Starting phenix.real_space_refine
on Wed Sep 17 09:26:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d7r_30610/09_2025/7d7r_30610.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d7r_30610/09_2025/7d7r_30610.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d7r_30610/09_2025/7d7r_30610.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d7r_30610/09_2025/7d7r_30610.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d7r_30610/09_2025/7d7r_30610.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d7r_30610/09_2025/7d7r_30610.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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      22      5.16       5
     C    4864      2.51       5
     N    1368      2.21       5
     O    1426      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7680
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 3840
          Classifications: {'peptide': 580}
          Incomplete info: {'truncation_to_alanine': 216}
          Link IDs: {'PTRANS': 12, 'TRANS': 567}
          Chain breaks: 1
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 773
          Unresolved non-hydrogen angles: 992
          Unresolved non-hydrogen dihedrals: 622
          Unresolved non-hydrogen chiralities: 82
          Planarities with less than four sites: {'ASP:plan': 17, 'PHE:plan': 9, 'ARG:plan': 22, 'TYR:plan': 6, 'TRP:plan': 2, 'GLN:plan1': 15, 'GLU:plan': 12, 'ASN:plan1': 7, 'HIS:plan': 5}
          Unresolved non-hydrogen planarities: 429
    Chain: "B"
      Number of atoms: 3840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 3840
          Classifications: {'peptide': 580}
          Incomplete info: {'truncation_to_alanine': 216}
          Link IDs: {'PTRANS': 12, 'TRANS': 567}
          Chain breaks: 1
          Unresolved chain link angles: 8
          Unresolved non-hydrogen bonds: 773
          Unresolved non-hydrogen angles: 992
          Unresolved non-hydrogen dihedrals: 622
          Unresolved non-hydrogen chiralities: 82
          Planarities with less than four sites: {'ASP:plan': 17, 'PHE:plan': 9, 'ARG:plan': 22, 'TYR:plan': 6, 'TRP:plan': 2, 'GLN:plan1': 15, 'GLU:plan': 12, 'ASN:plan1': 7, 'HIS:plan': 5}
          Unresolved non-hydrogen planarities: 429
  Time building chain proxies: 2.02, per 1000 atoms: 0.26
  Number of scatterers: 7680
  At special positions: 0
  Unit cell: (86.32, 107.12, 134.16, 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      22     16.00
     O    1426      8.00
     N    1368      7.00
     C    4864      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: 0.65
  Conformation dependent library (CDL) restraints added in 431.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      68.7% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 261 through 297
      removed outlier: 3.947A  pdb=" N   ARG A 276 " --> pdb=" O   MET A 272 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
    Processing helix  chain 'A' and resid 306 through 321
      removed outlier: 4.207A  pdb=" N   LEU A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 353
      removed outlier: 4.020A  pdb=" N   ARG A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 363
      removed outlier: 3.970A  pdb=" N   GLY A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 390
      removed outlier: 3.516A  pdb=" N   VAL A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 409
    Processing helix  chain 'A' and resid 412 through 459
      removed outlier: 4.322A  pdb=" N   LYS A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE A 438 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ASN A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 471 through 523
      removed outlier: 4.148A  pdb=" N   LEU A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 542
      removed outlier: 3.613A  pdb=" N   PHE A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE A 537 " --> pdb=" O   PHE A 533 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 549
    Processing helix  chain 'A' and resid 550 through 568
      removed outlier: 3.740A  pdb=" N   GLN A 555 " --> pdb=" O   TYR A 551 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ASN A 563 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET A 564 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 637
    Processing helix  chain 'A' and resid 659 through 664
    Processing helix  chain 'A' and resid 680 through 686
    Processing helix  chain 'A' and resid 692 through 704
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 728 through 744
    Processing helix  chain 'A' and resid 758 through 774
    Processing helix  chain 'A' and resid 807 through 815
    Processing helix  chain 'A' and resid 816 through 827
      removed outlier: 4.106A  pdb=" N   ASP A 820 " --> pdb=" O   GLY A 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 253
    Processing helix  chain 'B' and resid 261 through 297
      removed outlier: 3.947A  pdb=" N   ARG B 276 " --> pdb=" O   MET B 272 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 306 through 321
      removed outlier: 4.206A  pdb=" N   LEU B 315 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 353
      removed outlier: 4.021A  pdb=" N   ARG B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 363
      removed outlier: 3.971A  pdb=" N   GLY B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 390
      removed outlier: 3.516A  pdb=" N   VAL B 369 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 409
    Processing helix  chain 'B' and resid 412 through 459
      removed outlier: 4.322A  pdb=" N   LYS B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE B 438 " --> pdb=" O   TRP B 434 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ASN B 459 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 466
    Processing helix  chain 'B' and resid 471 through 523
      removed outlier: 4.148A  pdb=" N   LEU B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 542
      removed outlier: 3.613A  pdb=" N   PHE B 533 " --> pdb=" O   ASP B 529 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE B 537 " --> pdb=" O   PHE B 533 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ILE B 538 " --> pdb=" O   GLY B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 549
    Processing helix  chain 'B' and resid 550 through 568
      removed outlier: 3.740A  pdb=" N   GLN B 555 " --> pdb=" O   TYR B 551 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ASN B 563 " --> pdb=" O   ILE B 559 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET B 564 " --> pdb=" O   ASP B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 637
    Processing helix  chain 'B' and resid 659 through 664
    Processing helix  chain 'B' and resid 680 through 686
    Processing helix  chain 'B' and resid 692 through 704
    Processing helix  chain 'B' and resid 705 through 712
    Processing helix  chain 'B' and resid 728 through 744
    Processing helix  chain 'B' and resid 758 through 774
    Processing helix  chain 'B' and resid 807 through 815
    Processing helix  chain 'B' and resid 816 through 827
      removed outlier: 4.105A  pdb=" N   ASP B 820 " --> pdb=" O   GLY B 816 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 611 through 613
    Processing sheet with id=AA2, first strand: chain 'A' and resid 666 through 669
      removed outlier: 6.362A  pdb=" N   GLY A 667 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   ASP A 751 " --> pdb=" O   GLY A 667 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL A 669 " --> pdb=" O   ASP A 751 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   ILE A 748 " --> pdb=" O   ILE A 779 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   VAL A 781 " --> pdb=" O   ILE A 748 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   LEU A 750 " --> pdb=" O   VAL A 781 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   LEU A 619 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   THR A 618 " --> pdb=" O   GLN A 793 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   LEU A 795 " --> pdb=" O   THR A 618 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ALA A 620 " --> pdb=" O   LEU A 795 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ILE A 797 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL A 622 " --> pdb=" O   ILE A 797 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ILE A 794 " --> pdb=" O   ARG A 805 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ARG A 805 " --> pdb=" O   ILE A 794 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   VAL A 796 " --> pdb=" O   VAL A 803 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 679
    Processing sheet with id=AA4, first strand: chain 'B' and resid 611 through 613
    Processing sheet with id=AA5, first strand: chain 'B' and resid 666 through 669
      removed outlier: 6.363A  pdb=" N   GLY B 667 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASP B 751 " --> pdb=" O   GLY B 667 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL B 669 " --> pdb=" O   ASP B 751 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   ILE B 748 " --> pdb=" O   ILE B 779 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   VAL B 781 " --> pdb=" O   ILE B 748 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   LEU B 750 " --> pdb=" O   VAL B 781 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   LEU B 619 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   THR B 618 " --> pdb=" O   GLN B 793 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   LEU B 795 " --> pdb=" O   THR B 618 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ALA B 620 " --> pdb=" O   LEU B 795 " (cutoff:3.500A)
      removed outlier: 7.647A  pdb=" N   ILE B 797 " --> pdb=" O   ALA B 620 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL B 622 " --> pdb=" O   ILE B 797 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ILE B 794 " --> pdb=" O   ARG B 805 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ARG B 805 " --> pdb=" O   ILE B 794 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   VAL B 796 " --> pdb=" O   VAL B 803 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 678 through 679

    609 hydrogen bonds defined for protein.
    1791 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2308
        1.34 -     1.45: 1217
        1.45 -     1.57: 4223
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 7786
  Sorted by residual:
  bond pdb=" C   PRO A 255 "
       pdb=" N   ARG A 256 "
    ideal  model  delta    sigma   weight residual
    1.325  1.270  0.055 1.41e-02 5.03e+03 1.54e+01
  bond pdb=" C   PRO B 255 "
       pdb=" N   ARG B 256 "
    ideal  model  delta    sigma   weight residual
    1.325  1.270  0.055 1.41e-02 5.03e+03 1.52e+01
  bond pdb=" C   ARG A 256 "
       pdb=" N   GLY A 257 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.46e-02 4.69e+03 4.93e+00
  bond pdb=" C   ARG B 256 "
       pdb=" N   GLY B 257 "
    ideal  model  delta    sigma   weight residual
    1.331  1.363 -0.032 1.46e-02 4.69e+03 4.87e+00
  bond pdb=" C   ILE B 392 "
       pdb=" N   PRO B 393 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.23e-02 6.61e+03 2.18e+00
  ... (remaining 7781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 10116
        1.89 -     3.78: 426
        3.78 -     5.67: 60
        5.67 -     7.56: 23
        7.56 -     9.45: 17
  Bond angle restraints: 10642
  Sorted by residual:
  angle pdb=" N   VAL B 282 "
        pdb=" CA  VAL B 282 "
        pdb=" C   VAL B 282 "
      ideal   model   delta    sigma   weight residual
     108.88  117.15   -8.27 2.16e+00 2.14e-01 1.47e+01
  angle pdb=" N   VAL A 282 "
        pdb=" CA  VAL A 282 "
        pdb=" C   VAL A 282 "
      ideal   model   delta    sigma   weight residual
     108.88  117.10   -8.22 2.16e+00 2.14e-01 1.45e+01
  angle pdb=" C   GLU B 593 "
        pdb=" N   ASN B 594 "
        pdb=" CA  ASN B 594 "
      ideal   model   delta    sigma   weight residual
     122.82  128.22   -5.40 1.42e+00 4.96e-01 1.45e+01
  angle pdb=" C   GLU A 593 "
        pdb=" N   ASN A 594 "
        pdb=" CA  ASN A 594 "
      ideal   model   delta    sigma   weight residual
     122.82  128.17   -5.35 1.42e+00 4.96e-01 1.42e+01
  angle pdb=" N   MET A 542 "
        pdb=" CA  MET A 542 "
        pdb=" C   MET A 542 "
      ideal   model   delta    sigma   weight residual
     109.81  117.37   -7.56 2.21e+00 2.05e-01 1.17e+01
  ... (remaining 10637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 4067
       17.39 -    34.78: 346
       34.78 -    52.17: 66
       52.17 -    69.56: 19
       69.56 -    86.94: 4
  Dihedral angle restraints: 4502
    sinusoidal: 1186
      harmonic: 3316
  Sorted by residual:
  dihedral pdb=" CA  PRO A 713 "
           pdb=" C   PRO A 713 "
           pdb=" N   GLU A 714 "
           pdb=" CA  GLU A 714 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.75  -27.25     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  PRO B 713 "
           pdb=" C   PRO B 713 "
           pdb=" N   GLU B 714 "
           pdb=" CA  GLU B 714 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.75  -27.25     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  LEU B 568 "
           pdb=" C   LEU B 568 "
           pdb=" N   LYS B 569 "
           pdb=" CA  LYS B 569 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.56  -25.44     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 4499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 950
       0.054 -    0.109: 288
       0.109 -    0.163: 52
       0.163 -    0.217: 8
       0.217 -    0.271: 2
  Chirality restraints: 1300
  Sorted by residual:
  chirality pdb=" CA  ASP A 799 "
            pdb=" N   ASP A 799 "
            pdb=" C   ASP A 799 "
            pdb=" CB  ASP A 799 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  ASP B 799 "
            pdb=" N   ASP B 799 "
            pdb=" C   ASP B 799 "
            pdb=" CB  ASP B 799 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CG  LEU A 333 "
            pdb=" CB  LEU A 333 "
            pdb=" CD1 LEU A 333 "
            pdb=" CD2 LEU A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1297 not shown)

  Planarity restraints: 1394
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 388 "    0.015 2.00e-02 2.50e+03   2.90e-02 8.40e+00
        pdb=" C   VAL B 388 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   VAL B 388 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PHE B 389 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 388 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.32e+00
        pdb=" C   VAL A 388 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL A 388 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   PHE A 389 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 542 "    0.047 5.00e-02 4.00e+02   7.02e-02 7.88e+00
        pdb=" N   PRO A 543 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 543 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 543 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1391 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2105
        2.80 -     3.32: 7386
        3.32 -     3.85: 12446
        3.85 -     4.37: 13459
        4.37 -     4.90: 22502
  Nonbonded interactions: 57898
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 476 "
            pdb=" OE1 GLU B 346 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OE1 GLN A 316 "
            pdb=" OG1 THR A 320 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OE1 GLN B 316 "
            pdb=" OG1 THR B 320 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   SER B 490 "
            pdb=" OG  SER B 493 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   SER A 490 "
            pdb=" OG  SER A 493 "
     model   vdw
     2.311 3.040
  ... (remaining 57893 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.240
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.140
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6003
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7786  Z= 0.242
  Angle     :  0.961   9.447  10642  Z= 0.529
  Chirality :  0.054   0.271   1300
  Planarity :  0.006   0.070   1394
  Dihedral  : 14.868  86.944   2374
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.65 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.95 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.66 (0.19), residues: 1152
  helix: -2.08 (0.14), residues: 758
  sheet: -1.05 (0.58), residues: 82
  loop : -3.22 (0.27), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 330 
 TYR   0.026   0.003   TYR B 541 
 PHE   0.032   0.002   PHE A 460 
 TRP   0.012   0.002   TRP B 334 
 HIS   0.004   0.002   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 7786)
  covalent geometry    : angle       0.96068 (10642)
  hydrogen bonds       : bond        0.10793 (  609)
  hydrogen bonds       : angle       6.32374 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 227
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  328 ASN cc_start: 0.8140 (m-40) cc_final: 0.7355 (m-40)
REVERT: A  330 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6597 (ttm110)
REVERT: A  464 LYS cc_start: 0.7621 (mptt) cc_final: 0.7417 (pttt)
REVERT: A  487 GLU cc_start: 0.7251 (tp30) cc_final: 0.6988 (tp30)
REVERT: A  532 LEU cc_start: 0.8246 (tp) cc_final: 0.7983 (tp)
REVERT: B  290 VAL cc_start: 0.7941 (m) cc_final: 0.7716 (t)
REVERT: B  294 THR cc_start: 0.6162 (p) cc_final: 0.5532 (p)
REVERT: B  328 ASN cc_start: 0.8051 (m-40) cc_final: 0.7311 (m-40)
REVERT: B  464 LYS cc_start: 0.7803 (mptt) cc_final: 0.7570 (pttt)
REVERT: B  519 PHE cc_start: 0.6365 (m-80) cc_final: 0.6157 (m-80)
REVERT: B  525 LEU cc_start: 0.4824 (pt) cc_final: 0.4539 (mp)
REVERT: B  532 LEU cc_start: 0.8210 (tp) cc_final: 0.7797 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 227
  average time/residue: 0.0843
  time to fit residues: 25.4244
Evaluate side-chains
  150 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 316 GLN
** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 555 GLN
B 279 ASN
B 316 GLN
** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 539 GLN
B 555 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.145157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.143779 restraints weight = 31786.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.142848 restraints weight = 33511.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.142807 restraints weight = 32411.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.142788 restraints weight = 30724.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.142808 restraints weight = 28689.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6042
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7786  Z= 0.210
  Angle     :  0.717   8.134  10642  Z= 0.393
  Chirality :  0.044   0.143   1300
  Planarity :  0.005   0.057   1394
  Dihedral  :  5.694  25.738   1226
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.60 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.99 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.22), residues: 1152
  helix: -0.57 (0.17), residues: 786
  sheet: -1.00 (0.54), residues: 82
  loop : -3.21 (0.27), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 330 
 TYR   0.030   0.003   TYR B 541 
 PHE   0.027   0.003   PHE B 565 
 TRP   0.025   0.003   TRP B 334 
 HIS   0.004   0.002   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 7786)
  covalent geometry    : angle       0.71661 (10642)
  hydrogen bonds       : bond        0.05169 (  609)
  hydrogen bonds       : angle       5.13777 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7792 (m) cc_final: 0.7485 (t)
REVERT: A  350 PHE cc_start: 0.7760 (t80) cc_final: 0.7546 (t80)
REVERT: A  509 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7337 (tt)
REVERT: B  290 VAL cc_start: 0.7702 (m) cc_final: 0.7435 (t)
REVERT: B  328 ASN cc_start: 0.7657 (m-40) cc_final: 0.7392 (m110)
REVERT: B  350 PHE cc_start: 0.7802 (t80) cc_final: 0.7556 (t80)
REVERT: B  561 MET cc_start: 0.5270 (ppp) cc_final: 0.5053 (tmm)
  outliers start: 14
  outliers final: 9
  residues processed: 166
  average time/residue: 0.0776
  time to fit residues: 17.7823
Evaluate side-chains
  153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:   40.0000
   chunk 24 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 63 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 328 ASN
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.147480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.143048 restraints weight = 31737.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.143439 restraints weight = 26055.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.143575 restraints weight = 21712.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.143920 restraints weight = 19463.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.143921 restraints weight = 16994.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6294
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7786  Z= 0.138
  Angle     :  0.652   7.919  10642  Z= 0.340
  Chirality :  0.042   0.131   1300
  Planarity :  0.004   0.084   1394
  Dihedral  :  5.009  23.449   1226
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.35 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.23), residues: 1152
  helix:  0.36 (0.17), residues: 780
  sheet: -0.90 (0.54), residues: 86
  loop : -2.91 (0.30), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 365 
 TYR   0.021   0.002   TYR A 541 
 PHE   0.018   0.002   PHE B 519 
 TRP   0.014   0.002   TRP B 334 
 HIS   0.004   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7786)
  covalent geometry    : angle       0.65224 (10642)
  hydrogen bonds       : bond        0.04444 (  609)
  hydrogen bonds       : angle       4.61944 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 ARG cc_start: 0.6960 (mtm-85) cc_final: 0.5905 (ttm110)
REVERT: A  350 PHE cc_start: 0.8544 (t80) cc_final: 0.8139 (t80)
REVERT: A  370 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7300 (tt)
REVERT: A  570 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5871 (mm-30)
REVERT: B  330 ARG cc_start: 0.7509 (ttm110) cc_final: 0.6776 (ttm110)
REVERT: B  350 PHE cc_start: 0.8535 (t80) cc_final: 0.8119 (t80)
  outliers start: 17
  outliers final: 12
  residues processed: 178
  average time/residue: 0.0739
  time to fit residues: 18.6409
Evaluate side-chains
  163 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  570 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 39 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   chunk 61 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 43 optimal weight:    9.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 390 ASN
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 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 = 0.4338 r_free = 0.4338 target = 0.146319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.143242 restraints weight = 32091.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.143108 restraints weight = 31946.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.143375 restraints weight = 31919.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.143408 restraints weight = 25587.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.143497 restraints weight = 19881.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.4304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6034
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7786  Z= 0.152
  Angle     :  0.668  10.092  10642  Z= 0.346
  Chirality :  0.042   0.128   1300
  Planarity :  0.004   0.061   1394
  Dihedral  :  4.777  22.472   1226
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 22.08 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.24), residues: 1152
  helix:  0.79 (0.18), residues: 780
  sheet: -0.72 (0.54), residues: 86
  loop : -2.74 (0.32), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 330 
 TYR   0.051   0.002   TYR A 424 
 PHE   0.014   0.002   PHE A 314 
 TRP   0.013   0.002   TRP A 334 
 HIS   0.005   0.002   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7786)
  covalent geometry    : angle       0.66806 (10642)
  hydrogen bonds       : bond        0.04446 (  609)
  hydrogen bonds       : angle       4.55641 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  445 GLN cc_start: 0.5702 (pt0) cc_final: 0.5434 (mm-40)
REVERT: A  570 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6145 (mm-30)
REVERT: B  330 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6951 (ttm170)
  outliers start: 26
  outliers final: 16
  residues processed: 174
  average time/residue: 0.0777
  time to fit residues: 18.7892
Evaluate side-chains
  162 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 97 optimal weight:   30.0000
   chunk 44 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 390 ASN
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 ASN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.158706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.151078 restraints weight = 30172.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.152500 restraints weight = 19527.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.153523 restraints weight = 13436.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.154278 restraints weight = 9816.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.154640 restraints weight = 7389.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6085
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7786  Z= 0.160
  Angle     :  0.688  10.132  10642  Z= 0.359
  Chirality :  0.043   0.145   1300
  Planarity :  0.004   0.072   1394
  Dihedral  :  4.763  22.015   1226
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.00 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.24), residues: 1152
  helix:  0.96 (0.18), residues: 780
  sheet: -0.75 (0.53), residues: 86
  loop : -2.65 (0.32), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 330 
 TYR   0.015   0.002   TYR A 541 
 PHE   0.016   0.002   PHE B 408 
 TRP   0.014   0.002   TRP A 334 
 HIS   0.005   0.002   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7786)
  covalent geometry    : angle       0.68781 (10642)
  hydrogen bonds       : bond        0.04529 (  609)
  hydrogen bonds       : angle       4.59082 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7576 (m) cc_final: 0.7276 (t)
REVERT: A  311 PHE cc_start: 0.3601 (OUTLIER) cc_final: -0.2064 (m-80)
REVERT: A  384 LEU cc_start: 0.8628 (pp) cc_final: 0.8357 (pp)
REVERT: A  464 LYS cc_start: 0.7299 (mmtm) cc_final: 0.6824 (pttt)
REVERT: B  290 VAL cc_start: 0.7605 (m) cc_final: 0.7309 (t)
REVERT: B  350 PHE cc_start: 0.8099 (t80) cc_final: 0.7899 (t80)
REVERT: B  502 ASN cc_start: 0.5849 (m-40) cc_final: 0.5484 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 165
  average time/residue: 0.0787
  time to fit residues: 17.8911
Evaluate side-chains
  163 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 94 optimal weight:    0.5980
   chunk 53 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 111 optimal weight:    9.9990
   chunk 109 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 39 optimal weight:   30.0000
   chunk 30 optimal weight:    0.1980
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 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 = 0.4357 r_free = 0.4357 target = 0.147019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.145104 restraints weight = 31858.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.144043 restraints weight = 41376.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.143598 restraints weight = 39828.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.143714 restraints weight = 37800.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.143748 restraints weight = 34253.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6041
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7786  Z= 0.136
  Angle     :  0.686  11.295  10642  Z= 0.349
  Chirality :  0.042   0.133   1300
  Planarity :  0.004   0.061   1394
  Dihedral  :  4.437  17.335   1226
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 27.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.24), residues: 1152
  helix:  1.26 (0.18), residues: 778
  sheet: -0.74 (0.52), residues: 88
  loop : -2.53 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 330 
 TYR   0.018   0.002   TYR A 541 
 PHE   0.017   0.001   PHE B 408 
 TRP   0.013   0.002   TRP B 412 
 HIS   0.005   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7786)
  covalent geometry    : angle       0.68614 (10642)
  hydrogen bonds       : bond        0.04257 (  609)
  hydrogen bonds       : angle       4.36473 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  311 PHE cc_start: 0.2994 (OUTLIER) cc_final: -0.1412 (m-10)
REVERT: A  350 PHE cc_start: 0.7846 (t80) cc_final: 0.7641 (t80)
REVERT: A  464 LYS cc_start: 0.7289 (mmtm) cc_final: 0.6704 (pttt)
REVERT: A  502 ASN cc_start: 0.5713 (m-40) cc_final: 0.5180 (t0)
REVERT: A  505 ILE cc_start: 0.7483 (mt) cc_final: 0.7260 (tp)
REVERT: B  311 PHE cc_start: 0.3159 (OUTLIER) cc_final: -0.2036 (m-80)
REVERT: B  502 ASN cc_start: 0.5797 (m-40) cc_final: 0.5344 (t0)
REVERT: B  505 ILE cc_start: 0.7635 (mt) cc_final: 0.7300 (tp)
  outliers start: 25
  outliers final: 15
  residues processed: 176
  average time/residue: 0.0810
  time to fit residues: 19.7518
Evaluate side-chains
  164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  569 LYS
Chi-restraints excluded: chain B residue  311 PHE
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 95 optimal weight:   20.0000
   chunk 82 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0270
   chunk 54 optimal weight:   30.0000
   overall best weight:    1.4044

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

Flipped N/Q/H residues before XYZ refinement:
A 459 ASN
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 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 = 0.4346 r_free = 0.4346 target = 0.146844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.142634 restraints weight = 31787.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.142987 restraints weight = 26682.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.142987 restraints weight = 22640.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.142987 restraints weight = 22626.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.142987 restraints weight = 22626.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5950
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7786  Z= 0.143
  Angle     :  0.704  13.031  10642  Z= 0.359
  Chirality :  0.043   0.169   1300
  Planarity :  0.004   0.065   1394
  Dihedral  :  4.370  16.768   1226
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 27.55 %
    Favored  : 68.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.24), residues: 1152
  helix:  1.34 (0.18), residues: 778
  sheet: -0.64 (0.52), residues: 88
  loop : -2.46 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 276 
 TYR   0.017   0.002   TYR A 550 
 PHE   0.017   0.002   PHE B 460 
 TRP   0.010   0.001   TRP B 412 
 HIS   0.005   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7786)
  covalent geometry    : angle       0.70361 (10642)
  hydrogen bonds       : bond        0.04275 (  609)
  hydrogen bonds       : angle       4.36525 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  384 LEU cc_start: 0.8589 (pp) cc_final: 0.8154 (pp)
REVERT: A  464 LYS cc_start: 0.7290 (mmtm) cc_final: 0.6725 (pttt)
REVERT: A  502 ASN cc_start: 0.5332 (m-40) cc_final: 0.5092 (t0)
REVERT: B  311 PHE cc_start: 0.3629 (OUTLIER) cc_final: -0.1729 (m-80)
REVERT: B  502 ASN cc_start: 0.5425 (m-40) cc_final: 0.5225 (t0)
  outliers start: 19
  outliers final: 18
  residues processed: 166
  average time/residue: 0.0759
  time to fit residues: 17.6819
Evaluate side-chains
  158 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain B residue  311 PHE
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 109 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0770
   chunk 85 optimal weight:    3.9990
   chunk 111 optimal weight:   40.0000
   chunk 2 optimal weight:    0.8980
   chunk 50 optimal weight:    0.1980
   overall best weight:    1.6342

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

Flipped N/Q/H residues before XYZ refinement:
A 459 ASN
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 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 = 0.4339 r_free = 0.4339 target = 0.145856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.144521 restraints weight = 32508.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 80)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.142908 restraints weight = 41545.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 76)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.142595 restraints weight = 36605.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.142546 restraints weight = 46009.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.142609 restraints weight = 40831.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6059
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7786  Z= 0.148
  Angle     :  0.721  12.511  10642  Z= 0.370
  Chirality :  0.044   0.207   1300
  Planarity :  0.003   0.054   1394
  Dihedral  :  4.357  16.360   1226
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 28.28 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.25), residues: 1152
  helix:  1.35 (0.18), residues: 778
  sheet: -0.63 (0.53), residues: 88
  loop : -2.37 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 276 
 TYR   0.015   0.002   TYR A 466 
 PHE   0.028   0.002   PHE A 408 
 TRP   0.045   0.002   TRP A 334 
 HIS   0.005   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7786)
  covalent geometry    : angle       0.72078 (10642)
  hydrogen bonds       : bond        0.04352 (  609)
  hydrogen bonds       : angle       4.37312 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 VAL cc_start: 0.7944 (m) cc_final: 0.7690 (t)
REVERT: A  464 LYS cc_start: 0.7289 (mmtm) cc_final: 0.6733 (pttt)
REVERT: A  502 ASN cc_start: 0.5659 (m-40) cc_final: 0.5232 (t0)
REVERT: A  505 ILE cc_start: 0.7629 (mt) cc_final: 0.7305 (tp)
REVERT: B  290 VAL cc_start: 0.7959 (m) cc_final: 0.7716 (t)
REVERT: B  464 LYS cc_start: 0.7524 (mmtm) cc_final: 0.7293 (pttt)
REVERT: B  502 ASN cc_start: 0.5777 (m-40) cc_final: 0.5405 (t0)
REVERT: B  505 ILE cc_start: 0.7670 (mt) cc_final: 0.7392 (tp)
  outliers start: 25
  outliers final: 21
  residues processed: 161
  average time/residue: 0.0769
  time to fit residues: 17.4292
Evaluate side-chains
  162 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  404 TYR
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  459 ASN
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 459 ASN
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 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 = 0.4290 r_free = 0.4290 target = 0.142971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.139916 restraints weight = 32515.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.139563 restraints weight = 38842.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.139864 restraints weight = 35291.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.139712 restraints weight = 32463.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.140041 restraints weight = 24784.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6092
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7786  Z= 0.203
  Angle     :  0.768  13.506  10642  Z= 0.406
  Chirality :  0.046   0.216   1300
  Planarity :  0.004   0.051   1394
  Dihedral  :  4.766  20.860   1226
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 29.56 %
    Favored  : 66.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.24), residues: 1152
  helix:  1.16 (0.18), residues: 766
  sheet: -0.45 (0.84), residues: 44
  loop : -2.27 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 330 
 TYR   0.022   0.002   TYR A 551 
 PHE   0.026   0.003   PHE B 350 
 TRP   0.054   0.003   TRP A 334 
 HIS   0.006   0.002   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 7786)
  covalent geometry    : angle       0.76825 (10642)
  hydrogen bonds       : bond        0.04807 (  609)
  hydrogen bonds       : angle       4.74225 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  290 VAL cc_start: 0.7929 (m) cc_final: 0.7595 (t)
REVERT: A  311 PHE cc_start: 0.3624 (OUTLIER) cc_final: -0.1597 (m-80)
REVERT: A  505 ILE cc_start: 0.7596 (mt) cc_final: 0.7342 (tp)
REVERT: B  290 VAL cc_start: 0.7884 (m) cc_final: 0.7610 (t)
REVERT: B  464 LYS cc_start: 0.7572 (mmtm) cc_final: 0.7287 (pttt)
REVERT: B  505 ILE cc_start: 0.7610 (mt) cc_final: 0.7349 (tp)
  outliers start: 21
  outliers final: 20
  residues processed: 140
  average time/residue: 0.0766
  time to fit residues: 15.2902
Evaluate side-chains
  148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  404 TYR
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  459 ASN
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  569 LYS
Chi-restraints excluded: chain B residue  272 MET
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 101 optimal weight:   20.0000
   chunk 73 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 69 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 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 = 0.4477 r_free = 0.4477 target = 0.156596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.149272 restraints weight = 30449.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.150668 restraints weight = 19477.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.151618 restraints weight = 13293.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.152334 restraints weight = 9654.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.152670 restraints weight = 7394.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6163
moved from start:          0.4716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7786  Z= 0.180
  Angle     :  0.760  13.958  10642  Z= 0.396
  Chirality :  0.045   0.195   1300
  Planarity :  0.004   0.038   1394
  Dihedral  :  4.742  21.799   1226
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 30.84 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.24), residues: 1152
  helix:  1.12 (0.18), residues: 766
  sheet: -0.47 (0.88), residues: 44
  loop : -2.33 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 276 
 TYR   0.057   0.003   TYR A 424 
 PHE   0.025   0.002   PHE A 408 
 TRP   0.046   0.002   TRP A 334 
 HIS   0.006   0.002   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7786)
  covalent geometry    : angle       0.76014 (10642)
  hydrogen bonds       : bond        0.04746 (  609)
  hydrogen bonds       : angle       4.71181 ( 1791)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  290 VAL cc_start: 0.7765 (m) cc_final: 0.7403 (t)
REVERT: A  505 ILE cc_start: 0.7531 (mt) cc_final: 0.7271 (tp)
REVERT: B  290 VAL cc_start: 0.7800 (m) cc_final: 0.7497 (t)
REVERT: B  464 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7388 (pttt)
REVERT: B  505 ILE cc_start: 0.7551 (mt) cc_final: 0.7306 (tp)
  outliers start: 17
  outliers final: 16
  residues processed: 140
  average time/residue: 0.0764
  time to fit residues: 15.2830
Evaluate side-chains
  143 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  493 SER
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 SER
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 103 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0670
   chunk 14 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 58 optimal weight:   20.0000
   chunk 22 optimal weight:    0.0870
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.1700

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

Flipped N/Q/H residues before XYZ refinement:
A 459 ASN
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 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 = 0.4324 r_free = 0.4324 target = 0.145288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.141590 restraints weight = 32210.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.141544 restraints weight = 29943.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.141604 restraints weight = 27506.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.141668 restraints weight = 24514.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.141683 restraints weight = 23404.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5985
moved from start:          0.4803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7786  Z= 0.145
  Angle     :  0.734  14.515  10642  Z= 0.376
  Chirality :  0.043   0.176   1300
  Planarity :  0.004   0.065   1394
  Dihedral  :  4.391  18.842   1226
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 30.66 %
    Favored  : 65.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.25), residues: 1152
  helix:  1.37 (0.18), residues: 776
  sheet: -0.52 (0.69), residues: 60
  loop : -2.19 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 276 
 TYR   0.057   0.002   TYR B 424 
 PHE   0.021   0.002   PHE A 408 
 TRP   0.038   0.002   TRP A 334 
 HIS   0.005   0.002   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7786)
  covalent geometry    : angle       0.73411 (10642)
  hydrogen bonds       : bond        0.04458 (  609)
  hydrogen bonds       : angle       4.45422 ( 1791)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1211.11 seconds
wall clock time: 21 minutes 36.62 seconds (1296.62 seconds total)