Starting phenix.real_space_refine
on Wed Mar  4 21:44:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vyv_32215/03_2026/7vyv_32215.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vyv_32215/03_2026/7vyv_32215.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vyv_32215/03_2026/7vyv_32215.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vyv_32215/03_2026/7vyv_32215.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vyv_32215/03_2026/7vyv_32215.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vyv_32215/03_2026/7vyv_32215.cif"
  }
  resolution = 2.32
  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=  -0.000 sd=   0.007
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      66      5.16       5
     C   10572      2.51       5
     N    2817      2.21       5
     O    3243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 125 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16698
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 720, 5566
          Classifications: {'peptide': 720}
          Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689}
    Chain: "B"
      Number of atoms: 5566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 720, 5566
          Classifications: {'peptide': 720}
          Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689}
    Chain: "C"
      Number of atoms: 5566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 720, 5566
          Classifications: {'peptide': 720}
          Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689}
  Time building chain proxies: 3.67, per 1000 atoms: 0.22
  Number of scatterers: 16698
  At special positions: 0
  Unit cell: (93.482, 92.395, 180.442, 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      66     16.00
     O    3243      8.00
     N    2817      7.00
     C   10572      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: 1.39
  Conformation dependent library (CDL) restraints added in 765.0 milliseconds
  

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3930

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 20 sheets defined
      17.2% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 186 through 192
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 205 through 211
    Processing helix  chain 'A' and resid 277 through 280
    Processing helix  chain 'A' and resid 301 through 316
    Processing helix  chain 'A' and resid 354 through 357
    Processing helix  chain 'A' and resid 473 through 479
    Processing helix  chain 'A' and resid 561 through 569
    Processing helix  chain 'A' and resid 643 through 646
    Processing helix  chain 'A' and resid 653 through 659
    Processing helix  chain 'A' and resid 662 through 665
    Processing helix  chain 'A' and resid 705 through 709
    Processing helix  chain 'A' and resid 741 through 746
    Processing helix  chain 'A' and resid 784 through 788
    Processing helix  chain 'A' and resid 823 through 827
    Processing helix  chain 'A' and resid 828 through 832
    Processing helix  chain 'A' and resid 862 through 867
    Processing helix  chain 'A' and resid 886 through 902
    Processing helix  chain 'B' and resid 187 through 192
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 205 through 211
    Processing helix  chain 'B' and resid 277 through 280
    Processing helix  chain 'B' and resid 301 through 316
    Processing helix  chain 'B' and resid 354 through 357
    Processing helix  chain 'B' and resid 473 through 479
    Processing helix  chain 'B' and resid 561 through 569
    Processing helix  chain 'B' and resid 643 through 646
    Processing helix  chain 'B' and resid 653 through 659
    Processing helix  chain 'B' and resid 662 through 665
    Processing helix  chain 'B' and resid 705 through 709
    Processing helix  chain 'B' and resid 741 through 746
    Processing helix  chain 'B' and resid 784 through 788
    Processing helix  chain 'B' and resid 823 through 827
    Processing helix  chain 'B' and resid 828 through 832
    Processing helix  chain 'B' and resid 862 through 867
    Processing helix  chain 'B' and resid 886 through 902
    Processing helix  chain 'C' and resid 187 through 192
    Processing helix  chain 'C' and resid 195 through 200
    Processing helix  chain 'C' and resid 205 through 211
    Processing helix  chain 'C' and resid 277 through 280
    Processing helix  chain 'C' and resid 301 through 316
    Processing helix  chain 'C' and resid 354 through 357
    Processing helix  chain 'C' and resid 473 through 479
    Processing helix  chain 'C' and resid 561 through 569
    Processing helix  chain 'C' and resid 643 through 646
    Processing helix  chain 'C' and resid 653 through 659
    Processing helix  chain 'C' and resid 662 through 665
    Processing helix  chain 'C' and resid 705 through 709
    Processing helix  chain 'C' and resid 741 through 746
    Processing helix  chain 'C' and resid 784 through 788
    Processing helix  chain 'C' and resid 823 through 827
    Processing helix  chain 'C' and resid 828 through 832
    Processing helix  chain 'C' and resid 862 through 867
    Processing helix  chain 'C' and resid 886 through 903
    Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 225
      removed outlier: 5.674A  pdb=" N   SER A 225 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   GLY A 239 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TYR A 263 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275
      removed outlier: 6.498A  pdb=" N   PHE A 274 " --> pdb=" O   ASN A 320 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 318 through 320
    current: chain 'A' and resid 375 through 382
      removed outlier: 7.150A  pdb=" N   LEU A 405 " --> pdb=" O   ARG A 375 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   SER A 377 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   HIS A 407 " --> pdb=" O   SER A 377 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   LEU A 405 " --> pdb=" O   HIS A 431 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 428 through 431
    current: chain 'A' and resid 640 through 641
    Processing sheet with id=AA3, first strand: chain 'A' and resid 334 through 336
      removed outlier: 6.428A  pdb=" N   LEU A 334 " --> pdb=" O   ASN A 367 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ALA A 364 " --> pdb=" O   GLY A 390 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   ASN A 392 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   MET A 366 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   LYS A 389 " --> pdb=" O   GLY A 416 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   TYR A 418 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE A 391 " --> pdb=" O   TYR A 418 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   GLY A 442 " --> pdb=" O   TRP A 415 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   GLN A 441 " --> pdb=" O   GLY A 499 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   GLN A 501 " --> pdb=" O   GLN A 441 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   GLY A 499 " --> pdb=" O   THR A 526 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LEU A 528 " --> pdb=" O   GLY A 499 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   THR A 530 " --> pdb=" O   GLN A 501 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   TYR A 503 " --> pdb=" O   THR A 530 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   THR A 532 " --> pdb=" O   TYR A 503 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   GLN A 505 " --> pdb=" O   THR A 532 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   ALA A 577 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   THR A 601 " --> pdb=" O   ALA A 576 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 480 through 482
    Processing sheet with id=AA5, first strand: chain 'A' and resid 795 through 801
      removed outlier: 3.744A  pdb=" N   TYR A 751 " --> pdb=" O   VAL A 844 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   THR A 757 " --> pdb=" O   PHE A 838 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   PHE A 838 " --> pdb=" O   THR A 757 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   HIS A 671 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ALA A 843 " --> pdb=" O   LEU A 669 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   LEU A 669 " --> pdb=" O   ALA A 843 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   TYR A 845 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   SER A 667 " --> pdb=" O   TYR A 845 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 711 through 712
    Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 732
      removed outlier: 3.972A  pdb=" N   LEU A 727 " --> pdb=" O   PHE A 813 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 859
      removed outlier: 6.445A  pdb=" N   ILE B 841 " --> pdb=" O   ILE B 670 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ASN B 672 " --> pdb=" O   LEU B 839 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU B 839 " --> pdb=" O   ASN B 672 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE B 838 " --> pdb=" O   THR B 757 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   THR B 757 " --> pdb=" O   PHE B 838 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 225
      removed outlier: 5.659A  pdb=" N   SER B 225 " --> pdb=" O   GLY B 239 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   GLY B 239 " --> pdb=" O   SER B 225 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   TYR B 263 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 275
      removed outlier: 6.392A  pdb=" N   PHE B 274 " --> pdb=" O   ASN B 320 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 480 through 482
    Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 712
    Processing sheet with id=AB4, first strand: chain 'B' and resid 727 through 732
      removed outlier: 3.974A  pdb=" N   LEU B 727 " --> pdb=" O   PHE B 813 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 858 through 859
      removed outlier: 6.393A  pdb=" N   ILE C 841 " --> pdb=" O   ILE C 670 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ASN C 672 " --> pdb=" O   LEU C 839 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU C 839 " --> pdb=" O   ASN C 672 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   PHE C 838 " --> pdb=" O   THR C 757 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   THR C 757 " --> pdb=" O   PHE C 838 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR C 751 " --> pdb=" O   VAL C 844 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 220 through 225
      removed outlier: 5.570A  pdb=" N   SER C 225 " --> pdb=" O   GLY C 239 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   GLY C 239 " --> pdb=" O   SER C 225 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR C 263 " --> pdb=" O   GLY C 260 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 273 through 275
      removed outlier: 6.519A  pdb=" N   PHE C 274 " --> pdb=" O   ASN C 320 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 318 through 320
    current: chain 'C' and resid 375 through 382
      removed outlier: 7.069A  pdb=" N   LEU C 405 " --> pdb=" O   ARG C 375 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   SER C 377 " --> pdb=" O   LEU C 405 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   HIS C 407 " --> pdb=" O   SER C 377 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LEU C 405 " --> pdb=" O   HIS C 431 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 428 through 431
    current: chain 'C' and resid 640 through 641
    Processing sheet with id=AB8, first strand: chain 'C' and resid 334 through 336
      removed outlier: 6.493A  pdb=" N   LEU C 334 " --> pdb=" O   ASN C 367 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ALA C 364 " --> pdb=" O   GLY C 390 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   ASN C 392 " --> pdb=" O   ALA C 364 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   MET C 366 " --> pdb=" O   ASN C 392 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   PHE C 417 " --> pdb=" O   GLY C 390 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   ASN C 392 " --> pdb=" O   PHE C 417 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   VAL C 419 " --> pdb=" O   ASN C 392 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TRP C 415 " --> pdb=" O   GLY C 442 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   PHE C 444 " --> pdb=" O   TRP C 415 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   PHE C 417 " --> pdb=" O   PHE C 444 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   GLU C 446 " --> pdb=" O   PHE C 417 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL C 419 " --> pdb=" O   GLU C 446 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   GLN C 441 " --> pdb=" O   GLY C 499 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   GLN C 501 " --> pdb=" O   GLN C 441 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   CYS C 500 " --> pdb=" O   THR C 526 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   LEU C 528 " --> pdb=" O   CYS C 500 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   ALA C 577 " --> pdb=" O   ASN C 525 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   SER C 527 " --> pdb=" O   ALA C 577 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   VAL C 579 " --> pdb=" O   SER C 527 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ALA C 529 " --> pdb=" O   VAL C 579 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   SER C 581 " --> pdb=" O   ALA C 529 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   ILE C 531 " --> pdb=" O   SER C 581 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR C 601 " --> pdb=" O   ALA C 576 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   TRP C 627 " --> pdb=" O   SER C 600 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE C 602 " --> pdb=" O   TRP C 627 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 480 through 482
    Processing sheet with id=AC1, first strand: chain 'C' and resid 711 through 712
    Processing sheet with id=AC2, first strand: chain 'C' and resid 727 through 732
      removed outlier: 3.916A  pdb=" N   LEU C 727 " --> pdb=" O   PHE C 813 " (cutoff:3.500A)

    370 hydrogen bonds defined for protein.
    966 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: 2.81

  Time building geometry restraints manager: 1.87 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 4700
        1.33 -     1.47: 5221
        1.47 -     1.60: 7086
        1.60 -     1.74: 1
        1.74 -     1.87: 104
  Bond restraints: 17112
  Sorted by residual:
  bond pdb=" CB  LYS A 216 "
       pdb=" CG  LYS A 216 "
    ideal  model  delta    sigma   weight residual
    1.520  1.419  0.101 3.00e-02 1.11e+03 1.14e+01
  bond pdb=" C   LEU A 212 "
       pdb=" N   LYS A 213 "
    ideal  model  delta    sigma   weight residual
    1.328  1.273  0.055 1.67e-02 3.59e+03 1.08e+01
  bond pdb=" CG  GLN A 755 "
       pdb=" CD  GLN A 755 "
    ideal  model  delta    sigma   weight residual
    1.516  1.595 -0.079 2.50e-02 1.60e+03 1.00e+01
  bond pdb=" CG  LEU B 311 "
       pdb=" CD1 LEU B 311 "
    ideal  model  delta    sigma   weight residual
    1.521  1.424  0.097 3.30e-02 9.18e+02 8.57e+00
  bond pdb=" CG  LEU C 311 "
       pdb=" CD1 LEU C 311 "
    ideal  model  delta    sigma   weight residual
    1.521  1.427  0.094 3.30e-02 9.18e+02 8.08e+00
  ... (remaining 17107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 21602
        1.95 -     3.89: 1350
        3.89 -     5.84: 222
        5.84 -     7.79: 53
        7.79 -     9.74: 11
  Bond angle restraints: 23238
  Sorted by residual:
  angle pdb=" N   LYS A 750 "
        pdb=" CA  LYS A 750 "
        pdb=" C   LYS A 750 "
      ideal   model   delta    sigma   weight residual
     112.12  120.32   -8.20 1.34e+00 5.57e-01 3.74e+01
  angle pdb=" N   ILE B 693 "
        pdb=" CA  ILE B 693 "
        pdb=" C   ILE B 693 "
      ideal   model   delta    sigma   weight residual
     110.62  116.49   -5.87 1.02e+00 9.61e-01 3.31e+01
  angle pdb=" N   ILE A 693 "
        pdb=" CA  ILE A 693 "
        pdb=" C   ILE A 693 "
      ideal   model   delta    sigma   weight residual
     110.62  116.47   -5.85 1.02e+00 9.61e-01 3.29e+01
  angle pdb=" N   GLU A 748 "
        pdb=" CA  GLU A 748 "
        pdb=" C   GLU A 748 "
      ideal   model   delta    sigma   weight residual
     111.36  117.34   -5.98 1.09e+00 8.42e-01 3.01e+01
  angle pdb=" N   GLU C 748 "
        pdb=" CA  GLU C 748 "
        pdb=" C   GLU C 748 "
      ideal   model   delta    sigma   weight residual
     111.36  117.33   -5.97 1.09e+00 8.42e-01 3.00e+01
  ... (remaining 23233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 9243
       17.95 -    35.90: 609
       35.90 -    53.84: 85
       53.84 -    71.79: 16
       71.79 -    89.74: 22
  Dihedral angle restraints: 9975
    sinusoidal: 3783
      harmonic: 6192
  Sorted by residual:
  dihedral pdb=" CA  ASP C 847 "
           pdb=" C   ASP C 847 "
           pdb=" N   LEU C 848 "
           pdb=" CA  LEU C 848 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.28  -29.72     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  ASP B 847 "
           pdb=" C   ASP B 847 "
           pdb=" N   LEU B 848 "
           pdb=" CA  LEU B 848 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.57  -29.43     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  ASN C 400 "
           pdb=" C   ASN C 400 "
           pdb=" N   ARG C 401 "
           pdb=" CA  ARG C 401 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.02  -26.98     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 9972 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 2013
       0.081 -    0.163: 455
       0.163 -    0.244: 43
       0.244 -    0.325: 6
       0.325 -    0.407: 3
  Chirality restraints: 2520
  Sorted by residual:
  chirality pdb=" CA  VAL A 885 "
            pdb=" N   VAL A 885 "
            pdb=" C   VAL A 885 "
            pdb=" CB  VAL A 885 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.03    0.41 2.00e-01 2.50e+01 4.13e+00
  chirality pdb=" CA  VAL B 885 "
            pdb=" N   VAL B 885 "
            pdb=" C   VAL B 885 "
            pdb=" CB  VAL B 885 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.04    0.40 2.00e-01 2.50e+01 4.08e+00
  chirality pdb=" CA  VAL C 885 "
            pdb=" N   VAL C 885 "
            pdb=" C   VAL C 885 "
            pdb=" CB  VAL C 885 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.04    0.40 2.00e-01 2.50e+01 3.96e+00
  ... (remaining 2517 not shown)

  Planarity restraints: 3051
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 782 "    0.095 2.00e-02 2.50e+03   6.74e-02 1.13e+02
        pdb=" CG  TRP B 782 "   -0.167 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 782 "    0.079 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 782 "   -0.033 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 782 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 782 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 782 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 782 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 782 "    0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 782 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 782 "   -0.078 2.00e-02 2.50e+03   5.92e-02 8.77e+01
        pdb=" CG  TRP C 782 "    0.153 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 782 "   -0.069 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 782 "    0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 782 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 782 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 782 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 782 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 782 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 782 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 782 "    0.080 2.00e-02 2.50e+03   5.92e-02 8.76e+01
        pdb=" CG  TRP A 782 "   -0.152 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 782 "    0.068 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 782 "   -0.022 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 782 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 782 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 782 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 782 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 782 "    0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 782 "    0.015 2.00e-02 2.50e+03
  ... (remaining 3048 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2883
        2.77 -     3.30: 15318
        3.30 -     3.83: 28079
        3.83 -     4.37: 36520
        4.37 -     4.90: 61142
  Nonbonded interactions: 143942
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 395 "
            pdb=" O   GLU B 423 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" NH1 ARG A 395 "
            pdb=" O   GLU A 423 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   PHE B 291 "
            pdb=" O   ASN B 384 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OD2 ASP C 572 "
            pdb=" OG  SER C 574 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   PHE A 291 "
            pdb=" O   ASN A 384 "
     model   vdw
     2.324 3.040
  ... (remaining 143937 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     15.950
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:6.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
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      :  0.009   0.101  17112  Z= 0.426
  Angle     :  1.098   9.735  23238  Z= 0.638
  Chirality :  0.068   0.407   2520
  Planarity :  0.007   0.067   3051
  Dihedral  : 13.116  89.740   6045
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.20 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -1.40 (0.17), residues: 2154
  helix: -0.99 (0.28), residues: 303
  sheet: -0.22 (0.21), residues: 639
  loop : -1.30 (0.16), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 375 
 TYR   0.027   0.004   TYR A 842 
 PHE   0.042   0.005   PHE B 382 
 TRP   0.167   0.010   TRP B 782 
 HIS   0.012   0.003   HIS C 461 

Details of bonding type rmsd
  covalent geometry    : bond        0.00930 (17112)
  covalent geometry    : angle       1.09833 (23238)
  hydrogen bonds       : bond        0.17346 (  370)
  hydrogen bonds       : angle       7.51172 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A  305 MET cc_start: 0.9226 (tpp) cc_final: 0.8839 (tpp)
REVERT: A  453 GLU cc_start: 0.7802 (pm20) cc_final: 0.7383 (pm20)
REVERT: B  563 ASP cc_start: 0.8068 (m-30) cc_final: 0.7805 (m-30)
REVERT: B  700 MET cc_start: 0.9342 (mmm) cc_final: 0.9077 (mmm)
REVERT: C  236 MET cc_start: 0.9186 (mmm) cc_final: 0.8844 (mmm)
REVERT: C  660 MET cc_start: 0.9143 (ttt) cc_final: 0.8698 (ttt)
REVERT: C  902 ASN cc_start: 0.8611 (m-40) cc_final: 0.8307 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.7800
  time to fit residues: 148.7465
Evaluate side-chains
  129 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 194 optimal weight:    6.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 200 optimal weight:    1.9990
   chunk 212 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 356 ASN
A 400 ASN
A 509 ASN
** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 HIS
A 889 ASN
A 902 ASN
B 193 GLN
B 292 ASN
B 384 ASN
B 400 ASN
B 427 GLN
B 431 HIS
B 456 HIS
B 464 ASN
B 509 ASN
B 744 ASN
B 755 GLN
B 826 HIS
B 873 GLN
B 889 ASN
C 211 ASN
C 219 GLN
C 292 ASN
C 501 GLN
C 607 ASN
C 625 ASN
C 744 ASN
C 873 GLN
C 902 ASN

Total number of N/Q/H flips: 30

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.092956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.072809 restraints weight = 19805.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 1.28
r_work: 0.2657 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2556 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8921
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  17112  Z= 0.115
  Angle     :  0.560   6.976  23238  Z= 0.312
  Chirality :  0.046   0.150   2520
  Planarity :  0.005   0.044   3051
  Dihedral  :  5.445  22.904   2337
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.53 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  5.81 %
    Favored  : 93.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -1.06 (0.17), residues: 2154
  helix: -0.09 (0.30), residues: 303
  sheet: -0.13 (0.20), residues: 678
  loop : -1.21 (0.16), residues: 1173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 267 
 TYR   0.017   0.001   TYR A 256 
 PHE   0.013   0.001   PHE C 382 
 TRP   0.044   0.003   TRP C 782 
 HIS   0.003   0.001   HIS C 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (17112)
  covalent geometry    : angle       0.56020 (23238)
  hydrogen bonds       : bond        0.04246 (  370)
  hydrogen bonds       : angle       5.86650 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.612 
Fit side-chains
REVERT: A  453 GLU cc_start: 0.7537 (pm20) cc_final: 0.7067 (pm20)
REVERT: A  548 ASN cc_start: 0.8843 (t0) cc_final: 0.8597 (t0)
REVERT: A  902 ASN cc_start: 0.8253 (m110) cc_final: 0.7311 (m110)
REVERT: B  198 ASP cc_start: 0.8192 (t0) cc_final: 0.7762 (t0)
REVERT: B  700 MET cc_start: 0.9326 (mmm) cc_final: 0.9023 (mmm)
REVERT: B  855 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8135 (pt0)
REVERT: C  236 MET cc_start: 0.9170 (mmm) cc_final: 0.8893 (mmm)
REVERT: C  660 MET cc_start: 0.9288 (ttt) cc_final: 0.9024 (ttt)
  outliers start: 16
  outliers final: 2
  residues processed: 154
  average time/residue: 0.7237
  time to fit residues: 122.2160
Evaluate side-chains
  133 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  855 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 111 optimal weight:    8.9990
   chunk 104 optimal weight:    9.9990
   chunk 201 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 137 optimal weight:    8.9990
   chunk 172 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 209 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 367 ASN
A 392 ASN
A 486 ASN
A 760 ASN
A 873 GLN
B 292 ASN
B 367 ASN
B 392 ASN
B 456 HIS
C 219 GLN
C 292 ASN
C 456 HIS
C 902 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.089507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.069371 restraints weight = 20142.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2694 rms_B_bonded: 1.28
r_work: 0.2599 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2495 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.2495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8974
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.077  17112  Z= 0.286
  Angle     :  0.761   8.787  23238  Z= 0.425
  Chirality :  0.056   0.227   2520
  Planarity :  0.006   0.049   3051
  Dihedral  :  5.940  26.699   2337
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.06 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  7.40 %
    Favored  : 91.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -1.16 (0.17), residues: 2154
  helix: -0.34 (0.29), residues: 303
  sheet: -0.23 (0.21), residues: 660
  loop : -1.18 (0.16), residues: 1191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 267 
 TYR   0.025   0.003   TYR C 609 
 PHE   0.031   0.003   PHE B 382 
 TRP   0.037   0.004   TRP A 782 
 HIS   0.007   0.002   HIS C 826 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 (17112)
  covalent geometry    : angle       0.76068 (23238)
  hydrogen bonds       : bond        0.06148 (  370)
  hydrogen bonds       : angle       6.19217 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.668 
Fit side-chains
REVERT: A  548 ASN cc_start: 0.8958 (t0) cc_final: 0.8683 (t0)
REVERT: A  853 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8579 (mp10)
REVERT: A  902 ASN cc_start: 0.8209 (m110) cc_final: 0.7419 (m110)
REVERT: B  198 ASP cc_start: 0.8196 (t0) cc_final: 0.7764 (t0)
REVERT: B  700 MET cc_start: 0.9203 (mmm) cc_final: 0.8813 (mmm)
REVERT: B  855 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8137 (pt0)
REVERT: C  660 MET cc_start: 0.9292 (ttt) cc_final: 0.8982 (ttt)
  outliers start: 28
  outliers final: 9
  residues processed: 149
  average time/residue: 0.6691
  time to fit residues: 109.9694
Evaluate side-chains
  140 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  853 GLN
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  325 THR
Chi-restraints excluded: chain C residue  855 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 145 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 110 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 164 optimal weight:    4.9990
   chunk 177 optimal weight:    0.6980
   chunk 195 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 292 ASN
A 760 ASN
B 292 ASN
B 456 HIS
C 219 GLN
C 292 ASN
C 431 HIS
C 456 HIS
C 873 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.091376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.071313 restraints weight = 19844.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2725 rms_B_bonded: 1.28
r_work: 0.2632 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2529 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.2529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  17112  Z= 0.164
  Angle     :  0.620   8.185  23238  Z= 0.345
  Chirality :  0.049   0.156   2520
  Planarity :  0.005   0.046   3051
  Dihedral  :  5.637  25.363   2337
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.13 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.61 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -1.08 (0.17), residues: 2154
  helix: -0.15 (0.30), residues: 303
  sheet: -0.18 (0.20), residues: 675
  loop : -1.17 (0.16), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 267 
 TYR   0.015   0.002   TYR C 609 
 PHE   0.023   0.002   PHE B 382 
 TRP   0.019   0.002   TRP A 782 
 HIS   0.005   0.001   HIS C 826 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (17112)
  covalent geometry    : angle       0.62030 (23238)
  hydrogen bonds       : bond        0.04718 (  370)
  hydrogen bonds       : angle       5.89568 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.588 
Fit side-chains
REVERT: A  548 ASN cc_start: 0.8855 (t0) cc_final: 0.8570 (t0)
REVERT: A  560 ASP cc_start: 0.8229 (m-30) cc_final: 0.8023 (m-30)
REVERT: A  694 MET cc_start: 0.9124 (mtp) cc_final: 0.8825 (mtp)
REVERT: A  853 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8651 (mp10)
REVERT: A  864 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8407 (ttm170)
REVERT: A  902 ASN cc_start: 0.8157 (m110) cc_final: 0.7299 (m110)
REVERT: B  198 ASP cc_start: 0.8172 (t0) cc_final: 0.7753 (t0)
REVERT: B  855 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8133 (pt0)
REVERT: C  573 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9047 (mm)
REVERT: C  660 MET cc_start: 0.9258 (ttt) cc_final: 0.8930 (ttt)
  outliers start: 20
  outliers final: 7
  residues processed: 145
  average time/residue: 0.6988
  time to fit residues: 111.6742
Evaluate side-chains
  140 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  853 GLN
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  855 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 91 optimal weight:    8.9990
   chunk 133 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 148 optimal weight:    0.2980
   chunk 131 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 200 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 175 optimal weight:    8.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 292 ASN
A 760 ASN
B 456 HIS
C 219 GLN
C 292 ASN
C 456 HIS
C 873 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.091021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.071171 restraints weight = 19961.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 1.28
r_work: 0.2628 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2524 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.2524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  17112  Z= 0.179
  Angle     :  0.634   8.386  23238  Z= 0.353
  Chirality :  0.050   0.160   2520
  Planarity :  0.005   0.046   3051
  Dihedral  :  5.624  24.989   2337
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.87 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  8.55 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -1.08 (0.17), residues: 2154
  helix: -0.15 (0.30), residues: 303
  sheet: -0.19 (0.20), residues: 675
  loop : -1.17 (0.16), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 267 
 TYR   0.017   0.002   TYR C 609 
 PHE   0.026   0.002   PHE B 382 
 TRP   0.016   0.002   TRP A 782 
 HIS   0.005   0.001   HIS C 826 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (17112)
  covalent geometry    : angle       0.63404 (23238)
  hydrogen bonds       : bond        0.04885 (  370)
  hydrogen bonds       : angle       5.89104 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A  548 ASN cc_start: 0.8871 (t0) cc_final: 0.8578 (t0)
REVERT: A  560 ASP cc_start: 0.8212 (m-30) cc_final: 0.7998 (m-30)
REVERT: A  853 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8649 (mp10)
REVERT: A  864 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8362 (ttm170)
REVERT: A  902 ASN cc_start: 0.8155 (m110) cc_final: 0.7306 (m110)
REVERT: B  198 ASP cc_start: 0.8169 (t0) cc_final: 0.7737 (t0)
REVERT: B  855 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8122 (pt0)
REVERT: C  573 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9060 (mm)
  outliers start: 31
  outliers final: 13
  residues processed: 152
  average time/residue: 0.6740
  time to fit residues: 113.0025
Evaluate side-chains
  146 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  853 GLN
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  325 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  855 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 124 optimal weight:    6.9990
   chunk 159 optimal weight:    0.1980
   chunk 152 optimal weight:    1.9990
   chunk 156 optimal weight:    0.9980
   chunk 163 optimal weight:    7.9990
   chunk 128 optimal weight:    7.9990
   chunk 212 optimal weight:    0.1980
   chunk 25 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 153 optimal weight:    6.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN
A 292 ASN
** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 760 ASN
B 219 GLN
B 456 HIS
C 219 GLN
C 292 ASN
C 456 HIS
C 873 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.093111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.073190 restraints weight = 19802.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.2747 rms_B_bonded: 1.29
r_work: 0.2654 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.2551 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.2551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8930
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  17112  Z= 0.121
  Angle     :  0.555   7.810  23238  Z= 0.308
  Chirality :  0.046   0.146   2520
  Planarity :  0.004   0.043   3051
  Dihedral  :  5.342  24.064   2337
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.85 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  8.88 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -1.01 (0.17), residues: 2154
  helix:  0.03 (0.30), residues: 303
  sheet: -0.15 (0.20), residues: 696
  loop : -1.17 (0.16), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 267 
 TYR   0.013   0.001   TYR A 256 
 PHE   0.020   0.001   PHE B 382 
 TRP   0.010   0.002   TRP A 782 
 HIS   0.004   0.001   HIS B 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (17112)
  covalent geometry    : angle       0.55451 (23238)
  hydrogen bonds       : bond        0.04046 (  370)
  hydrogen bonds       : angle       5.68147 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A  548 ASN cc_start: 0.8785 (t0) cc_final: 0.8463 (t0)
REVERT: A  560 ASP cc_start: 0.8217 (m-30) cc_final: 0.8011 (m-30)
REVERT: A  853 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8655 (mp10)
REVERT: A  864 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8328 (ttm170)
REVERT: A  902 ASN cc_start: 0.8173 (m110) cc_final: 0.7306 (m110)
REVERT: B  198 ASP cc_start: 0.8154 (t0) cc_final: 0.7761 (t0)
REVERT: B  855 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8098 (pt0)
REVERT: C  492 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8820 (ptp)
  outliers start: 25
  outliers final: 6
  residues processed: 151
  average time/residue: 0.6734
  time to fit residues: 112.2130
Evaluate side-chains
  140 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  853 GLN
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain B residue  544 LEU
Chi-restraints excluded: chain B residue  822 SER
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  492 MET
Chi-restraints excluded: chain C residue  855 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 97 optimal weight:    6.9990
   chunk 206 optimal weight:    8.9990
   chunk 89 optimal weight:    0.0970
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 212 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 193 optimal weight:    9.9990
   overall best weight:    3.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 271 ASN
A 292 ASN
A 760 ASN
B 456 HIS
C 219 GLN
C 292 ASN
C 456 HIS
C 902 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.091082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.071217 restraints weight = 19848.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 1.27
r_work: 0.2617 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2513 rms_B_bonded: 2.56 restraints_weight: 0.2500
r_work (final): 0.2513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  17112  Z= 0.229
  Angle     :  0.688   8.530  23238  Z= 0.383
  Chirality :  0.052   0.172   2520
  Planarity :  0.005   0.044   3051
  Dihedral  :  5.717  25.476   2337
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.97 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  8.55 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -1.10 (0.17), residues: 2154
  helix: -0.21 (0.29), residues: 303
  sheet: -0.19 (0.20), residues: 675
  loop : -1.18 (0.16), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 267 
 TYR   0.019   0.002   TYR C 609 
 PHE   0.029   0.002   PHE B 382 
 TRP   0.013   0.002   TRP A 695 
 HIS   0.005   0.001   HIS C 826 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (17112)
  covalent geometry    : angle       0.68779 (23238)
  hydrogen bonds       : bond        0.05373 (  370)
  hydrogen bonds       : angle       5.96690 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A  548 ASN cc_start: 0.8890 (t0) cc_final: 0.8603 (t0)
REVERT: A  864 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8321 (ttm170)
REVERT: A  902 ASN cc_start: 0.8152 (m110) cc_final: 0.7303 (m110)
REVERT: B  198 ASP cc_start: 0.8180 (t0) cc_final: 0.7763 (t0)
REVERT: B  855 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8153 (pt0)
REVERT: C  486 ASN cc_start: 0.9001 (m-40) cc_final: 0.8771 (m110)
REVERT: C  492 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8763 (ptp)
  outliers start: 37
  outliers final: 16
  residues processed: 161
  average time/residue: 0.6476
  time to fit residues: 115.5184
Evaluate side-chains
  151 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  292 ASN
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  822 SER
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  325 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  456 HIS
Chi-restraints excluded: chain C residue  492 MET
Chi-restraints excluded: chain C residue  855 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 109 optimal weight:    0.6980
   chunk 203 optimal weight:    4.9990
   chunk 180 optimal weight:    1.9990
   chunk 210 optimal weight:    6.9990
   chunk 102 optimal weight:    7.9990
   chunk 181 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   chunk 67 optimal weight:    7.9990
   chunk 173 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 292 ASN
** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 760 ASN
B 359 ASN
B 456 HIS
C 219 GLN
C 292 ASN
C 456 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.092854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.072935 restraints weight = 19888.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 1.29
r_work: 0.2651 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2549 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.2549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  17112  Z= 0.122
  Angle     :  0.566   7.842  23238  Z= 0.313
  Chirality :  0.047   0.146   2520
  Planarity :  0.004   0.044   3051
  Dihedral  :  5.425  24.609   2337
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.13 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  9.65 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -1.02 (0.17), residues: 2154
  helix: -0.01 (0.30), residues: 303
  sheet: -0.16 (0.20), residues: 696
  loop : -1.17 (0.16), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 267 
 TYR   0.013   0.001   TYR A 256 
 PHE   0.020   0.001   PHE B 382 
 TRP   0.010   0.002   TRP A 695 
 HIS   0.024   0.001   HIS C 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (17112)
  covalent geometry    : angle       0.56636 (23238)
  hydrogen bonds       : bond        0.04126 (  370)
  hydrogen bonds       : angle       5.70739 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A  548 ASN cc_start: 0.8788 (t0) cc_final: 0.8481 (t0)
REVERT: A  864 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8333 (ttm170)
REVERT: A  902 ASN cc_start: 0.8163 (m110) cc_final: 0.7305 (m110)
REVERT: B  198 ASP cc_start: 0.8157 (t0) cc_final: 0.7744 (t0)
REVERT: B  599 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.8942 (tt)
REVERT: B  855 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8129 (pt0)
REVERT: C  492 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8775 (ptp)
  outliers start: 23
  outliers final: 10
  residues processed: 152
  average time/residue: 0.6160
  time to fit residues: 104.0888
Evaluate side-chains
  148 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  599 LEU
Chi-restraints excluded: chain B residue  822 SER
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  325 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  492 MET
Chi-restraints excluded: chain C residue  855 GLU
Chi-restraints excluded: chain C residue  898 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 200 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 191 optimal weight:    0.0970
   chunk 127 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 207 optimal weight:    7.9990
   chunk 95 optimal weight:    0.2980
   chunk 211 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 755 GLN
A 760 ASN
B 359 ASN
B 456 HIS
C 219 GLN
C 292 ASN
C 456 HIS
C 902 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.092341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.072429 restraints weight = 19864.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.2735 rms_B_bonded: 1.29
r_work: 0.2642 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2539 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.2539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  17112  Z= 0.148
  Angle     :  0.592   7.978  23238  Z= 0.328
  Chirality :  0.048   0.151   2520
  Planarity :  0.005   0.042   3051
  Dihedral  :  5.430  24.709   2337
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.74 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.70 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -0.98 (0.17), residues: 2154
  helix:  0.00 (0.30), residues: 303
  sheet: -0.14 (0.20), residues: 675
  loop : -1.12 (0.16), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 267 
 TYR   0.015   0.002   TYR C 609 
 PHE   0.023   0.002   PHE B 382 
 TRP   0.011   0.002   TRP A 695 
 HIS   0.004   0.001   HIS C 826 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (17112)
  covalent geometry    : angle       0.59178 (23238)
  hydrogen bonds       : bond        0.04417 (  370)
  hydrogen bonds       : angle       5.75663 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A  548 ASN cc_start: 0.8808 (t0) cc_final: 0.8505 (t0)
REVERT: A  864 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8303 (ttm170)
REVERT: A  902 ASN cc_start: 0.8137 (m110) cc_final: 0.7288 (m110)
REVERT: B  198 ASP cc_start: 0.8158 (t0) cc_final: 0.7743 (t0)
REVERT: B  599 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.8918 (tt)
REVERT: B  855 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8113 (pt0)
REVERT: C  492 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8750 (ptp)
REVERT: C  573 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9043 (mm)
  outliers start: 26
  outliers final: 12
  residues processed: 154
  average time/residue: 0.6383
  time to fit residues: 109.2266
Evaluate side-chains
  150 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  456 HIS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  599 LEU
Chi-restraints excluded: chain B residue  822 SER
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  325 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  492 MET
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  855 GLU
Chi-restraints excluded: chain C residue  898 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 186 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 129 optimal weight:    0.4980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 161 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 760 ASN
** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
B 456 HIS
C 219 GLN
C 292 ASN
C 456 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.093735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.073905 restraints weight = 19721.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.2762 rms_B_bonded: 1.28
r_work: 0.2671 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2568 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8922
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  17112  Z= 0.108
  Angle     :  0.534   7.551  23238  Z= 0.296
  Chirality :  0.046   0.145   2520
  Planarity :  0.004   0.042   3051
  Dihedral  :  5.206  23.551   2337
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.99 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.03 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -0.93 (0.17), residues: 2154
  helix:  0.06 (0.30), residues: 303
  sheet: -0.10 (0.20), residues: 696
  loop : -1.11 (0.16), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.013   0.001   TYR A 256 
 PHE   0.018   0.001   PHE B 382 
 TRP   0.010   0.001   TRP A 695 
 HIS   0.004   0.001   HIS B 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (17112)
  covalent geometry    : angle       0.53427 (23238)
  hydrogen bonds       : bond        0.03791 (  370)
  hydrogen bonds       : angle       5.59981 (  966)

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

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

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4308 Ramachandran restraints generated.
    2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A  548 ASN cc_start: 0.8715 (t0) cc_final: 0.8390 (t0)
REVERT: A  864 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8295 (ttm170)
REVERT: A  902 ASN cc_start: 0.8065 (m110) cc_final: 0.7186 (m110)
REVERT: B  198 ASP cc_start: 0.8132 (t0) cc_final: 0.7735 (t0)
REVERT: B  599 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.8914 (tt)
REVERT: B  855 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8056 (pt0)
REVERT: C  198 ASP cc_start: 0.8271 (t0) cc_final: 0.7832 (t0)
REVERT: C  492 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8806 (ptp)
  outliers start: 20
  outliers final: 10
  residues processed: 153
  average time/residue: 0.6366
  time to fit residues: 108.0999
Evaluate side-chains
  147 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  567 SER
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  756 THR
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain B residue  599 LEU
Chi-restraints excluded: chain B residue  822 SER
Chi-restraints excluded: chain B residue  855 GLU
Chi-restraints excluded: chain C residue  325 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  492 MET
Chi-restraints excluded: chain C residue  855 GLU
Chi-restraints excluded: chain C residue  898 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 123 optimal weight:    8.9990
   chunk 16 optimal weight:    0.6980
   chunk 165 optimal weight:    1.9990
   chunk 194 optimal weight:    2.9990
   chunk 192 optimal weight:    3.9990
   chunk 134 optimal weight:    0.0970
   chunk 135 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 760 ASN
** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 ASN
B 456 HIS
C 219 GLN
C 292 ASN
C 456 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.093681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.073811 restraints weight = 19735.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 1.29
r_work: 0.2667 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.2565 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8922
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17112  Z= 0.113
  Angle     :  0.538   7.622  23238  Z= 0.298
  Chirality :  0.046   0.147   2520
  Planarity :  0.004   0.041   3051
  Dihedral  :  5.160  23.172   2337
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.60 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.98 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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 are not related in a simple way.
  whole: -0.88 (0.17), residues: 2154
  helix:  0.11 (0.30), residues: 303
  sheet: -0.08 (0.20), residues: 696
  loop : -1.07 (0.16), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 395 
 TYR   0.013   0.001   TYR A 256 
 PHE   0.019   0.001   PHE B 382 
 TRP   0.010   0.001   TRP A 695 
 HIS   0.004   0.001   HIS B 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (17112)
  covalent geometry    : angle       0.53829 (23238)
  hydrogen bonds       : bond        0.03833 (  370)
  hydrogen bonds       : angle       5.58987 (  966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5517.42 seconds
wall clock time: 94 minutes 42.30 seconds (5682.30 seconds total)