc_final: -0.0013 (pmm)
REVERT: B  380 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7848 (tp30)
REVERT: D  417 ASP cc_start: 0.7690 (t70) cc_final: 0.7397 (t70)
  outliers start: 34
  outliers final: 16
  residues processed: 204
  average time/residue: 0.0939
  time to fit residues: 29.0638
Evaluate side-chains
  183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ASP
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  663 MET
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  387 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 127 optimal weight:   30.0000
   chunk 89 optimal weight:    0.9980
   chunk 48 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 111 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A  89 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.162611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.113148 restraints weight = 16838.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.116519 restraints weight = 9865.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.118719 restraints weight = 7239.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.119840 restraints weight = 6042.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.120632 restraints weight = 5491.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11750  Z= 0.188
  Angle     :  0.561   7.705  15826  Z= 0.296
  Chirality :  0.042   0.166   1712
  Planarity :  0.003   0.050   2026
  Dihedral  :  4.783  36.320   1552
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.81 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.23), residues: 1422
  helix:  0.60 (0.22), residues: 580
  sheet: -1.52 (0.41), residues: 154
  loop : -0.07 (0.25), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 205 
 TYR   0.019   0.002   TYR C 422 
 PHE   0.020   0.002   PHE B 350 
 TRP   0.019   0.001   TRP D 655 
 HIS   0.005   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (11750)
  covalent geometry    : angle       0.56118 (15826)
  hydrogen bonds       : bond        0.03669 (  473)
  hydrogen bonds       : angle       5.19345 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 183
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8164 (mp10) cc_final: 0.7863 (mp10)
REVERT: A   17 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.6533 (mt)
REVERT: A  265 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7123 (tm-30)
REVERT: C  431 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8408 (pp)
REVERT: C  517 MET cc_start: 0.1587 (ppp) cc_final: 0.0448 (pmm)
REVERT: C  547 MET cc_start: 0.8439 (mmm) cc_final: 0.8181 (mtt)
REVERT: B  123 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9053 (p)
REVERT: B  190 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7981 (mt0)
REVERT: B  380 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7877 (tp30)
  outliers start: 40
  outliers final: 24
  residues processed: 207
  average time/residue: 0.0905
  time to fit residues: 28.5576
Evaluate side-chains
  194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  663 MET
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  416 LYS
Chi-restraints excluded: chain D residue  566 ILE
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 136 optimal weight:    0.6980
   chunk 77 optimal weight:    0.3980
   chunk 100 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 90 optimal weight:    0.0050
   chunk 139 optimal weight:    0.7980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 497 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.166950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.116641 restraints weight = 17104.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.120557 restraints weight = 9393.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.122972 restraints weight = 6660.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124359 restraints weight = 5477.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.125215 restraints weight = 4922.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  11750  Z= 0.105
  Angle     :  0.509   7.318  15826  Z= 0.268
  Chirality :  0.041   0.163   1712
  Planarity :  0.003   0.049   2026
  Dihedral  :  4.657  36.143   1552
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 20.56 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.23), residues: 1422
  helix:  0.70 (0.22), residues: 582
  sheet: -1.96 (0.41), residues: 150
  loop :  0.03 (0.25), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   6 
 TYR   0.012   0.001   TYR C 422 
 PHE   0.016   0.001   PHE D 605 
 TRP   0.018   0.001   TRP D 655 
 HIS   0.003   0.000   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (11750)
  covalent geometry    : angle       0.50874 (15826)
  hydrogen bonds       : bond        0.03124 (  473)
  hydrogen bonds       : angle       4.95616 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 185
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8134 (mp10) cc_final: 0.7860 (mp10)
REVERT: A   17 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6429 (mt)
REVERT: A  265 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6945 (tm-30)
REVERT: C  431 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8477 (pp)
REVERT: C  447 MET cc_start: 0.4935 (tmm) cc_final: 0.4710 (tmm)
REVERT: C  547 MET cc_start: 0.8326 (mmm) cc_final: 0.8094 (mtt)
REVERT: B  123 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.9009 (p)
REVERT: B  190 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8018 (mt0)
REVERT: B  380 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7818 (tp30)
REVERT: D  417 ASP cc_start: 0.7606 (t70) cc_final: 0.7312 (t70)
REVERT: D  517 MET cc_start: 0.3409 (pmm) cc_final: 0.3194 (ppp)
  outliers start: 46
  outliers final: 24
  residues processed: 213
  average time/residue: 0.0914
  time to fit residues: 29.8457
Evaluate side-chains
  202 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 174
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  318 ASP
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain D residue  409 THR
Chi-restraints excluded: chain D residue  566 ILE
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  662 LEU
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 134 optimal weight:    4.9990
   chunk 91 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 131 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   chunk 85 optimal weight:    0.0020
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
A  26 ASN
A  81 GLN
A  89 ASN
** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 497 ASN
C 642 GLN
D 432 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.170118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123147 restraints weight = 17255.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.124191 restraints weight = 9872.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.124737 restraints weight = 7180.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.125627 restraints weight = 7114.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.125793 restraints weight = 6413.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11750  Z= 0.103
  Angle     :  0.514   7.983  15826  Z= 0.268
  Chirality :  0.041   0.168   1712
  Planarity :  0.003   0.052   2026
  Dihedral  :  4.569  36.732   1552
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 21.61 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.23), residues: 1422
  helix:  0.78 (0.22), residues: 580
  sheet: -1.91 (0.41), residues: 148
  loop :  0.02 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   6 
 TYR   0.025   0.001   TYR D 422 
 PHE   0.019   0.001   PHE B 350 
 TRP   0.018   0.001   TRP D 655 
 HIS   0.004   0.000   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (11750)
  covalent geometry    : angle       0.51371 (15826)
  hydrogen bonds       : bond        0.03022 (  473)
  hydrogen bonds       : angle       4.82986 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 183
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8189 (mp10) cc_final: 0.7888 (mp10)
REVERT: A  265 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6918 (tm-30)
REVERT: C  431 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8558 (pp)
REVERT: C  517 MET cc_start: 0.2195 (ppp) cc_final: -0.0097 (ptt)
REVERT: C  583 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7856 (tp40)
REVERT: B  190 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8210 (mt0)
REVERT: B  265 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6929 (tm-30)
REVERT: B  380 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7907 (tp30)
REVERT: B  413 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: D  417 ASP cc_start: 0.7531 (t70) cc_final: 0.7271 (t70)
  outliers start: 42
  outliers final: 29
  residues processed: 210
  average time/residue: 0.0886
  time to fit residues: 28.9244
Evaluate side-chains
  204 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 173
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ASN
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  386 ASP
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain D residue  409 THR
Chi-restraints excluded: chain D residue  556 THR
Chi-restraints excluded: chain D residue  566 ILE
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  662 LEU
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 114 optimal weight:    0.2980
   chunk 51 optimal weight:    5.9990
   chunk 124 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 90 optimal weight:    0.3980
   chunk 34 optimal weight:    5.9990
   chunk 103 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 130 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 230 HIS
** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
D 432 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.171255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121019 restraints weight = 17085.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124780 restraints weight = 9617.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.127295 restraints weight = 6954.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.128579 restraints weight = 5748.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.129531 restraints weight = 5172.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11750  Z= 0.108
  Angle     :  0.525   6.800  15826  Z= 0.274
  Chirality :  0.041   0.178   1712
  Planarity :  0.003   0.053   2026
  Dihedral  :  4.539  36.418   1552
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.85 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.23), residues: 1422
  helix:  0.80 (0.22), residues: 582
  sheet: -1.83 (0.41), residues: 148
  loop : -0.04 (0.25), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   6 
 TYR   0.014   0.001   TYR D 422 
 PHE   0.023   0.001   PHE C 573 
 TRP   0.018   0.001   TRP C 655 
 HIS   0.004   0.000   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11750)
  covalent geometry    : angle       0.52536 (15826)
  hydrogen bonds       : bond        0.02931 (  473)
  hydrogen bonds       : angle       4.69162 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 187
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8143 (mp10) cc_final: 0.7834 (mp10)
REVERT: A  265 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6923 (tm-30)
REVERT: C  431 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8466 (pp)
REVERT: C  517 MET cc_start: 0.1898 (ppp) cc_final: -0.0167 (ptt)
REVERT: C  583 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7811 (tp40)
REVERT: B  190 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8098 (mt0)
REVERT: B  265 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6958 (tm-30)
REVERT: B  380 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7812 (tp30)
REVERT: B  413 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7792 (mt-10)
REVERT: D  417 ASP cc_start: 0.7557 (t70) cc_final: 0.7245 (t70)
  outliers start: 41
  outliers final: 31
  residues processed: 210
  average time/residue: 0.0859
  time to fit residues: 27.6988
Evaluate side-chains
  209 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  663 MET
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain D residue  409 THR
Chi-restraints excluded: chain D residue  556 THR
Chi-restraints excluded: chain D residue  566 ILE
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  662 LEU
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 7 optimal weight:    0.3980
   chunk 73 optimal weight:    0.6980
   chunk 138 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 78 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   chunk 131 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 432 HIS
B  81 GLN
D 432 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.170951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120863 restraints weight = 16959.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.124549 restraints weight = 9590.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.127011 restraints weight = 6936.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.128403 restraints weight = 5753.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.129082 restraints weight = 5167.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11750  Z= 0.112
  Angle     :  0.535   7.686  15826  Z= 0.277
  Chirality :  0.041   0.200   1712
  Planarity :  0.003   0.054   2026
  Dihedral  :  4.526  35.930   1552
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.26 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.23), residues: 1422
  helix:  0.84 (0.22), residues: 580
  sheet: -1.78 (0.42), residues: 148
  loop : -0.04 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   6 
 TYR   0.014   0.001   TYR D 422 
 PHE   0.018   0.001   PHE A 350 
 TRP   0.019   0.001   TRP C 655 
 HIS   0.004   0.000   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11750)
  covalent geometry    : angle       0.53540 (15826)
  hydrogen bonds       : bond        0.02922 (  473)
  hydrogen bonds       : angle       4.64376 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 186
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8107 (mp10) cc_final: 0.7608 (mp10)
REVERT: A   17 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6420 (mt)
REVERT: A  265 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6964 (tm-30)
REVERT: C  431 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8524 (pp)
REVERT: C  445 TRP cc_start: 0.6734 (OUTLIER) cc_final: 0.5859 (m100)
REVERT: C  517 MET cc_start: 0.1712 (ppp) cc_final: -0.0411 (ptt)
REVERT: C  583 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7811 (tp40)
REVERT: C  659 PHE cc_start: 0.6804 (m-80) cc_final: 0.6393 (m-80)
REVERT: B  190 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8108 (mt0)
REVERT: B  265 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6954 (tm-30)
REVERT: B  380 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7807 (tp30)
REVERT: B  413 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7768 (mt-10)
REVERT: D  417 ASP cc_start: 0.7567 (t70) cc_final: 0.7267 (t70)
  outliers start: 42
  outliers final: 31
  residues processed: 209
  average time/residue: 0.0926
  time to fit residues: 29.2443
Evaluate side-chains
  217 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 182
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  414 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  445 TRP
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  663 MET
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain D residue  409 THR
Chi-restraints excluded: chain D residue  566 ILE
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  662 LEU
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
D 642 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.169466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.119150 restraints weight = 16994.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.122781 restraints weight = 9707.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.125168 restraints weight = 7064.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.126458 restraints weight = 5875.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.127003 restraints weight = 5310.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11750  Z= 0.132
  Angle     :  0.559   7.654  15826  Z= 0.286
  Chirality :  0.041   0.212   1712
  Planarity :  0.003   0.055   2026
  Dihedral  :  4.560  35.460   1552
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.50 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.23), residues: 1422
  helix:  0.85 (0.22), residues: 580
  sheet: -1.82 (0.42), residues: 150
  loop : -0.03 (0.25), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   6 
 TYR   0.020   0.001   TYR D 422 
 PHE   0.021   0.001   PHE B 350 
 TRP   0.029   0.002   TRP C 445 
 HIS   0.005   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (11750)
  covalent geometry    : angle       0.55915 (15826)
  hydrogen bonds       : bond        0.02968 (  473)
  hydrogen bonds       : angle       4.62619 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 185
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8081 (mp10) cc_final: 0.7561 (mp10)
REVERT: A   17 LEU cc_start: 0.7499 (tt) cc_final: 0.6560 (mt)
REVERT: A  265 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6985 (tm-30)
REVERT: A  297 LEU cc_start: 0.7965 (mm) cc_final: 0.7383 (tp)
REVERT: C  431 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8595 (pp)
REVERT: C  517 MET cc_start: 0.1871 (ppp) cc_final: -0.0305 (ptt)
REVERT: C  583 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7774 (tp40)
REVERT: C  655 TRP cc_start: 0.8437 (p-90) cc_final: 0.8224 (p-90)
REVERT: B  190 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8150 (mt0)
REVERT: B  265 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6971 (tm-30)
REVERT: B  380 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7827 (tp30)
REVERT: B  413 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7760 (mt-10)
REVERT: D  417 ASP cc_start: 0.7625 (t70) cc_final: 0.7341 (t70)
  outliers start: 40
  outliers final: 35
  residues processed: 208
  average time/residue: 0.0885
  time to fit residues: 28.5946
Evaluate side-chains
  213 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 176
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  414 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  663 MET
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  411 LEU
Chi-restraints excluded: chain D residue  409 THR
Chi-restraints excluded: chain D residue  566 ILE
Chi-restraints excluded: chain D residue  629 LEU
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  662 LEU
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 123 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 116 optimal weight:    6.9990
   chunk 91 optimal weight:    0.8980
   chunk 77 optimal weight:    0.3980
   chunk 125 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 132 optimal weight:    0.3980
   chunk 54 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN
B 103 ASN
D 642 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.163904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.112784 restraints weight = 17052.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.116392 restraints weight = 9827.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.118606 restraints weight = 7219.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.119785 restraints weight = 6067.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.120594 restraints weight = 5516.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11750  Z= 0.205
  Angle     :  0.619  10.174  15826  Z= 0.318
  Chirality :  0.043   0.243   1712
  Planarity :  0.004   0.056   2026
  Dihedral  :  4.785  34.400   1552
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.98 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.23), residues: 1422
  helix:  0.74 (0.22), residues: 584
  sheet: -1.90 (0.42), residues: 150
  loop : -0.07 (0.25), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   6 
 TYR   0.028   0.002   TYR D 422 
 PHE   0.028   0.002   PHE B 359 
 TRP   0.024   0.002   TRP C 445 
 HIS   0.005   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (11750)
  covalent geometry    : angle       0.61931 (15826)
  hydrogen bonds       : bond        0.03286 (  473)
  hydrogen bonds       : angle       4.78903 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 173
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8181 (mp10) cc_final: 0.7600 (mp10)
REVERT: A   17 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.6654 (mt)
REVERT: A  265 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7179 (tm-30)
REVERT: C  431 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8621 (pp)
REVERT: C  583 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7827 (tp40)
REVERT: B  123 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.9129 (p)
REVERT: B  190 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8197 (mt0)
REVERT: B  265 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7096 (tm-30)
REVERT: B  380 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7908 (tp30)
REVERT: D  517 MET cc_start: 0.3324 (pmm) cc_final: 0.2882 (ppp)
  outliers start: 41
  outliers final: 33
  residues processed: 199
  average time/residue: 0.0901
  time to fit residues: 27.7477
Evaluate side-chains
  209 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 172
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  414 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  663 MET
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain D residue  409 THR
Chi-restraints excluded: chain D residue  566 ILE
Chi-restraints excluded: chain D residue  629 LEU
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  662 LEU
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 127 optimal weight:   30.0000
   chunk 120 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 111 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  26 ASN
A  81 GLN
A 160 ASN
** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.166453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.116248 restraints weight = 17004.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.119993 restraints weight = 9575.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.122298 restraints weight = 6920.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.123430 restraints weight = 5758.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124365 restraints weight = 5229.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11750  Z= 0.135
  Angle     :  0.591   9.446  15826  Z= 0.302
  Chirality :  0.042   0.235   1712
  Planarity :  0.003   0.055   2026
  Dihedral  :  4.752  37.793   1552
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.98 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.23), residues: 1422
  helix:  0.78 (0.22), residues: 582
  sheet: -1.87 (0.42), residues: 150
  loop : -0.08 (0.25), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   6 
 TYR   0.030   0.001   TYR D 422 
 PHE   0.032   0.002   PHE A 359 
 TRP   0.025   0.002   TRP C 655 
 HIS   0.004   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11750)
  covalent geometry    : angle       0.59093 (15826)
  hydrogen bonds       : bond        0.03019 (  473)
  hydrogen bonds       : angle       4.73334 ( 1305)

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

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

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2844 Ramachandran restraints generated.
    1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 GLN cc_start: 0.8073 (mp10) cc_final: 0.7513 (mp10)
REVERT: A   17 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.6750 (mt)
REVERT: A  265 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7169 (tm-30)
REVERT: C  431 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8600 (pp)
REVERT: B  123 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.9084 (p)
REVERT: B  190 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (mt0)
REVERT: B  265 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7056 (tm-30)
REVERT: B  380 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7865 (tp30)
REVERT: B  413 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7812 (mt-10)
REVERT: D  517 MET cc_start: 0.3108 (pmm) cc_final: 0.2733 (ppp)
  outliers start: 40
  outliers final: 33
  residues processed: 203
  average time/residue: 0.0944
  time to fit residues: 29.4114
Evaluate side-chains
  205 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 168
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain C residue  409 THR
Chi-restraints excluded: chain C residue  414 THR
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  663 MET
Chi-restraints excluded: chain B residue    7 ASP
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  123 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  190 GLN
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain D residue  409 THR
Chi-restraints excluded: chain D residue  566 ILE
Chi-restraints excluded: chain D residue  629 LEU
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  662 LEU
Chi-restraints excluded: chain D residue  663 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 19 optimal weight:    0.0020
   chunk 2 optimal weight:    7.9990
   chunk 124 optimal weight:   20.0000
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.168024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.121297 restraints weight = 17040.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121755 restraints weight = 10426.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.123025 restraints weight = 7475.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.123427 restraints weight = 6862.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.123698 restraints weight = 6433.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11750  Z= 0.122
  Angle     :  0.582   9.316  15826  Z= 0.299
  Chirality :  0.042   0.225   1712
  Planarity :  0.003   0.055   2026
  Dihedral  :  4.740  43.753   1552
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.63 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.23), residues: 1422
  helix:  0.83 (0.22), residues: 578
  sheet: -1.82 (0.42), residues: 150
  loop : -0.00 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   6 
 TYR   0.027   0.001   TYR D 422 
 PHE   0.032   0.002   PHE A 359 
 TRP   0.025   0.002   TRP C 655 
 HIS   0.004   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11750)
  covalent geometry    : angle       0.58230 (15826)
  hydrogen bonds       : bond        0.02999 (  473)
  hydrogen bonds       : angle       4.71443 ( 1305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2154.40 seconds
wall clock time: 38 minutes 3.06 seconds (2283.06 seconds total)