Starting phenix.real_space_refine
on Sat Aug 23 10:12:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qzc_18774/08_2025/8qzc_18774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qzc_18774/08_2025/8qzc_18774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qzc_18774/08_2025/8qzc_18774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qzc_18774/08_2025/8qzc_18774.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qzc_18774/08_2025/8qzc_18774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qzc_18774/08_2025/8qzc_18774.map"
  }
  resolution = 3.29
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      72      5.16       5
     C    7472      2.51       5
     N    1888      2.21       5
     O    2032      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11468
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 701, 5732
          Classifications: {'peptide': 701}
          Link IDs: {'PTRANS': 30, 'TRANS': 670}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 5732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 701, 5732
          Classifications: {'peptide': 701}
          Link IDs: {'PTRANS': 30, 'TRANS': 670}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.88, per 1000 atoms: 0.25
  Number of scatterers: 11468
  At special positions: 0
  Unit cell: (90.283, 121.915, 113.348, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      72     16.00
     O    2032      8.00
     N    1888      7.00
     C    7472      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 386 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 625 " - pdb=" SG  CYS A 630 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 386 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 625 " - pdb=" SG  CYS B 630 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 456.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 10 sheets defined
      67.4% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 180
      removed outlier: 4.041A  pdb=" N   MET A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
    Processing helix  chain 'A' and resid 204 through 213
      removed outlier: 3.643A  pdb=" N   LYS A 208 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   HIS A 212 " --> pdb=" O   LYS A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 226
      removed outlier: 3.648A  pdb=" N   SER A 225 " --> pdb=" O   TYR A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 3.672A  pdb=" N   PHE A 240 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE A 241 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 237 through 241'
    Processing helix  chain 'A' and resid 242 through 257
    Processing helix  chain 'A' and resid 268 through 275
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.650A  pdb=" N   VAL A 310 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   PHE A 311 " --> pdb=" O   TYR A 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 307 through 311'
    Processing helix  chain 'A' and resid 316 through 358
      removed outlier: 7.524A  pdb=" N   GLU A 326 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
      removed outlier: 9.043A  pdb=" N   LYS A 327 " --> pdb=" O   TYR A 323 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
    Processing helix  chain 'A' and resid 359 through 362
    Processing helix  chain 'A' and resid 363 through 371
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 394 through 402
      removed outlier: 3.665A  pdb=" N   ALA A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 405
      No H-bonds generated for 'chain 'A' and resid 403 through 405'
    Processing helix  chain 'A' and resid 406 through 439
      removed outlier: 3.531A  pdb=" N   VAL A 410 " --> pdb=" O   ASN A 406 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   MET A 432 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 465
    Processing helix  chain 'A' and resid 489 through 527
      removed outlier: 3.724A  pdb=" N   ALA A 519 " --> pdb=" O   ARG A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 569
      removed outlier: 4.070A  pdb=" N   GLU A 555 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   VAL A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLU A 568 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A 569 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 601
      Proline residue:  A 595  - end of helix
    Processing helix  chain 'A' and resid 617 through 619
      No H-bonds generated for 'chain 'A' and resid 617 through 619'
    Processing helix  chain 'A' and resid 630 through 651
      removed outlier: 3.937A  pdb=" N   LYS A 645 " --> pdb=" O   ILE A 641 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLN A 646 " --> pdb=" O   MET A 642 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLN A 649 " --> pdb=" O   LYS A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 693
      removed outlier: 3.728A  pdb=" N   VAL A 689 " --> pdb=" O   GLN A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 716
      removed outlier: 3.652A  pdb=" N   GLU A 705 " --> pdb=" O   PRO A 701 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   MET A 706 " --> pdb=" O   GLU A 702 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE A 716 " --> pdb=" O   PHE A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 744
      removed outlier: 3.938A  pdb=" N   VAL A 733 " --> pdb=" O   LEU A 729 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG A 736 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 782
      removed outlier: 3.933A  pdb=" N   ASN A 762 " --> pdb=" O   GLY A 758 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL A 772 " --> pdb=" O   GLY A 768 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ILE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 795
    Processing helix  chain 'A' and resid 803 through 809
    Processing helix  chain 'A' and resid 815 through 817
      No H-bonds generated for 'chain 'A' and resid 815 through 817'
    Processing helix  chain 'A' and resid 854 through 886
      removed outlier: 3.783A  pdb=" N   TRP A 858 " --> pdb=" O   SER A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 910
      removed outlier: 3.906A  pdb=" N   ARG A 910 " --> pdb=" O   GLU A 906 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 181
      removed outlier: 4.011A  pdb=" N   MET B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      Proline residue:  B 177  - end of helix
    Processing helix  chain 'B' and resid 202 through 204
      No H-bonds generated for 'chain 'B' and resid 202 through 204'
    Processing helix  chain 'B' and resid 205 through 213
      removed outlier: 3.847A  pdb=" N   HIS B 212 " --> pdb=" O   LYS B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 226
      removed outlier: 3.543A  pdb=" N   SER B 225 " --> pdb=" O   TYR B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 241
      removed outlier: 3.726A  pdb=" N   PHE B 240 " --> pdb=" O   ARG B 237 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 237 through 241'
    Processing helix  chain 'B' and resid 242 through 257
    Processing helix  chain 'B' and resid 268 through 275
    Processing helix  chain 'B' and resid 296 through 305
    Processing helix  chain 'B' and resid 307 through 311
      removed outlier: 3.631A  pdb=" N   VAL B 310 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE B 311 " --> pdb=" O   TYR B 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 307 through 311'
    Processing helix  chain 'B' and resid 316 through 358
      removed outlier: 7.512A  pdb=" N   GLU B 326 " --> pdb=" O   LYS B 322 " (cutoff:3.500A)
      removed outlier: 9.017A  pdb=" N   LYS B 327 " --> pdb=" O   TYR B 323 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   VAL B 328 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE B 343 " --> pdb=" O   THR B 339 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
    Processing helix  chain 'B' and resid 359 through 362
    Processing helix  chain 'B' and resid 363 through 371
    Processing helix  chain 'B' and resid 391 through 393
      No H-bonds generated for 'chain 'B' and resid 391 through 393'
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 3.662A  pdb=" N   ALA B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 405
      No H-bonds generated for 'chain 'B' and resid 403 through 405'
    Processing helix  chain 'B' and resid 406 through 439
      removed outlier: 3.523A  pdb=" N   VAL B 410 " --> pdb=" O   ASN B 406 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   MET B 432 " --> pdb=" O   LYS B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 465
    Processing helix  chain 'B' and resid 489 through 527
      removed outlier: 3.715A  pdb=" N   ALA B 519 " --> pdb=" O   ARG B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 569
      removed outlier: 4.068A  pdb=" N   GLU B 555 " --> pdb=" O   ILE B 551 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL B 556 " --> pdb=" O   LEU B 552 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU B 568 " --> pdb=" O   LEU B 564 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL B 569 " --> pdb=" O   THR B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 601
      Proline residue:  B 595  - end of helix
    Processing helix  chain 'B' and resid 617 through 619
      No H-bonds generated for 'chain 'B' and resid 617 through 619'
    Processing helix  chain 'B' and resid 630 through 651
      removed outlier: 3.959A  pdb=" N   LYS B 645 " --> pdb=" O   ILE B 641 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLN B 646 " --> pdb=" O   MET B 642 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN B 649 " --> pdb=" O   LYS B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 685 through 693
      removed outlier: 3.701A  pdb=" N   VAL B 689 " --> pdb=" O   GLN B 685 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 699 through 716
      removed outlier: 3.655A  pdb=" N   GLU B 705 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET B 706 " --> pdb=" O   GLU B 702 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE B 716 " --> pdb=" O   PHE B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 744
      removed outlier: 3.921A  pdb=" N   VAL B 733 " --> pdb=" O   LEU B 729 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ARG B 736 " --> pdb=" O   ILE B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 782
      removed outlier: 3.942A  pdb=" N   ASN B 762 " --> pdb=" O   GLY B 758 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL B 772 " --> pdb=" O   GLY B 768 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   ILE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 795
    Processing helix  chain 'B' and resid 803 through 809
    Processing helix  chain 'B' and resid 815 through 817
      No H-bonds generated for 'chain 'B' and resid 815 through 817'
    Processing helix  chain 'B' and resid 854 through 886
      removed outlier: 3.780A  pdb=" N   TRP B 858 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 910
      removed outlier: 3.893A  pdb=" N   ARG B 910 " --> pdb=" O   GLU B 906 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126
      removed outlier: 3.893A  pdb=" N   ALA A 279 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 190
      removed outlier: 3.525A  pdb=" N   THR A 187 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218
    Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616
    Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813
    Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 126
      removed outlier: 3.939A  pdb=" N   ALA B 279 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190
      removed outlier: 3.583A  pdb=" N   THR B 187 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 218
    Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 616
    Processing sheet with id=AB1, first strand: chain 'B' and resid 810 through 813

    661 hydrogen bonds defined for protein.
    1947 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3562
        1.34 -     1.46: 2914
        1.46 -     1.58: 5160
        1.58 -     1.70: 0
        1.70 -     1.82: 118
  Bond restraints: 11754
  Sorted by residual:
  bond pdb=" CB  GLU A 555 "
       pdb=" CG  GLU A 555 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.14e+00
  bond pdb=" CB  GLU B 555 "
       pdb=" CG  GLU B 555 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.10e+00
  bond pdb=" SD  MET A 416 "
       pdb=" CE  MET A 416 "
    ideal  model  delta    sigma   weight residual
    1.791  1.755  0.036 2.50e-02 1.60e+03 2.02e+00
  bond pdb=" SD  MET B 416 "
       pdb=" CE  MET B 416 "
    ideal  model  delta    sigma   weight residual
    1.791  1.756  0.035 2.50e-02 1.60e+03 2.01e+00
  bond pdb=" CB  ASP B 883 "
       pdb=" CG  ASP B 883 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.75e+00
  ... (remaining 11749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 15678
        2.68 -     5.37: 178
        5.37 -     8.05: 44
        8.05 -    10.74: 6
       10.74 -    13.42: 6
  Bond angle restraints: 15912
  Sorted by residual:
  angle pdb=" CB  MET A 424 "
        pdb=" CG  MET A 424 "
        pdb=" SD  MET A 424 "
      ideal   model   delta    sigma   weight residual
     112.70  124.93  -12.23 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C   TYR B 288 "
        pdb=" N   GLU B 289 "
        pdb=" CA  GLU B 289 "
      ideal   model   delta    sigma   weight residual
     122.08  127.90   -5.82 1.47e+00 4.63e-01 1.56e+01
  angle pdb=" CB  MET B 424 "
        pdb=" CG  MET B 424 "
        pdb=" SD  MET B 424 "
      ideal   model   delta    sigma   weight residual
     112.70  124.42  -11.72 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" C   TYR A 288 "
        pdb=" N   GLU A 289 "
        pdb=" CA  GLU A 289 "
      ideal   model   delta    sigma   weight residual
     122.08  127.81   -5.73 1.47e+00 4.63e-01 1.52e+01
  angle pdb=" CA  LEU B 191 "
        pdb=" CB  LEU B 191 "
        pdb=" CG  LEU B 191 "
      ideal   model   delta    sigma   weight residual
     116.30  129.72  -13.42 3.50e+00 8.16e-02 1.47e+01
  ... (remaining 15907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 6166
       16.03 -    32.06: 702
       32.06 -    48.08: 127
       48.08 -    64.11: 21
       64.11 -    80.14: 6
  Dihedral angle restraints: 7022
    sinusoidal: 2870
      harmonic: 4152
  Sorted by residual:
  dihedral pdb=" CB  CYS B 382 "
           pdb=" SG  CYS B 382 "
           pdb=" SG  CYS B 386 "
           pdb=" CB  CYS B 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.60   63.60     1      1.00e+01 1.00e-02 5.33e+01
  dihedral pdb=" CB  CYS A 382 "
           pdb=" SG  CYS A 382 "
           pdb=" SG  CYS A 386 "
           pdb=" CB  CYS A 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.37   63.37     1      1.00e+01 1.00e-02 5.30e+01
  dihedral pdb=" CB  CYS B 625 "
           pdb=" SG  CYS B 625 "
           pdb=" SG  CYS B 630 "
           pdb=" CB  CYS B 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -46.12  -39.88     1      1.00e+01 1.00e-02 2.23e+01
  ... (remaining 7019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1314
       0.051 -    0.102: 352
       0.102 -    0.154: 80
       0.154 -    0.205: 3
       0.205 -    0.256: 5
  Chirality restraints: 1754
  Sorted by residual:
  chirality pdb=" CA  GLU B 425 "
            pdb=" N   GLU B 425 "
            pdb=" C   GLU B 425 "
            pdb=" CB  GLU B 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  VAL A 569 "
            pdb=" CA  VAL A 569 "
            pdb=" CG1 VAL A 569 "
            pdb=" CG2 VAL A 569 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  VAL B 750 "
            pdb=" CA  VAL B 750 "
            pdb=" CG1 VAL B 750 "
            pdb=" CG2 VAL B 750 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1751 not shown)

  Planarity restraints: 1998
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 176 "   -0.038 5.00e-02 4.00e+02   5.77e-02 5.32e+00
        pdb=" N   PRO A 177 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 177 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 177 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 176 "    0.037 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO B 177 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 177 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 177 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 406 "   -0.030 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO B 407 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 407 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 407 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1995 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2328
        2.78 -     3.31: 10850
        3.31 -     3.84: 18851
        3.84 -     4.37: 21116
        4.37 -     4.90: 37307
  Nonbonded interactions: 90452
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 590 "
            pdb=" OG1 THR B 594 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   VAL A 590 "
            pdb=" OG1 THR A 594 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   LYS A 175 "
            pdb=" OG1 THR A 178 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER A 387 "
            pdb=" OD2 ASP A 828 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG  SER B 387 "
            pdb=" OD2 ASP B 828 "
     model   vdw
     2.291 3.040
  ... (remaining 90447 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'
}

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:             4.350
  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:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.700
  Find NCS groups from input model:        0.170
  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:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
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      :  0.004   0.047  11762  Z= 0.187
  Angle     :  0.816  13.424  15928  Z= 0.421
  Chirality :  0.049   0.256   1754
  Planarity :  0.006   0.058   1998
  Dihedral  : 13.360  80.141   4310
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.20), residues: 1382
  helix: -0.05 (0.16), residues: 856
  sheet: -1.79 (0.99), residues: 28
  loop : -2.35 (0.24), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 128 
 TYR   0.026   0.002   TYR B 222 
 PHE   0.028   0.002   PHE B 324 
 TRP   0.016   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (11754)
  covalent geometry    : angle       0.81325 (15912)
  SS BOND              : bond        0.00489 (    8)
  SS BOND              : angle       2.21171 (   16)
  hydrogen bonds       : bond        0.09950 (  661)
  hydrogen bonds       : angle       5.81106 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A  827 LEU cc_start: 0.7498 (mt) cc_final: 0.7217 (mp)
REVERT: A  909 MET cc_start: 0.5081 (ttm) cc_final: 0.3630 (tpt)
REVERT: B  827 LEU cc_start: 0.7553 (mt) cc_final: 0.7310 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1132
  time to fit residues: 27.8072
Evaluate side-chains
  130 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.187721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.144754 restraints weight = 13995.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.90
r_work: 0.3579 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11762  Z= 0.187
  Angle     :  0.622   8.499  15928  Z= 0.324
  Chirality :  0.043   0.183   1754
  Planarity :  0.004   0.048   1998
  Dihedral  :  4.303  16.228   1546
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.85 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.22), residues: 1382
  helix:  0.87 (0.17), residues: 854
  sheet: -2.85 (0.59), residues: 58
  loop : -2.03 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 128 
 TYR   0.015   0.002   TYR B 838 
 PHE   0.019   0.002   PHE A 126 
 TRP   0.015   0.002   TRP A 427 
 HIS   0.008   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (11754)
  covalent geometry    : angle       0.61927 (15912)
  SS BOND              : bond        0.00296 (    8)
  SS BOND              : angle       1.99072 (   16)
  hydrogen bonds       : bond        0.04284 (  661)
  hydrogen bonds       : angle       4.24834 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7402 (pp30) cc_final: 0.6424 (pp30)
REVERT: A  691 PHE cc_start: 0.8420 (t80) cc_final: 0.8214 (t80)
REVERT: A  752 ILE cc_start: 0.8254 (tt) cc_final: 0.7608 (mm)
REVERT: B  215 GLN cc_start: 0.7497 (pp30) cc_final: 0.7246 (pt0)
REVERT: B  752 ILE cc_start: 0.8215 (tt) cc_final: 0.7579 (mm)
  outliers start: 11
  outliers final: 9
  residues processed: 150
  average time/residue: 0.1056
  time to fit residues: 23.2414
Evaluate side-chains
  142 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  733 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 91 optimal weight:    7.9990
   chunk 127 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   chunk 74 optimal weight:    8.9990
   chunk 90 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.196380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.157926 restraints weight = 14252.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 1.91
r_work: 0.3716 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11762  Z= 0.122
  Angle     :  0.553   7.751  15928  Z= 0.284
  Chirality :  0.040   0.194   1754
  Planarity :  0.004   0.046   1998
  Dihedral  :  4.040  14.272   1546
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 10.26 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.22), residues: 1382
  helix:  1.35 (0.17), residues: 854
  sheet: -3.14 (0.59), residues: 48
  loop : -1.99 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 188 
 TYR   0.011   0.001   TYR B 355 
 PHE   0.028   0.001   PHE A 126 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (11754)
  covalent geometry    : angle       0.55096 (15912)
  SS BOND              : bond        0.00283 (    8)
  SS BOND              : angle       1.45534 (   16)
  hydrogen bonds       : bond        0.03731 (  661)
  hydrogen bonds       : angle       3.96308 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7285 (pp30) cc_final: 0.6363 (pp30)
REVERT: A  691 PHE cc_start: 0.8444 (t80) cc_final: 0.8208 (t80)
REVERT: A  752 ILE cc_start: 0.8340 (tt) cc_final: 0.7810 (mm)
REVERT: A  909 MET cc_start: 0.4880 (ttm) cc_final: 0.3545 (tpt)
REVERT: B  215 GLN cc_start: 0.7427 (pp30) cc_final: 0.7187 (pt0)
REVERT: B  752 ILE cc_start: 0.8215 (tt) cc_final: 0.7618 (mm)
  outliers start: 10
  outliers final: 4
  residues processed: 148
  average time/residue: 0.1044
  time to fit residues: 22.8099
Evaluate side-chains
  136 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  616 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 136 optimal weight:    0.5980
   chunk 100 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 132 optimal weight:    7.9990
   chunk 43 optimal weight:    0.7980
   chunk 119 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 122 optimal weight:    3.9990
   chunk 125 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.196594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.157013 restraints weight = 14411.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 1.69
r_work: 0.3748 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11762  Z= 0.122
  Angle     :  0.561   7.916  15928  Z= 0.288
  Chirality :  0.040   0.194   1754
  Planarity :  0.003   0.045   1998
  Dihedral  :  4.046  21.434   1546
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 11.94 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.22), residues: 1382
  helix:  1.52 (0.17), residues: 854
  sheet: -3.10 (0.60), residues: 48
  loop : -1.93 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 188 
 TYR   0.010   0.001   TYR A 838 
 PHE   0.027   0.001   PHE A 126 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (11754)
  covalent geometry    : angle       0.55757 (15912)
  SS BOND              : bond        0.00353 (    8)
  SS BOND              : angle       2.13125 (   16)
  hydrogen bonds       : bond        0.03665 (  661)
  hydrogen bonds       : angle       3.91355 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 GLN cc_start: 0.7223 (pp30) cc_final: 0.6911 (pt0)
REVERT: A  691 PHE cc_start: 0.8448 (t80) cc_final: 0.8216 (t80)
REVERT: A  752 ILE cc_start: 0.8379 (tt) cc_final: 0.7838 (mm)
REVERT: A  909 MET cc_start: 0.4910 (ttm) cc_final: 0.3578 (tpt)
REVERT: B  752 ILE cc_start: 0.8222 (tt) cc_final: 0.7590 (mm)
  outliers start: 9
  outliers final: 5
  residues processed: 149
  average time/residue: 0.1141
  time to fit residues: 24.9299
Evaluate side-chains
  143 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  616 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 125 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 70 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 136 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.194861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.156041 restraints weight = 14296.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 1.96
r_work: 0.3695 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11762  Z= 0.138
  Angle     :  0.572   8.341  15928  Z= 0.293
  Chirality :  0.041   0.184   1754
  Planarity :  0.003   0.043   1998
  Dihedral  :  4.049  19.302   1546
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 11.62 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.22), residues: 1382
  helix:  1.56 (0.17), residues: 854
  sheet: -2.89 (0.60), residues: 58
  loop : -1.87 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 188 
 TYR   0.012   0.001   TYR A 687 
 PHE   0.028   0.001   PHE A 126 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (11754)
  covalent geometry    : angle       0.56797 (15912)
  SS BOND              : bond        0.00264 (    8)
  SS BOND              : angle       2.16922 (   16)
  hydrogen bonds       : bond        0.03831 (  661)
  hydrogen bonds       : angle       3.89368 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7233 (pp30) cc_final: 0.6972 (pt0)
REVERT: A  730 ASN cc_start: 0.8352 (t0) cc_final: 0.8087 (m-40)
REVERT: A  752 ILE cc_start: 0.8390 (tt) cc_final: 0.7845 (mm)
REVERT: A  909 MET cc_start: 0.4896 (ttm) cc_final: 0.3588 (tpt)
REVERT: B  730 ASN cc_start: 0.8341 (t0) cc_final: 0.8066 (m-40)
REVERT: B  752 ILE cc_start: 0.8249 (tt) cc_final: 0.7623 (mm)
  outliers start: 15
  outliers final: 12
  residues processed: 148
  average time/residue: 0.1106
  time to fit residues: 24.0152
Evaluate side-chains
  146 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 134 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0870
   chunk 61 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 116 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 129 optimal weight:    1.9990
   overall best weight:    1.0164

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.194708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.156097 restraints weight = 14274.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 1.95
r_work: 0.3696 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11762  Z= 0.137
  Angle     :  0.575   8.559  15928  Z= 0.294
  Chirality :  0.041   0.167   1754
  Planarity :  0.003   0.042   1998
  Dihedral  :  4.023  17.869   1546
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.70 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.23), residues: 1382
  helix:  1.62 (0.18), residues: 854
  sheet: -2.81 (0.63), residues: 58
  loop : -1.86 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 188 
 TYR   0.013   0.001   TYR B 838 
 PHE   0.028   0.001   PHE A 126 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (11754)
  covalent geometry    : angle       0.57137 (15912)
  SS BOND              : bond        0.00235 (    8)
  SS BOND              : angle       1.99004 (   16)
  hydrogen bonds       : bond        0.03764 (  661)
  hydrogen bonds       : angle       3.94539 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  215 GLN cc_start: 0.7204 (pp30) cc_final: 0.7002 (pt0)
REVERT: A  730 ASN cc_start: 0.8341 (t0) cc_final: 0.8083 (m-40)
REVERT: A  752 ILE cc_start: 0.8374 (tt) cc_final: 0.7826 (mm)
REVERT: A  909 MET cc_start: 0.4858 (ttm) cc_final: 0.3581 (tpt)
REVERT: B  730 ASN cc_start: 0.8345 (t0) cc_final: 0.8085 (m-40)
REVERT: B  752 ILE cc_start: 0.8259 (tt) cc_final: 0.7639 (mm)
  outliers start: 24
  outliers final: 16
  residues processed: 158
  average time/residue: 0.1148
  time to fit residues: 25.8184
Evaluate side-chains
  148 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 130 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0870
   chunk 77 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 692 ASN
** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.190423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.151684 restraints weight = 14183.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.00
r_work: 0.3637 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3508 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11762  Z= 0.215
  Angle     :  0.649   9.356  15928  Z= 0.337
  Chirality :  0.044   0.189   1754
  Planarity :  0.004   0.042   1998
  Dihedral  :  4.303  18.455   1546
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.50 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.22), residues: 1382
  helix:  1.31 (0.17), residues: 854
  sheet: -2.97 (0.63), residues: 58
  loop : -1.95 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 128 
 TYR   0.016   0.002   TYR A 838 
 PHE   0.027   0.002   PHE A 126 
 TRP   0.013   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (11754)
  covalent geometry    : angle       0.64665 (15912)
  SS BOND              : bond        0.00194 (    8)
  SS BOND              : angle       2.01821 (   16)
  hydrogen bonds       : bond        0.04346 (  661)
  hydrogen bonds       : angle       4.16025 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  175 LYS cc_start: 0.7927 (tptm) cc_final: 0.7333 (ttpp)
REVERT: A  215 GLN cc_start: 0.7223 (pp30) cc_final: 0.6993 (pt0)
REVERT: A  752 ILE cc_start: 0.8468 (tt) cc_final: 0.7891 (mm)
REVERT: B  752 ILE cc_start: 0.8439 (tt) cc_final: 0.7856 (mm)
  outliers start: 21
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1146
  time to fit residues: 24.9115
Evaluate side-chains
  147 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  690 ASP
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 127 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 138 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 130 optimal weight:    0.5980
   chunk 101 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 206 GLN
B 692 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.194671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.155465 restraints weight = 14221.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 1.89
r_work: 0.3700 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11762  Z= 0.123
  Angle     :  0.579   8.961  15928  Z= 0.295
  Chirality :  0.040   0.170   1754
  Planarity :  0.003   0.033   1998
  Dihedral  :  4.110  21.508   1546
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.90 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.23), residues: 1382
  helix:  1.60 (0.18), residues: 854
  sheet: -3.05 (0.62), residues: 58
  loop : -1.84 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 753 
 TYR   0.011   0.001   TYR A 687 
 PHE   0.031   0.001   PHE A 126 
 TRP   0.015   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (11754)
  covalent geometry    : angle       0.57603 (15912)
  SS BOND              : bond        0.00273 (    8)
  SS BOND              : angle       1.89040 (   16)
  hydrogen bonds       : bond        0.03699 (  661)
  hydrogen bonds       : angle       3.94514 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A  175 LYS cc_start: 0.8013 (tptm) cc_final: 0.7412 (ttpp)
REVERT: A  215 GLN cc_start: 0.7192 (pp30) cc_final: 0.6947 (pt0)
REVERT: A  730 ASN cc_start: 0.8306 (t0) cc_final: 0.8076 (m-40)
REVERT: A  752 ILE cc_start: 0.8419 (tt) cc_final: 0.8202 (tp)
REVERT: A  909 MET cc_start: 0.4841 (ttm) cc_final: 0.3664 (tpt)
REVERT: B  730 ASN cc_start: 0.8311 (t0) cc_final: 0.8070 (m-40)
REVERT: B  752 ILE cc_start: 0.8396 (tt) cc_final: 0.7860 (mm)
  outliers start: 20
  outliers final: 18
  residues processed: 154
  average time/residue: 0.1073
  time to fit residues: 24.2225
Evaluate side-chains
  146 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  690 ASP
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0030
   overall best weight:    0.8592

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.194153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.155200 restraints weight = 14105.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 1.87
r_work: 0.3704 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11762  Z= 0.131
  Angle     :  0.580   9.071  15928  Z= 0.298
  Chirality :  0.040   0.165   1754
  Planarity :  0.003   0.035   1998
  Dihedral  :  4.056  16.089   1546
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.98 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.23), residues: 1382
  helix:  1.66 (0.18), residues: 854
  sheet: -3.08 (0.61), residues: 58
  loop : -1.82 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 753 
 TYR   0.011   0.001   TYR A 687 
 PHE   0.030   0.001   PHE A 126 
 TRP   0.015   0.001   TRP A 427 
 HIS   0.003   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (11754)
  covalent geometry    : angle       0.57754 (15912)
  SS BOND              : bond        0.00238 (    8)
  SS BOND              : angle       1.82554 (   16)
  hydrogen bonds       : bond        0.03764 (  661)
  hydrogen bonds       : angle       3.96033 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  175 LYS cc_start: 0.8012 (tptm) cc_final: 0.7454 (ttpp)
REVERT: A  215 GLN cc_start: 0.7167 (pp30) cc_final: 0.6958 (pt0)
REVERT: A  730 ASN cc_start: 0.8327 (t0) cc_final: 0.8083 (m-40)
REVERT: A  752 ILE cc_start: 0.8421 (tt) cc_final: 0.8218 (tp)
REVERT: A  909 MET cc_start: 0.4857 (ttm) cc_final: 0.3676 (tpt)
REVERT: B  730 ASN cc_start: 0.8338 (t0) cc_final: 0.8091 (m-40)
  outliers start: 20
  outliers final: 18
  residues processed: 147
  average time/residue: 0.0799
  time to fit residues: 17.3641
Evaluate side-chains
  147 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 134 optimal weight:    3.9990
   chunk 109 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   chunk 117 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 206 GLN
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.194359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.155091 restraints weight = 14294.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.90
r_work: 0.3697 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11762  Z= 0.132
  Angle     :  0.588   9.258  15928  Z= 0.300
  Chirality :  0.041   0.161   1754
  Planarity :  0.003   0.031   1998
  Dihedral  :  4.033  19.490   1546
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.62 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.23), residues: 1382
  helix:  1.64 (0.18), residues: 860
  sheet: -3.17 (0.60), residues: 58
  loop : -1.89 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 753 
 TYR   0.011   0.001   TYR A 687 
 PHE   0.034   0.001   PHE A 126 
 TRP   0.014   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11754)
  covalent geometry    : angle       0.58579 (15912)
  SS BOND              : bond        0.00226 (    8)
  SS BOND              : angle       1.78106 (   16)
  hydrogen bonds       : bond        0.03749 (  661)
  hydrogen bonds       : angle       3.94942 ( 1947)

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

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

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2764 Ramachandran restraints generated.
    1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  175 LYS cc_start: 0.8128 (tptm) cc_final: 0.7527 (ttpp)
REVERT: A  197 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7154 (t)
REVERT: A  730 ASN cc_start: 0.8328 (t0) cc_final: 0.8079 (m-40)
REVERT: A  909 MET cc_start: 0.4828 (ttm) cc_final: 0.3682 (tpt)
REVERT: B  730 ASN cc_start: 0.8340 (t0) cc_final: 0.8082 (m-40)
  outliers start: 22
  outliers final: 19
  residues processed: 150
  average time/residue: 0.0999
  time to fit residues: 22.0856
Evaluate side-chains
  149 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  717 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  616 ILE
Chi-restraints excluded: chain B residue  717 VAL
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  757 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 68 optimal weight:    0.2980
   chunk 135 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 115 optimal weight:    0.6980
   chunk 99 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 114 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 692 ASN
B 692 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.195515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.152591 restraints weight = 14233.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 1.95
r_work: 0.3743 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11762  Z= 0.121
  Angle     :  0.580   9.141  15928  Z= 0.294
  Chirality :  0.040   0.165   1754
  Planarity :  0.003   0.032   1998
  Dihedral  :  3.953  19.038   1546
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.86 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.23), residues: 1382
  helix:  1.73 (0.18), residues: 860
  sheet: -3.16 (0.60), residues: 58
  loop : -1.85 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 753 
 TYR   0.011   0.001   TYR A 687 
 PHE   0.033   0.001   PHE A 126 
 TRP   0.014   0.001   TRP A 427 
 HIS   0.004   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (11754)
  covalent geometry    : angle       0.57733 (15912)
  SS BOND              : bond        0.00259 (    8)
  SS BOND              : angle       1.69328 (   16)
  hydrogen bonds       : bond        0.03615 (  661)
  hydrogen bonds       : angle       3.89721 ( 1947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3135.63 seconds
wall clock time: 54 minutes 25.34 seconds (3265.34 seconds total)