Starting phenix.real_space_refine
on Wed Jul 30 21:11:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a9a_15274/07_2025/8a9a_15274.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a9a_15274/07_2025/8a9a_15274.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a9a_15274/07_2025/8a9a_15274.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a9a_15274/07_2025/8a9a_15274.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a9a_15274/07_2025/8a9a_15274.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a9a_15274/07_2025/8a9a_15274.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.033
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      16      5.16       5
     C    8240      2.51       5
     N    2054      2.21       5
     O    2462      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12772
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 809, 6386
          Classifications: {'peptide': 809}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 22, 'TRANS': 786}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 22
  Restraints were copied for chains:
    B
  Time building chain proxies: 16.01, per 1000 atoms: 1.25
  Number of scatterers: 12772
  At special positions: 0
  Unit cell: (86.1, 115.5, 257.25, 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      16     16.00
     O    2462      8.00
     N    2054      7.00
     C    8240      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: 2.99
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3060

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 6 sheets defined
      46.2% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'B' and resid 95 through 106
      removed outlier: 4.063A  pdb=" N   GLY B  99 " --> pdb=" O   ASP B  95 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   PHE B 104 " --> pdb=" O   GLU B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 125
      removed outlier: 3.766A  pdb=" N   ALA B 113 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 256
      removed outlier: 4.171A  pdb=" N   ASN B 255 " --> pdb=" O   GLU B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 267
    Processing helix  chain 'B' and resid 268 through 294
      removed outlier: 3.554A  pdb=" N   ILE B 280 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 304
      removed outlier: 3.649A  pdb=" N   GLU B 300 " --> pdb=" O   LYS B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 319
      removed outlier: 4.023A  pdb=" N   LYS B 318 " --> pdb=" O   LYS B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 331
      removed outlier: 3.708A  pdb=" N   ARG B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 342
      removed outlier: 3.663A  pdb=" N   LYS B 339 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 361
      removed outlier: 3.598A  pdb=" N   ASP B 360 " --> pdb=" O   LYS B 356 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ASN B 361 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 371
    Processing helix  chain 'B' and resid 376 through 382
      removed outlier: 3.866A  pdb=" N   SER B 380 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 388
    Processing helix  chain 'B' and resid 393 through 415
      removed outlier: 4.583A  pdb=" N   ASP B 406 " --> pdb=" O   GLN B 402 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   LEU B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
      Proline residue:  B 410  - end of helix
    Processing helix  chain 'B' and resid 421 through 429
      removed outlier: 3.690A  pdb=" N   ILE B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 443
    Processing helix  chain 'B' and resid 443 through 462
    Processing helix  chain 'B' and resid 465 through 477
    Processing helix  chain 'B' and resid 478 through 486
      removed outlier: 3.882A  pdb=" N   LEU B 484 " --> pdb=" O   ALA B 481 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY B 486 " --> pdb=" O   ASP B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 499
      removed outlier: 4.189A  pdb=" N   ALA B 495 " --> pdb=" O   VAL B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 514
      removed outlier: 3.976A  pdb=" N   ASP B 514 " --> pdb=" O   GLU B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 525
    Processing helix  chain 'B' and resid 532 through 540
    Processing helix  chain 'B' and resid 552 through 557
      removed outlier: 4.108A  pdb=" N   GLU B 556 " --> pdb=" O   VAL B 552 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ALA B 557 " --> pdb=" O   ALA B 553 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 552 through 557'
    Processing helix  chain 'B' and resid 565 through 584
      removed outlier: 4.136A  pdb=" N   GLU B 569 " --> pdb=" O   ASP B 565 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA B 571 " --> pdb=" O   LYS B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 593
      removed outlier: 4.018A  pdb=" N   LYS B 593 " --> pdb=" O   THR B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 644
      removed outlier: 3.584A  pdb=" N   LEU B 644 " --> pdb=" O   MET B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 659
    Processing helix  chain 'B' and resid 663 through 674
    Processing helix  chain 'B' and resid 685 through 690
    Processing helix  chain 'B' and resid 691 through 701
      removed outlier: 3.819A  pdb=" N   PHE B 697 " --> pdb=" O   ILE B 693 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ILE B 701 " --> pdb=" O   PHE B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 716
    Processing helix  chain 'B' and resid 719 through 723
    Processing helix  chain 'B' and resid 797 through 816
    Processing helix  chain 'A' and resid 95 through 106
      removed outlier: 4.062A  pdb=" N   GLY A  99 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE A 104 " --> pdb=" O   GLU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 125
      removed outlier: 3.767A  pdb=" N   ALA A 113 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 4.171A  pdb=" N   ASN A 255 " --> pdb=" O   GLU A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 267
    Processing helix  chain 'A' and resid 268 through 294
      removed outlier: 3.554A  pdb=" N   ILE A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 304
      removed outlier: 3.649A  pdb=" N   GLU A 300 " --> pdb=" O   LYS A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 319
      removed outlier: 4.023A  pdb=" N   LYS A 318 " --> pdb=" O   LYS A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 331
      removed outlier: 3.708A  pdb=" N   ARG A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 342
      removed outlier: 3.663A  pdb=" N   LYS A 339 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 3.598A  pdb=" N   ASP A 360 " --> pdb=" O   LYS A 356 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ASN A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 371
    Processing helix  chain 'A' and resid 376 through 382
      removed outlier: 3.867A  pdb=" N   SER A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 393 through 415
      removed outlier: 4.584A  pdb=" N   ASP A 406 " --> pdb=" O   GLN A 402 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   LEU A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
      Proline residue:  A 410  - end of helix
    Processing helix  chain 'A' and resid 421 through 429
      removed outlier: 3.690A  pdb=" N   ILE A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 443
    Processing helix  chain 'A' and resid 443 through 462
    Processing helix  chain 'A' and resid 465 through 477
    Processing helix  chain 'A' and resid 478 through 486
      removed outlier: 3.882A  pdb=" N   LEU A 484 " --> pdb=" O   ALA A 481 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 486 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 499
      removed outlier: 4.189A  pdb=" N   ALA A 495 " --> pdb=" O   VAL A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 514
      removed outlier: 3.977A  pdb=" N   ASP A 514 " --> pdb=" O   GLU A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 525
    Processing helix  chain 'A' and resid 532 through 540
    Processing helix  chain 'A' and resid 552 through 557
      removed outlier: 4.110A  pdb=" N   GLU A 556 " --> pdb=" O   VAL A 552 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ALA A 557 " --> pdb=" O   ALA A 553 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 552 through 557'
    Processing helix  chain 'A' and resid 565 through 584
      removed outlier: 4.137A  pdb=" N   GLU A 569 " --> pdb=" O   ASP A 565 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA A 571 " --> pdb=" O   LYS A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 593
      removed outlier: 4.017A  pdb=" N   LYS A 593 " --> pdb=" O   THR A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 644
      removed outlier: 3.583A  pdb=" N   LEU A 644 " --> pdb=" O   MET A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 659
    Processing helix  chain 'A' and resid 663 through 674
    Processing helix  chain 'A' and resid 685 through 690
    Processing helix  chain 'A' and resid 691 through 701
      removed outlier: 3.818A  pdb=" N   PHE A 697 " --> pdb=" O   ILE A 693 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE A 701 " --> pdb=" O   PHE A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 716
    Processing helix  chain 'A' and resid 719 through 723
    Processing helix  chain 'A' and resid 797 through 816
    Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 143
      removed outlier: 5.485A  pdb=" N   LEU B 136 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   THR B 160 " --> pdb=" O   LEU B 136 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   ALA B 138 " --> pdb=" O   ARG B 158 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ARG B 158 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ARG B 140 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ALA B 151 " --> pdb=" O   ALA B 193 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ALA B 193 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 184 through 194
    current: chain 'B' and resid 211 through 219
      removed outlier: 7.590A  pdb=" N   MET B 213 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   SER B 228 " --> pdb=" O   MET B 213 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   ASP B 215 " --> pdb=" O   LYS B 226 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE B 217 " --> pdb=" O   VAL B 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168
      removed outlier: 3.551A  pdb=" N   VAL B 179 " --> pdb=" O   GLN B 167 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 595 through 598
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 595 through 598
    current: chain 'B' and resid 615 through 620
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 615 through 620
    current: chain 'B' and resid 728 through 750
      removed outlier: 9.593A  pdb=" N   TYR B 740 " --> pdb=" O   ILE B 770 " (cutoff:3.500A)
      removed outlier: 9.544A  pdb=" N   ILE B 770 " --> pdb=" O   TYR B 740 " (cutoff:3.500A)
      removed outlier: 10.191A  pdb=" N   GLY B 742 " --> pdb=" O   THR B 768 " (cutoff:3.500A)
      removed outlier: 9.987A  pdb=" N   THR B 768 " --> pdb=" O   GLY B 742 " (cutoff:3.500A)
      removed outlier: 11.562A  pdb=" N   ASN B 744 " --> pdb=" O   VAL B 766 " (cutoff:3.500A)
      removed outlier: 8.654A  pdb=" N   VAL B 766 " --> pdb=" O   ASN B 744 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   ASN B 746 " --> pdb=" O   ILE B 764 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 143
      removed outlier: 5.485A  pdb=" N   LEU A 136 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   THR A 160 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   ALA A 138 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   ARG A 158 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   ARG A 140 " --> pdb=" O   ILE A 156 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   ALA A 151 " --> pdb=" O   ALA A 193 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ALA A 193 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 184 through 194
    current: chain 'A' and resid 211 through 219
      removed outlier: 7.589A  pdb=" N   MET A 213 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   SER A 228 " --> pdb=" O   MET A 213 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   ASP A 215 " --> pdb=" O   LYS A 226 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A 217 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 168
      removed outlier: 3.552A  pdb=" N   VAL A 179 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 598
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 595 through 598
    current: chain 'A' and resid 615 through 620
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 615 through 620
    current: chain 'A' and resid 728 through 750
      removed outlier: 9.594A  pdb=" N   TYR A 740 " --> pdb=" O   ILE A 770 " (cutoff:3.500A)
      removed outlier: 9.544A  pdb=" N   ILE A 770 " --> pdb=" O   TYR A 740 " (cutoff:3.500A)
      removed outlier: 10.192A  pdb=" N   GLY A 742 " --> pdb=" O   THR A 768 " (cutoff:3.500A)
      removed outlier: 9.987A  pdb=" N   THR A 768 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
      removed outlier: 11.562A  pdb=" N   ASN A 744 " --> pdb=" O   VAL A 766 " (cutoff:3.500A)
      removed outlier: 8.655A  pdb=" N   VAL A 766 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   ASN A 746 " --> pdb=" O   ILE A 764 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1332 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.59

  Time building geometry restraints manager: 3.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4078
        1.34 -     1.46: 2682
        1.46 -     1.58: 6202
        1.58 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 12994
  Sorted by residual:
  bond pdb=" CB  LYS A 363 "
       pdb=" CG  LYS A 363 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.40e+00
  bond pdb=" CB  LYS B 363 "
       pdb=" CG  LYS B 363 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.37e+00
  bond pdb=" N   PRO B  61 "
       pdb=" CA  PRO B  61 "
    ideal  model  delta    sigma   weight residual
    1.469  1.454  0.014 1.28e-02 6.10e+03 1.26e+00
  bond pdb=" N   PRO A  61 "
       pdb=" CA  PRO A  61 "
    ideal  model  delta    sigma   weight residual
    1.469  1.455  0.014 1.28e-02 6.10e+03 1.23e+00
  bond pdb=" CB  ASN B 328 "
       pdb=" CG  ASN B 328 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.11e-01
  ... (remaining 12989 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 17081
        1.80 -     3.60: 340
        3.60 -     5.40: 53
        5.40 -     7.20: 22
        7.20 -     9.00: 16
  Bond angle restraints: 17512
  Sorted by residual:
  angle pdb=" N   PRO A  61 "
        pdb=" CA  PRO A  61 "
        pdb=" CB  PRO A  61 "
      ideal   model   delta    sigma   weight residual
     103.25  110.58   -7.33 1.05e+00 9.07e-01 4.88e+01
  angle pdb=" N   PRO B  61 "
        pdb=" CA  PRO B  61 "
        pdb=" CB  PRO B  61 "
      ideal   model   delta    sigma   weight residual
     103.25  110.55   -7.30 1.05e+00 9.07e-01 4.83e+01
  angle pdb=" N   LEU B 546 "
        pdb=" CA  LEU B 546 "
        pdb=" C   LEU B 546 "
      ideal   model   delta    sigma   weight residual
     114.31  109.99    4.32 1.29e+00 6.01e-01 1.12e+01
  angle pdb=" N   LEU A 546 "
        pdb=" CA  LEU A 546 "
        pdb=" C   LEU A 546 "
      ideal   model   delta    sigma   weight residual
     114.31  110.03    4.28 1.29e+00 6.01e-01 1.10e+01
  angle pdb=" CA  LYS B 363 "
        pdb=" CB  LYS B 363 "
        pdb=" CG  LYS B 363 "
      ideal   model   delta    sigma   weight residual
     114.10  120.36   -6.26 2.00e+00 2.50e-01 9.80e+00
  ... (remaining 17507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 6597
       17.65 -    35.29: 991
       35.29 -    52.94: 244
       52.94 -    70.59: 46
       70.59 -    88.24: 20
  Dihedral angle restraints: 7898
    sinusoidal: 3178
      harmonic: 4720
  Sorted by residual:
  dihedral pdb=" CA  PHE B 817 "
           pdb=" C   PHE B 817 "
           pdb=" N   GLN B 818 "
           pdb=" CA  GLN B 818 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.77  -23.23     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  PHE A 817 "
           pdb=" C   PHE A 817 "
           pdb=" N   GLN A 818 "
           pdb=" CA  GLN A 818 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.79  -23.21     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  LEU B 524 "
           pdb=" C   LEU B 524 "
           pdb=" N   LEU B 525 "
           pdb=" CA  LEU B 525 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.57   17.43     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 7895 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1509
       0.044 -    0.088: 378
       0.088 -    0.132: 94
       0.132 -    0.176: 11
       0.176 -    0.219: 6
  Chirality restraints: 1998
  Sorted by residual:
  chirality pdb=" CA  PRO B  61 "
            pdb=" N   PRO B  61 "
            pdb=" C   PRO B  61 "
            pdb=" CB  PRO B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  PRO A  61 "
            pdb=" N   PRO A  61 "
            pdb=" C   PRO A  61 "
            pdb=" CB  PRO A  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  PHE B 111 "
            pdb=" N   PHE B 111 "
            pdb=" C   PHE B 111 "
            pdb=" CB  PHE B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1995 not shown)

  Planarity restraints: 2242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 331 "    0.059 5.00e-02 4.00e+02   8.98e-02 1.29e+01
        pdb=" N   PRO B 332 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO B 332 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 332 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 331 "    0.059 5.00e-02 4.00e+02   8.95e-02 1.28e+01
        pdb=" N   PRO A 332 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 374 "   -0.053 5.00e-02 4.00e+02   8.07e-02 1.04e+01
        pdb=" N   PRO A 375 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "   -0.045 5.00e-02 4.00e+02
  ... (remaining 2239 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 265
        2.67 -     3.23: 12490
        3.23 -     3.79: 19940
        3.79 -     4.34: 27205
        4.34 -     4.90: 44018
  Nonbonded interactions: 103918
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 144 "
            pdb=" OG  SER B 152 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" OG1 THR A 144 "
            pdb=" OG  SER A 152 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" O   THR A 610 "
            pdb=" OG1 THR A 613 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   THR B 610 "
            pdb=" OG1 THR B 613 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ILE B 816 "
            pdb=" OH  TYR B 821 "
     model   vdw
     2.233 3.040
  ... (remaining 103913 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: 0.06
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:             115.110
  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:          0.570
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     38.120
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  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:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  157.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5657
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      :  0.003   0.036  12994  Z= 0.138
  Angle     :  0.666   8.999  17512  Z= 0.345
  Chirality :  0.043   0.219   1998
  Planarity :  0.005   0.090   2242
  Dihedral  : 18.003  88.236   4838
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.53 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 29.36 %
    Favored  : 70.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.21), residues: 1614
  helix:  0.19 (0.21), residues: 640
  sheet: -0.07 (0.46), residues: 136
  loop : -2.12 (0.20), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 681 
 HIS   0.005   0.001   HIS B 580 
 PHE   0.016   0.001   PHE B 485 
 TYR   0.010   0.001   TYR A 761 
 ARG   0.003   0.000   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15909 (  464)
  hydrogen bonds       : angle       7.16635 ( 1332)
  covalent geometry    : bond        0.00295 (12994)
  covalent geometry    : angle       0.66562 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 284
  time to evaluate  : 1.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  210 LEU cc_start: 0.8492 (mt) cc_final: 0.8268 (mt)
REVERT: B  465 MET cc_start: 0.5288 (mmp) cc_final: 0.5043 (mmm)
REVERT: B  711 PHE cc_start: 0.7701 (m-80) cc_final: 0.7487 (m-80)
REVERT: A  534 ASP cc_start: 0.4215 (t70) cc_final: 0.3934 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 286
  average time/residue: 0.2824
  time to fit residues: 113.2792
Evaluate side-chains
  148 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 1.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  781 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 81 optimal weight:   20.0000
   chunk 64 optimal weight:    0.9980
   chunk 125 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 76 optimal weight:    0.3980
   chunk 93 optimal weight:   20.0000
   chunk 145 optimal weight:    0.9980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  98 GLN
B 279 ASN
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 ASN
B 746 ASN
A 235 ASN
A 584 ASN
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 799 GLN
A 803 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.223986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.192848 restraints weight = 19417.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.4381 rms_B_bonded: 2.33
r_work: 0.4044 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  12994  Z= 0.268
  Angle     :  0.792   8.483  17512  Z= 0.409
  Chirality :  0.049   0.259   1998
  Planarity :  0.005   0.073   2242
  Dihedral  :  5.499  34.226   1682
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.21 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 24.36 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.20), residues: 1614
  helix: -0.56 (0.20), residues: 648
  sheet: -0.69 (0.44), residues: 156
  loop : -1.99 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 681 
 HIS   0.008   0.002   HIS B 580 
 PHE   0.021   0.002   PHE B 458 
 TYR   0.023   0.002   TYR A 623 
 ARG   0.005   0.001   ARG A 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04832 (  464)
  hydrogen bonds       : angle       5.80815 ( 1332)
  covalent geometry    : bond        0.00620 (12994)
  covalent geometry    : angle       0.79165 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 148
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  213 MET cc_start: 0.6649 (ppp) cc_final: 0.6302 (ppp)
REVERT: B  667 MET cc_start: 0.7680 (tmm) cc_final: 0.7340 (tmm)
REVERT: B  695 ASN cc_start: 0.7667 (t0) cc_final: 0.7184 (t0)
REVERT: A  393 ASP cc_start: 0.4412 (OUTLIER) cc_final: 0.3724 (t70)
REVERT: A  500 THR cc_start: 0.7619 (m) cc_final: 0.6880 (p)
REVERT: A  669 ASP cc_start: 0.8440 (m-30) cc_final: 0.8225 (m-30)
REVERT: A  695 ASN cc_start: 0.6521 (t0) cc_final: 0.6035 (t0)
REVERT: A  714 MET cc_start: 0.8272 (ttt) cc_final: 0.8041 (ttt)
  outliers start: 76
  outliers final: 31
  residues processed: 217
  average time/residue: 0.2423
  time to fit residues: 78.3855
Evaluate side-chains
  151 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  270 GLU
Chi-restraints excluded: chain B residue  361 ASN
Chi-restraints excluded: chain B residue  371 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  574 LEU
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  746 ASN
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  704 THR
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  773 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 129 optimal weight:    0.0030
   chunk 101 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 133 optimal weight:    0.9990
   chunk 46 optimal weight:    0.4980
   chunk 144 optimal weight:    0.9980
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 GLN
B 746 ASN
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 GLN
A 449 ASN
** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 803 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.224612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.194521 restraints weight = 19706.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.4380 rms_B_bonded: 2.25
r_work: 0.4027 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12994  Z= 0.171
  Angle     :  0.672  13.380  17512  Z= 0.344
  Chirality :  0.044   0.162   1998
  Planarity :  0.004   0.055   2242
  Dihedral  :  5.158  25.976   1680
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.91 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 25.93 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.20), residues: 1614
  helix: -0.58 (0.19), residues: 660
  sheet: -0.63 (0.45), residues: 144
  loop : -2.13 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 121 
 HIS   0.007   0.002   HIS A 580 
 PHE   0.018   0.001   PHE B 232 
 TYR   0.017   0.001   TYR B  79 
 ARG   0.006   0.001   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04133 (  464)
  hydrogen bonds       : angle       5.55156 ( 1332)
  covalent geometry    : bond        0.00388 (12994)
  covalent geometry    : angle       0.67202 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 136
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7599 (tt)
REVERT: B  667 MET cc_start: 0.7541 (tmm) cc_final: 0.7283 (tmm)
REVERT: B  695 ASN cc_start: 0.7509 (t0) cc_final: 0.7052 (t0)
REVERT: B  864 LEU cc_start: 0.4937 (tp) cc_final: 0.4647 (tp)
REVERT: A  347 GLN cc_start: 0.6760 (tp-100) cc_final: 0.5437 (mp10)
REVERT: A  427 GLU cc_start: 0.4080 (OUTLIER) cc_final: 0.2166 (mt-10)
REVERT: A  496 GLU cc_start: 0.8551 (tm-30) cc_final: 0.7714 (tt0)
REVERT: A  500 THR cc_start: 0.7626 (m) cc_final: 0.6866 (p)
REVERT: A  668 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6556 (tttt)
REVERT: A  669 ASP cc_start: 0.8418 (m-30) cc_final: 0.8173 (m-30)
REVERT: A  695 ASN cc_start: 0.6536 (t0) cc_final: 0.6059 (t0)
REVERT: A  748 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7051 (pp)
  outliers start: 68
  outliers final: 32
  residues processed: 196
  average time/residue: 0.2605
  time to fit residues: 77.9435
Evaluate side-chains
  150 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 114
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  376 GLU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  427 GLU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  668 LYS
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  773 THR
Chi-restraints excluded: chain A residue  835 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 159 optimal weight:    6.9990
   chunk 57 optimal weight:    0.4980
   chunk 146 optimal weight:    1.9990
   chunk 83 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 51 optimal weight:    0.6980
   chunk 10 optimal weight:    9.9990
   chunk 145 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 ASN
B 367 ASN
A 303 ASN
A 304 GLN
** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 584 ASN
A 601 ASN
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 803 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.220259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.189762 restraints weight = 19378.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.4350 rms_B_bonded: 2.21
r_work: 0.3982 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.5204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12994  Z= 0.222
  Angle     :  0.721  12.514  17512  Z= 0.369
  Chirality :  0.045   0.166   1998
  Planarity :  0.004   0.048   2242
  Dihedral  :  5.319  22.268   1680
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.15 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 25.07 %
    Favored  : 69.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.20), residues: 1614
  helix: -0.81 (0.19), residues: 652
  sheet: -1.09 (0.43), residues: 158
  loop : -2.10 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 681 
 HIS   0.006   0.001   HIS B 580 
 PHE   0.020   0.002   PHE A 327 
 TYR   0.015   0.002   TYR A 623 
 ARG   0.006   0.001   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04269 (  464)
  hydrogen bonds       : angle       5.64963 ( 1332)
  covalent geometry    : bond        0.00515 (12994)
  covalent geometry    : angle       0.72133 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 122
  time to evaluate  : 1.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  213 MET cc_start: 0.6672 (ppp) cc_final: 0.6408 (ppp)
REVERT: B  341 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7769 (tt)
REVERT: B  667 MET cc_start: 0.7554 (tmm) cc_final: 0.7311 (tmm)
REVERT: B  695 ASN cc_start: 0.7675 (t0) cc_final: 0.7204 (t0)
REVERT: B  864 LEU cc_start: 0.4810 (tp) cc_final: 0.4578 (tp)
REVERT: A   97 LEU cc_start: 0.1543 (OUTLIER) cc_final: 0.1282 (pt)
REVERT: A  347 GLN cc_start: 0.6707 (tp-100) cc_final: 0.5354 (mp-120)
REVERT: A  496 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8069 (tt0)
REVERT: A  668 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6547 (tttt)
REVERT: A  669 ASP cc_start: 0.8339 (m-30) cc_final: 0.8085 (m-30)
REVERT: A  695 ASN cc_start: 0.6878 (t0) cc_final: 0.6319 (t0)
REVERT: A  739 LYS cc_start: 0.6515 (mmtt) cc_final: 0.6262 (tptp)
REVERT: A  748 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7092 (pp)
  outliers start: 78
  outliers final: 44
  residues processed: 191
  average time/residue: 0.3204
  time to fit residues: 94.8320
Evaluate side-chains
  153 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 105
  time to evaluate  : 2.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  270 GLU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  361 ASN
Chi-restraints excluded: chain B residue  376 GLU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  427 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  570 GLN
Chi-restraints excluded: chain B residue  574 LEU
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  668 LYS
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  835 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 151 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 93 optimal weight:    5.9990
   chunk 135 optimal weight:    0.0270
   chunk 69 optimal weight:    0.6980
   chunk 96 optimal weight:    9.9990
   chunk 139 optimal weight:    0.3980
   chunk 126 optimal weight:    0.4980
   chunk 12 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 ASN
** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 803 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.219381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.189342 restraints weight = 19605.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.4365 rms_B_bonded: 2.29
r_work: 0.4011 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12994  Z= 0.167
  Angle     :  0.674  10.411  17512  Z= 0.343
  Chirality :  0.044   0.151   1998
  Planarity :  0.004   0.044   2242
  Dihedral  :  5.218  24.489   1680
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.66 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 26.00 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.20), residues: 1614
  helix: -0.72 (0.19), residues: 650
  sheet: -1.05 (0.43), residues: 158
  loop : -2.10 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 121 
 HIS   0.007   0.001   HIS A 580 
 PHE   0.026   0.001   PHE B 454 
 TYR   0.014   0.001   TYR B  79 
 ARG   0.009   0.001   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  464)
  hydrogen bonds       : angle       5.61576 ( 1332)
  covalent geometry    : bond        0.00380 (12994)
  covalent geometry    : angle       0.67384 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 121
  time to evaluate  : 2.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7734 (tt)
REVERT: B  404 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6911 (t80)
REVERT: B  427 GLU cc_start: 0.5734 (OUTLIER) cc_final: 0.5123 (pt0)
REVERT: B  695 ASN cc_start: 0.7508 (t0) cc_final: 0.7064 (t0)
REVERT: B  864 LEU cc_start: 0.4674 (tp) cc_final: 0.4413 (tp)
REVERT: A  294 MET cc_start: 0.7141 (ptm) cc_final: 0.6831 (ptt)
REVERT: A  347 GLN cc_start: 0.6680 (tp-100) cc_final: 0.5371 (mp10)
REVERT: A  364 THR cc_start: 0.5698 (OUTLIER) cc_final: 0.5184 (m)
REVERT: A  496 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8137 (tt0)
REVERT: A  668 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6705 (tttt)
REVERT: A  695 ASN cc_start: 0.7037 (t0) cc_final: 0.6503 (t0)
REVERT: A  739 LYS cc_start: 0.6605 (mmtt) cc_final: 0.6349 (tptt)
REVERT: A  748 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.7032 (pp)
REVERT: A  799 GLN cc_start: 0.7308 (tm130) cc_final: 0.6849 (tm-30)
  outliers start: 78
  outliers final: 48
  residues processed: 188
  average time/residue: 0.2893
  time to fit residues: 85.1624
Evaluate side-chains
  160 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 106
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  270 GLU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  361 ASN
Chi-restraints excluded: chain B residue  376 GLU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  404 PHE
Chi-restraints excluded: chain B residue  427 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  570 GLN
Chi-restraints excluded: chain B residue  574 LEU
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain B residue  805 TRP
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  668 LYS
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  808 MET
Chi-restraints excluded: chain A residue  835 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 144 optimal weight:    0.0980
   chunk 118 optimal weight:    0.2980
   chunk 40 optimal weight:    0.0270
   chunk 125 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0980
   overall best weight:    0.2038

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

Flipped N/Q/H residues before XYZ refinement:
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 343 GLN
** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 343 GLN
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.224705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.196403 restraints weight = 19678.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.4423 rms_B_bonded: 2.16
r_work: 0.4081 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.5608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12994  Z= 0.122
  Angle     :  0.634   8.820  17512  Z= 0.322
  Chirality :  0.043   0.163   1998
  Planarity :  0.004   0.042   2242
  Dihedral  :  4.980  24.657   1680
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.48 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 26.93 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.20), residues: 1614
  helix: -0.56 (0.19), residues: 668
  sheet: -1.02 (0.43), residues: 158
  loop : -2.17 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 121 
 HIS   0.006   0.001   HIS A 580 
 PHE   0.019   0.001   PHE B 111 
 TYR   0.014   0.001   TYR B  79 
 ARG   0.009   0.001   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (  464)
  hydrogen bonds       : angle       5.49222 ( 1332)
  covalent geometry    : bond        0.00264 (12994)
  covalent geometry    : angle       0.63429 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 117
  time to evaluate  : 1.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7594 (tt)
REVERT: B  404 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7184 (m-80)
REVERT: B  427 GLU cc_start: 0.5320 (OUTLIER) cc_final: 0.4705 (pt0)
REVERT: B  667 MET cc_start: 0.7571 (tmm) cc_final: 0.7322 (tmm)
REVERT: B  695 ASN cc_start: 0.7205 (t0) cc_final: 0.6868 (t0)
REVERT: A  364 THR cc_start: 0.5348 (OUTLIER) cc_final: 0.4808 (m)
REVERT: A  487 GLU cc_start: 0.6708 (pp20) cc_final: 0.6435 (pp20)
REVERT: A  668 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6765 (tttt)
REVERT: A  695 ASN cc_start: 0.6783 (t0) cc_final: 0.6309 (t0)
REVERT: A  748 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7019 (pp)
REVERT: A  799 GLN cc_start: 0.7233 (tm130) cc_final: 0.6808 (tm-30)
  outliers start: 61
  outliers final: 33
  residues processed: 171
  average time/residue: 0.2324
  time to fit residues: 61.1009
Evaluate side-chains
  138 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 99
  time to evaluate  : 1.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  404 PHE
Chi-restraints excluded: chain B residue  427 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  483 ASP
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  570 GLN
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  668 LYS
Chi-restraints excluded: chain A residue  748 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 128 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0970
   chunk 76 optimal weight:    0.5980
   chunk 99 optimal weight:    0.2980
   chunk 105 optimal weight:    0.5980
   chunk 90 optimal weight:   20.0000
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
** B  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 ASN
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.223676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.194418 restraints weight = 19469.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.4382 rms_B_bonded: 2.19
r_work: 0.4022 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.5889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12994  Z= 0.152
  Angle     :  0.664   8.770  17512  Z= 0.337
  Chirality :  0.043   0.146   1998
  Planarity :  0.004   0.040   2242
  Dihedral  :  5.021  22.771   1680
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.66 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 27.29 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.20), residues: 1614
  helix: -0.62 (0.19), residues: 658
  sheet: -0.97 (0.44), residues: 154
  loop : -2.18 (0.21), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 121 
 HIS   0.006   0.001   HIS B 580 
 PHE   0.027   0.001   PHE B 454 
 TYR   0.012   0.001   TYR B  79 
 ARG   0.009   0.001   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  464)
  hydrogen bonds       : angle       5.53041 ( 1332)
  covalent geometry    : bond        0.00344 (12994)
  covalent geometry    : angle       0.66418 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 113
  time to evaluate  : 1.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7688 (tt)
REVERT: B  427 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.4981 (pt0)
REVERT: B  695 ASN cc_start: 0.7414 (t0) cc_final: 0.7029 (t0)
REVERT: A  364 THR cc_start: 0.5563 (OUTLIER) cc_final: 0.5034 (m)
REVERT: A  487 GLU cc_start: 0.6755 (pp20) cc_final: 0.6246 (pp20)
REVERT: A  668 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6778 (tttt)
REVERT: A  714 MET cc_start: 0.8249 (ttt) cc_final: 0.8046 (ttt)
  outliers start: 60
  outliers final: 40
  residues processed: 166
  average time/residue: 0.2132
  time to fit residues: 54.7453
Evaluate side-chains
  148 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 104
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  376 GLU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  427 GLU
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  570 GLN
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain B residue  805 TRP
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  668 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 137 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 144 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 133 optimal weight:    0.0870
   chunk 139 optimal weight:    0.3980
   chunk 127 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 84 optimal weight:    8.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 303 ASN
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.221245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.189222 restraints weight = 19344.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.4335 rms_B_bonded: 2.32
r_work: 0.3966 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.6226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12994  Z= 0.176
  Angle     :  0.697  10.303  17512  Z= 0.352
  Chirality :  0.044   0.154   1998
  Planarity :  0.004   0.040   2242
  Dihedral  :  5.177  23.624   1680
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.72 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 27.71 %
    Favored  : 68.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.20), residues: 1614
  helix: -0.71 (0.19), residues: 674
  sheet: -1.03 (0.44), residues: 158
  loop : -2.17 (0.21), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 121 
 HIS   0.006   0.001   HIS B 580 
 PHE   0.022   0.002   PHE B 232 
 TYR   0.015   0.001   TYR B  79 
 ARG   0.009   0.001   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  464)
  hydrogen bonds       : angle       5.60636 ( 1332)
  covalent geometry    : bond        0.00404 (12994)
  covalent geometry    : angle       0.69673 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 109
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 ASP cc_start: 0.6516 (m-30) cc_final: 0.6315 (m-30)
REVERT: B  341 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7748 (tt)
REVERT: B  404 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7044 (m-80)
REVERT: B  453 ASN cc_start: 0.7353 (p0) cc_final: 0.7110 (p0)
REVERT: B  620 ASP cc_start: 0.6789 (p0) cc_final: 0.6073 (p0)
REVERT: B  695 ASN cc_start: 0.7523 (t0) cc_final: 0.6887 (t0)
REVERT: A  364 THR cc_start: 0.5676 (OUTLIER) cc_final: 0.5136 (m)
REVERT: A  450 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6328 (pp)
REVERT: A  487 GLU cc_start: 0.6932 (pp20) cc_final: 0.6510 (pp20)
REVERT: A  668 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6744 (tttt)
REVERT: A  714 MET cc_start: 0.8318 (ttt) cc_final: 0.8111 (ttt)
  outliers start: 60
  outliers final: 43
  residues processed: 162
  average time/residue: 0.2105
  time to fit residues: 52.3987
Evaluate side-chains
  150 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 102
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  270 GLU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  376 GLU
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  404 PHE
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  570 GLN
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain B residue  805 TRP
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  668 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 116 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 24 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 159 optimal weight:    0.8980
   chunk 135 optimal weight:    0.9980
   chunk 147 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.220230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.189423 restraints weight = 19285.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.4345 rms_B_bonded: 2.27
r_work: 0.3971 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.6534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12994  Z= 0.180
  Angle     :  0.709  10.200  17512  Z= 0.360
  Chirality :  0.044   0.176   1998
  Planarity :  0.004   0.042   2242
  Dihedral  :  5.209  23.684   1680
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.21 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 27.86 %
    Favored  : 68.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.20), residues: 1614
  helix: -0.76 (0.19), residues: 674
  sheet: -1.11 (0.46), residues: 154
  loop : -2.22 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 121 
 HIS   0.006   0.001   HIS B 580 
 PHE   0.024   0.001   PHE B 232 
 TYR   0.014   0.001   TYR B  79 
 ARG   0.009   0.001   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  464)
  hydrogen bonds       : angle       5.60878 ( 1332)
  covalent geometry    : bond        0.00416 (12994)
  covalent geometry    : angle       0.70941 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 107
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7746 (tt)
REVERT: B  359 PHE cc_start: 0.5317 (t80) cc_final: 0.4935 (t80)
REVERT: B  404 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6994 (m-80)
REVERT: B  453 ASN cc_start: 0.7179 (p0) cc_final: 0.6889 (p0)
REVERT: B  695 ASN cc_start: 0.7523 (t0) cc_final: 0.6887 (t0)
REVERT: A  364 THR cc_start: 0.5916 (OUTLIER) cc_final: 0.5394 (m)
REVERT: A  450 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6346 (pp)
REVERT: A  487 GLU cc_start: 0.6896 (pp20) cc_final: 0.6216 (pp20)
REVERT: A  668 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6730 (tttt)
REVERT: A  714 MET cc_start: 0.8353 (ttt) cc_final: 0.8142 (ttt)
  outliers start: 58
  outliers final: 45
  residues processed: 158
  average time/residue: 0.2106
  time to fit residues: 52.1231
Evaluate side-chains
  147 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 97
  time to evaluate  : 1.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  270 GLU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  376 GLU
Chi-restraints excluded: chain B residue  404 PHE
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  483 ASP
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  570 GLN
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  723 VAL
Chi-restraints excluded: chain B residue  735 SER
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain B residue  805 TRP
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  386 VAL
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  570 GLN
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  668 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 100 optimal weight:    0.1980
   chunk 81 optimal weight:   30.0000
   chunk 107 optimal weight:    0.0570
   chunk 50 optimal weight:    0.7980
   chunk 58 optimal weight:    0.2980
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 138 optimal weight:    0.2980
   chunk 76 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   chunk 130 optimal weight:    0.4980
   overall best weight:    0.1898

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

Flipped N/Q/H residues before XYZ refinement:
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 756 ASN
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.221755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.198408 restraints weight = 19511.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.4453 rms_B_bonded: 1.87
r_work: 0.4104 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.6584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  12994  Z= 0.125
  Angle     :  0.670   9.122  17512  Z= 0.339
  Chirality :  0.043   0.172   1998
  Planarity :  0.004   0.042   2242
  Dihedral  :  4.905  24.753   1680
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.60 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 29.07 %
    Favored  : 68.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.20), residues: 1614
  helix: -0.54 (0.19), residues: 672
  sheet: -0.93 (0.45), residues: 154
  loop : -2.21 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 121 
 HIS   0.004   0.001   HIS B 580 
 PHE   0.023   0.001   PHE A 404 
 TYR   0.016   0.001   TYR B  79 
 ARG   0.010   0.001   ARG A 400 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03597 (  464)
  hydrogen bonds       : angle       5.40219 ( 1332)
  covalent geometry    : bond        0.00273 (12994)
  covalent geometry    : angle       0.66967 (17512)

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

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

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3228 Ramachandran restraints generated.
    1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 1.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7689 (tt)
REVERT: B  404 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6602 (m-80)
REVERT: B  453 ASN cc_start: 0.6970 (p0) cc_final: 0.6641 (p0)
REVERT: B  695 ASN cc_start: 0.7204 (t0) cc_final: 0.6864 (t0)
REVERT: A  364 THR cc_start: 0.5147 (OUTLIER) cc_final: 0.4571 (m)
REVERT: A  487 GLU cc_start: 0.6639 (pp20) cc_final: 0.6421 (pp20)
REVERT: A  499 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7726 (mt)
REVERT: A  668 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6791 (tttt)
REVERT: A  756 ASN cc_start: 0.5765 (OUTLIER) cc_final: 0.5436 (p0)
  outliers start: 41
  outliers final: 28
  residues processed: 148
  average time/residue: 0.2352
  time to fit residues: 53.9796
Evaluate side-chains
  130 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 LEU
Chi-restraints excluded: chain B residue  152 SER
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  376 GLU
Chi-restraints excluded: chain B residue  404 PHE
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  483 ASP
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  570 GLN
Chi-restraints excluded: chain B residue  595 THR
Chi-restraints excluded: chain B residue  613 THR
Chi-restraints excluded: chain B residue  654 LEU
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  767 ASP
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  788 SER
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  668 LYS
Chi-restraints excluded: chain A residue  756 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 100 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0170
   chunk 36 optimal weight:    0.4980
   chunk 111 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   chunk 103 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 65 optimal weight:    0.2980
   chunk 32 optimal weight:    3.9990
   chunk 129 optimal weight:    5.9990
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.3418

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

Flipped N/Q/H residues before XYZ refinement:
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 756 ASN
** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.221577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.197452 restraints weight = 19382.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.4449 rms_B_bonded: 1.90
r_work: 0.4074 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.6614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.200  12994  Z= 0.213
  Angle     :  0.916  59.101  17512  Z= 0.516
  Chirality :  0.048   0.898   1998
  Planarity :  0.004   0.046   2242
  Dihedral  :  4.905  24.581   1680
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.79 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 29.36 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.20), residues: 1614
  helix: -0.53 (0.19), residues: 672
  sheet: -0.93 (0.45), residues: 154
  loop : -2.20 (0.21), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 121 
 HIS   0.005   0.001   HIS B 580 
 PHE   0.063   0.002   PHE B 134 
 TYR   0.015   0.001   TYR B  79 
 ARG   0.003   0.000   ARG A 548 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03605 (  464)
  hydrogen bonds       : angle       5.39669 ( 1332)
  covalent geometry    : bond        0.00465 (12994)
  covalent geometry    : angle       0.91644 (17512)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7466.57 seconds
wall clock time: 136 minutes 41.73 seconds (8201.73 seconds total)