Starting phenix.real_space_refine
on Tue Mar 11 14:30:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uy9_42796/03_2025/8uy9_42796.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uy9_42796/03_2025/8uy9_42796.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uy9_42796/03_2025/8uy9_42796.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uy9_42796/03_2025/8uy9_42796.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uy9_42796/03_2025/8uy9_42796.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uy9_42796/03_2025/8uy9_42796.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      28      5.16       5
     C    3830      2.51       5
     N    1033      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5982
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 859, 5981
          Classifications: {'peptide': 859}
          Incomplete info: {'truncation_to_alanine': 198}
          Link IDs: {'PTRANS': 40, 'TRANS': 818}
          Unresolved non-hydrogen bonds: 702
          Unresolved non-hydrogen angles: 900
          Unresolved non-hydrogen dihedrals: 568
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 14, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 5, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 27, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 418
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.24, per 1000 atoms: 0.88
  Number of scatterers: 5982
  At special positions: 0
  Unit cell: (80.51, 84.66, 131.97, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     Mg      1     11.99
     O    1090      8.00
     N    1033      7.00
     C    3830      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 980.7 milliseconds
  

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1618

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      56.6% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 48
      removed outlier: 3.713A  pdb=" N   HIS A  41 " --> pdb=" O   SER A  37 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   CYS A  42 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   LEU A  43 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 65 through 77
    Processing helix  chain 'A' and resid 88 through 96
      removed outlier: 3.682A  pdb=" N   TRP A  94 " --> pdb=" O   TRP A  90 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A  95 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 115
    Processing helix  chain 'A' and resid 117 through 146
      removed outlier: 3.531A  pdb=" N   ALA A 121 " --> pdb=" O   ASP A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 179
      No H-bonds generated for 'chain 'A' and resid 177 through 179'
    Processing helix  chain 'A' and resid 258 through 262
    Processing helix  chain 'A' and resid 279 through 310
      Proline residue:  A 301  - end of helix
      removed outlier: 3.953A  pdb=" N   GLY A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 328
      removed outlier: 3.782A  pdb=" N   LEU A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 350
      removed outlier: 3.868A  pdb=" N   LYS A 350 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 367
      removed outlier: 4.157A  pdb=" N   ILE A 361 " --> pdb=" O   HIS A 357 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLN A 362 " --> pdb=" O   LEU A 358 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASN A 363 " --> pdb=" O   ASP A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 409
      removed outlier: 3.660A  pdb=" N   LEU A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ASN A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 425
      removed outlier: 3.638A  pdb=" N   THR A 425 " --> pdb=" O   VAL A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 437
    Processing helix  chain 'A' and resid 470 through 477
    Processing helix  chain 'A' and resid 491 through 509
    Processing helix  chain 'A' and resid 528 through 532
    Processing helix  chain 'A' and resid 550 through 561
      removed outlier: 3.548A  pdb=" N   LYS A 559 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 584
      removed outlier: 3.538A  pdb=" N   HIS A 581 " --> pdb=" O   ALA A 577 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLU A 582 " --> pdb=" O   LYS A 578 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL A 583 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 599
      removed outlier: 3.743A  pdb=" N   GLU A 597 " --> pdb=" O   GLY A 593 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   THR A 598 " --> pdb=" O   SER A 594 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU A 599 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 593 through 599'
    Processing helix  chain 'A' and resid 600 through 610
      removed outlier: 3.741A  pdb=" N   ARG A 610 " --> pdb=" O   ASN A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 630
    Processing helix  chain 'A' and resid 642 through 644
      No H-bonds generated for 'chain 'A' and resid 642 through 644'
    Processing helix  chain 'A' and resid 645 through 652
    Processing helix  chain 'A' and resid 662 through 668
    Processing helix  chain 'A' and resid 677 through 716
      removed outlier: 3.536A  pdb=" N   ILE A 699 " --> pdb=" O   MET A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 741
    Processing helix  chain 'A' and resid 742 through 747
      Proline residue:  A 745  - end of helix
      No H-bonds generated for 'chain 'A' and resid 742 through 747'
    Processing helix  chain 'A' and resid 752 through 756
      removed outlier: 4.220A  pdb=" N   LYS A 756 " --> pdb=" O   GLN A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 790
      removed outlier: 3.809A  pdb=" N   LEU A 765 " --> pdb=" O   ASN A 761 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ARG A 767 " --> pdb=" O   ALA A 763 " (cutoff:3.500A)
      Proline residue:  A 774  - end of helix
      removed outlier: 3.770A  pdb=" N   PHE A 779 " --> pdb=" O   ILE A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 797
      No H-bonds generated for 'chain 'A' and resid 795 through 797'
    Processing helix  chain 'A' and resid 798 through 822
      removed outlier: 3.972A  pdb=" N   PHE A 802 " --> pdb=" O   THR A 798 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL A 809 " --> pdb=" O   GLY A 805 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR A 815 " --> pdb=" O   LEU A 811 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL A 818 " --> pdb=" O   GLN A 814 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   HIS A 819 " --> pdb=" O   THR A 815 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   MET A 820 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 851
    Processing helix  chain 'A' and resid 855 through 860
      removed outlier: 4.325A  pdb=" N   TYR A 859 " --> pdb=" O   PRO A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 889
      removed outlier: 4.235A  pdb=" N   TRP A 872 " --> pdb=" O   SER A 868 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLY A 889 " --> pdb=" O   GLN A 885 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 159
    Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 187
      removed outlier: 6.935A  pdb=" N   VAL A 246 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   VAL A 207 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU A 205 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A 250 " --> pdb=" O   ARG A 203 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   MET A 254 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   ILE A 199 " --> pdb=" O   MET A 254 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LEU A 205 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 187
      removed outlier: 6.935A  pdb=" N   VAL A 246 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   VAL A 207 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU A 205 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A 250 " --> pdb=" O   ARG A 203 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   MET A 254 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   ILE A 199 " --> pdb=" O   MET A 254 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355
      removed outlier: 6.849A  pdb=" N   VAL A 636 " --> pdb=" O   ILE A 654 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   ILE A 656 " --> pdb=" O   VAL A 636 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   PHE A 638 " --> pdb=" O   ILE A 656 " (cutoff:3.500A)
      removed outlier: 8.435A  pdb=" N   VAL A 658 " --> pdb=" O   PHE A 638 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   LEU A 370 " --> pdb=" O   LYS A 566 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LEU A 568 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   THR A 372 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 8.529A  pdb=" N   PHE A 614 " --> pdb=" O   VAL A 565 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE A 567 " --> pdb=" O   PHE A 614 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   VAL A 591 " --> pdb=" O   ALA A 615 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 389
      removed outlier: 5.325A  pdb=" N   LEU A 385 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU A 544 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ASN A 387 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ALA A 542 " --> pdb=" O   ASN A 387 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A 389 " --> pdb=" O   TYR A 540 " (cutoff:3.500A)
      removed outlier: 8.650A  pdb=" N   LEU A 535 " --> pdb=" O   TYR A 519 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   TYR A 519 " --> pdb=" O   LEU A 535 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   LEU A 537 " --> pdb=" O   THR A 517 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   THR A 517 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY A 469 " --> pdb=" O   ALA A 514 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ARG A 451 " --> pdb=" O   PHE A 445 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   PHE A 445 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   ALA A 457 " --> pdb=" O   LYS A 439 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   LYS A 439 " --> pdb=" O   ALA A 457 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 384 through 389
      removed outlier: 5.325A  pdb=" N   LEU A 385 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU A 544 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ASN A 387 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ALA A 542 " --> pdb=" O   ASN A 387 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A 389 " --> pdb=" O   TYR A 540 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   CYS A 478 " --> pdb=" O   LEU A 535 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   LEU A 537 " --> pdb=" O   CYS A 478 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   GLN A 480 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      removed outlier: 8.423A  pdb=" N   GLY A 539 " --> pdb=" O   GLN A 480 " (cutoff:3.500A)
      removed outlier: 9.016A  pdb=" N   ARG A 482 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
      removed outlier: 12.394A  pdb=" N   ILE A 541 " --> pdb=" O   ARG A 482 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.03

  Time building geometry restraints manager: 1.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1438
        1.33 -     1.45: 1109
        1.45 -     1.57: 3497
        1.57 -     1.70: 1
        1.70 -     1.82: 49
  Bond restraints: 6094
  Sorted by residual:
  bond pdb=" CA  ILE A 744 "
       pdb=" CB  ILE A 744 "
    ideal  model  delta    sigma   weight residual
    1.534  1.552 -0.017 6.80e-03 2.16e+04 6.61e+00
  bond pdb=" C   ARG A 690 "
       pdb=" O   ARG A 690 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.17e-02 7.31e+03 5.64e+00
  bond pdb=" C   THR A 691 "
       pdb=" O   THR A 691 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.027 1.17e-02 7.31e+03 5.34e+00
  bond pdb=" C   GLN A 803 "
       pdb=" O   GLN A 803 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.17e-02 7.31e+03 4.39e+00
  bond pdb=" N   ASN A 387 "
       pdb=" CA  ASN A 387 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.66e+00
  ... (remaining 6089 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 8132
        1.98 -     3.96: 174
        3.96 -     5.93: 31
        5.93 -     7.91: 8
        7.91 -     9.89: 4
  Bond angle restraints: 8349
  Sorted by residual:
  angle pdb=" C   VAL A 826 "
        pdb=" N   PRO A 827 "
        pdb=" CA  PRO A 827 "
      ideal   model   delta    sigma   weight residual
     119.05  126.51   -7.46 1.11e+00 8.12e-01 4.52e+01
  angle pdb=" N   ILE A 744 "
        pdb=" CA  ILE A 744 "
        pdb=" CB  ILE A 744 "
      ideal   model   delta    sigma   weight residual
     110.50  113.80   -3.30 6.30e-01 2.52e+00 2.75e+01
  angle pdb=" N   ARG A 689 "
        pdb=" CA  ARG A 689 "
        pdb=" C   ARG A 689 "
      ideal   model   delta    sigma   weight residual
     112.90  106.68    6.22 1.31e+00 5.83e-01 2.25e+01
  angle pdb=" N   PRO A 827 "
        pdb=" CA  PRO A 827 "
        pdb=" C   PRO A 827 "
      ideal   model   delta    sigma   weight residual
     113.53  119.44   -5.91 1.39e+00 5.18e-01 1.81e+01
  angle pdb=" N   ASN A 387 "
        pdb=" CA  ASN A 387 "
        pdb=" C   ASN A 387 "
      ideal   model   delta    sigma   weight residual
     110.80  118.82   -8.02 2.13e+00 2.20e-01 1.42e+01
  ... (remaining 8344 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 3232
       16.44 -    32.88: 303
       32.88 -    49.32: 83
       49.32 -    65.76: 17
       65.76 -    82.20: 4
  Dihedral angle restraints: 3639
    sinusoidal: 1153
      harmonic: 2486
  Sorted by residual:
  dihedral pdb=" N   ASN A 387 "
           pdb=" C   ASN A 387 "
           pdb=" CA  ASN A 387 "
           pdb=" CB  ASN A 387 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.45  -13.65     0      2.50e+00 1.60e-01 2.98e+01
  dihedral pdb=" C   ASN A 387 "
           pdb=" N   ASN A 387 "
           pdb=" CA  ASN A 387 "
           pdb=" CB  ASN A 387 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.30   12.70     0      2.50e+00 1.60e-01 2.58e+01
  dihedral pdb=" C   ILE A 744 "
           pdb=" N   ILE A 744 "
           pdb=" CA  ILE A 744 "
           pdb=" CB  ILE A 744 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.29   10.29     0      2.50e+00 1.60e-01 1.69e+01
  ... (remaining 3636 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1006
       0.111 -    0.221: 19
       0.221 -    0.332: 3
       0.332 -    0.443: 0
       0.443 -    0.553: 1
  Chirality restraints: 1029
  Sorted by residual:
  chirality pdb=" CA  ASN A 387 "
            pdb=" N   ASN A 387 "
            pdb=" C   ASN A 387 "
            pdb=" CB  ASN A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.65e+00
  chirality pdb=" CA  PHE A 828 "
            pdb=" N   PHE A 828 "
            pdb=" C   PHE A 828 "
            pdb=" CB  PHE A 828 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.32 2.00e-01 2.50e+01 2.48e+00
  chirality pdb=" CA  ILE A 744 "
            pdb=" N   ILE A 744 "
            pdb=" C   ILE A 744 "
            pdb=" CB  ILE A 744 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.16    0.28 2.00e-01 2.50e+01 1.92e+00
  ... (remaining 1026 not shown)

  Planarity restraints: 1081
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 825 "    0.012 2.00e-02 2.50e+03   2.36e-02 5.59e+00
        pdb=" C   ARG A 825 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ARG A 825 "    0.016 2.00e-02 2.50e+03
        pdb=" N   VAL A 826 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 827 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.83e+00
        pdb=" C   PRO A 827 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   PRO A 827 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 828 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 826 "    0.009 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" C   VAL A 826 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   VAL A 826 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PRO A 827 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1078 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 18
        2.52 -     3.11: 4588
        3.11 -     3.71: 9423
        3.71 -     4.30: 11838
        4.30 -     4.90: 20535
  Nonbonded interactions: 46402
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 709 "
            pdb="MG    MG A1001 "
     model   vdw
     1.921 2.170
  nonbonded pdb=" OG  SER A 776 "
            pdb=" OH  TYR A 880 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OD1 ASP A 780 "
            pdb=" NE1 TRP A 806 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O   ASN A 748 "
            pdb=" NH2 ARG A 822 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" NH1 ARG A 822 "
            pdb=" O   CYS A 832 "
     model   vdw
     2.310 3.120
  ... (remaining 46397 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.000
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
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   0.051   6094  Z= 0.272
  Angle     :  0.726   9.889   8349  Z= 0.407
  Chirality :  0.050   0.553   1029
  Planarity :  0.004   0.046   1081
  Dihedral  : 14.676  82.201   2021
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 21.36 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.29), residues: 857
  helix:  1.26 (0.25), residues: 450
  sheet: -0.03 (0.56), residues: 90
  loop : -0.41 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.012   0.001   PHE A 136 
 TYR   0.033   0.003   TYR A  97 
 ARG   0.005   0.000   ARG A 689 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 ASN cc_start: 0.8455 (m-40) cc_final: 0.8050 (m-40)
REVERT: A  401 HIS cc_start: 0.8836 (m-70) cc_final: 0.8507 (m-70)
  outliers start: 2
  outliers final: 2
  residues processed: 93
  average time/residue: 0.1862
  time to fit residues: 23.0696
Evaluate side-chains
  90 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  691 THR
Chi-restraints excluded: chain A residue  742 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0980
   chunk 22 optimal weight:   40.0000
   chunk 43 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 66 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0050
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.3594

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 HIS ** 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 = 0.4084 r_free = 0.4084 target = 0.177200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.123616 restraints weight = 8197.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.118476 restraints weight = 5932.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.120276 restraints weight = 4605.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6094  Z= 0.175
  Angle     :  0.574   9.947   8349  Z= 0.282
  Chirality :  0.042   0.149   1029
  Planarity :  0.004   0.042   1081
  Dihedral  :  3.764  23.717    894
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.85 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.29), residues: 857
  helix:  1.58 (0.25), residues: 454
  sheet: -0.26 (0.54), residues: 86
  loop : -0.35 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 388 
 PHE   0.013   0.001   PHE A 802 
 TYR   0.009   0.001   TYR A 113 
 ARG   0.003   0.000   ARG A 822 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8913 (m-70) cc_final: 0.8308 (m-70)
  outliers start: 12
  outliers final: 7
  residues processed: 109
  average time/residue: 0.1753
  time to fit residues: 25.3311
Evaluate side-chains
  95 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0470
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:   40.0000
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:   20.0000
   chunk 11 optimal weight:   30.0000
   chunk 0 optimal weight:   30.0000
   chunk 81 optimal weight:    0.5980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.8880

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

Flipped N/Q/H residues before XYZ refinement:
A 307 ASN
A 819 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.174051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.110340 restraints weight = 8204.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.113526 restraints weight = 4675.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.115490 restraints weight = 3334.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6094  Z= 0.288
  Angle     :  0.609  11.094   8349  Z= 0.295
  Chirality :  0.043   0.169   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.778  18.166    892
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.79 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.29), residues: 857
  helix:  1.46 (0.25), residues: 455
  sheet: -0.23 (0.54), residues: 85
  loop : -0.41 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 788 
 HIS   0.004   0.001   HIS A 819 
 PHE   0.013   0.002   PHE A 802 
 TYR   0.008   0.001   TYR A 880 
 ARG   0.002   0.000   ARG A 616 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8752 (m-70) cc_final: 0.8200 (m-70)
REVERT: A  404 TRP cc_start: 0.7851 (t60) cc_final: 0.7500 (t-100)
REVERT: A  816 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8898 (mp)
  outliers start: 22
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1680
  time to fit residues: 23.7740
Evaluate side-chains
  103 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0770
   chunk 71 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.4516

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.176584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.120039 restraints weight = 8364.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.118250 restraints weight = 5293.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.118489 restraints weight = 4187.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6094  Z= 0.185
  Angle     :  0.562  11.714   8349  Z= 0.270
  Chirality :  0.042   0.146   1029
  Planarity :  0.004   0.045   1081
  Dihedral  :  3.631  16.842    892
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 21.55 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.29), residues: 857
  helix:  1.68 (0.25), residues: 455
  sheet: -0.22 (0.53), residues: 85
  loop : -0.32 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 788 
 HIS   0.003   0.000   HIS A 401 
 PHE   0.011   0.001   PHE A 802 
 TYR   0.029   0.002   TYR A  97 
 ARG   0.002   0.000   ARG A 511 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.9006 (m-70) cc_final: 0.8426 (m-70)
REVERT: A  667 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8107 (mp0)
REVERT: A  816 LEU cc_start: 0.9337 (mm) cc_final: 0.9050 (mp)
  outliers start: 23
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1577
  time to fit residues: 23.1500
Evaluate side-chains
  102 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  667 GLU
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 12 optimal weight:   50.0000
   chunk 69 optimal weight:    0.0970
   chunk 36 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 HIS ** 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 = 0.4064 r_free = 0.4064 target = 0.175409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.115945 restraints weight = 8200.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.116750 restraints weight = 6076.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.117222 restraints weight = 4194.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6094  Z= 0.202
  Angle     :  0.568  13.054   8349  Z= 0.270
  Chirality :  0.042   0.142   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.574  16.139    892
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 22.87 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.29), residues: 857
  helix:  1.66 (0.25), residues: 457
  sheet: -0.15 (0.53), residues: 85
  loop : -0.33 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 404 
 HIS   0.003   0.001   HIS A 408 
 PHE   0.011   0.001   PHE A 802 
 TYR   0.010   0.001   TYR A 113 
 ARG   0.001   0.000   ARG A 822 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8902 (m-70) cc_final: 0.8395 (m-70)
REVERT: A  422 LEU cc_start: 0.9255 (tp) cc_final: 0.9018 (mm)
REVERT: A  816 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9002 (mp)
  outliers start: 25
  outliers final: 19
  residues processed: 106
  average time/residue: 0.1632
  time to fit residues: 23.7257
Evaluate side-chains
  105 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  281 PHE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 19 optimal weight:    0.6980
   chunk 52 optimal weight:    0.2980
   chunk 80 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 83 optimal weight:    0.5980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.175566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.115677 restraints weight = 8185.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.118646 restraints weight = 5426.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.118802 restraints weight = 3917.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6094  Z= 0.194
  Angle     :  0.573  12.385   8349  Z= 0.272
  Chirality :  0.042   0.266   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.509  16.823    892
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 22.12 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.29), residues: 857
  helix:  1.70 (0.25), residues: 457
  sheet: -0.47 (0.52), residues: 92
  loop : -0.28 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 404 
 HIS   0.002   0.000   HIS A 401 
 PHE   0.011   0.001   PHE A 802 
 TYR   0.029   0.002   TYR A  97 
 ARG   0.001   0.000   ARG A  98 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8992 (m-70) cc_final: 0.8439 (m-70)
REVERT: A  422 LEU cc_start: 0.9229 (tp) cc_final: 0.8958 (mm)
REVERT: A  816 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9032 (mp)
REVERT: A  883 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8172 (tt)
  outliers start: 29
  outliers final: 20
  residues processed: 113
  average time/residue: 0.1492
  time to fit residues: 23.1199
Evaluate side-chains
  109 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  281 PHE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  883 LEU
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 61 optimal weight:    0.2980
   chunk 21 optimal weight:   50.0000
   chunk 26 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 2 optimal weight:    0.3980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
** A 388 HIS ** 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 = 0.4068 r_free = 0.4068 target = 0.175625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.131989 restraints weight = 8336.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.121589 restraints weight = 6854.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.125192 restraints weight = 6981.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6094  Z= 0.192
  Angle     :  0.567  11.476   8349  Z= 0.270
  Chirality :  0.042   0.247   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.506  16.069    892
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 22.87 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.29), residues: 857
  helix:  1.72 (0.25), residues: 457
  sheet: -0.41 (0.52), residues: 92
  loop : -0.25 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 404 
 HIS   0.002   0.000   HIS A 401 
 PHE   0.010   0.001   PHE A 802 
 TYR   0.013   0.001   TYR A 113 
 ARG   0.001   0.000   ARG A  98 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.9023 (m-70) cc_final: 0.8592 (m-70)
REVERT: A  422 LEU cc_start: 0.9274 (tp) cc_final: 0.9012 (mm)
REVERT: A  816 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9041 (mp)
REVERT: A  883 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8192 (tt)
  outliers start: 27
  outliers final: 19
  residues processed: 108
  average time/residue: 0.1503
  time to fit residues: 22.6588
Evaluate side-chains
  105 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  281 PHE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  883 LEU
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 19 optimal weight:    8.9990
   chunk 3 optimal weight:   50.0000
   chunk 18 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.173004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.109821 restraints weight = 8323.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.112941 restraints weight = 5135.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.114640 restraints weight = 3867.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6094  Z= 0.292
  Angle     :  0.626  13.052   8349  Z= 0.298
  Chirality :  0.044   0.243   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.671  16.785    892
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.82 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.29), residues: 857
  helix:  1.51 (0.25), residues: 457
  sheet: -0.35 (0.52), residues: 92
  loop : -0.30 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 404 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.013   0.002   PHE A 802 
 TYR   0.029   0.002   TYR A  97 
 ARG   0.002   0.000   ARG A 511 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8873 (m-70) cc_final: 0.8524 (m-70)
REVERT: A  422 LEU cc_start: 0.9271 (tp) cc_final: 0.9042 (mm)
REVERT: A  753 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7852 (mp10)
REVERT: A  816 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8935 (mp)
REVERT: A  883 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8279 (tt)
  outliers start: 25
  outliers final: 20
  residues processed: 103
  average time/residue: 0.1640
  time to fit residues: 23.0717
Evaluate side-chains
  108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  281 PHE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  739 VAL
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  883 LEU
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 HIS ** 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 = 0.4046 r_free = 0.4046 target = 0.173555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.110807 restraints weight = 8399.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114315 restraints weight = 5123.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.116059 restraints weight = 3758.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6094  Z= 0.261
  Angle     :  0.610  12.473   8349  Z= 0.289
  Chirality :  0.043   0.230   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.670  16.499    892
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 24.39 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.29), residues: 857
  helix:  1.52 (0.25), residues: 457
  sheet: -0.39 (0.53), residues: 89
  loop : -0.29 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 404 
 HIS   0.002   0.001   HIS A 401 
 PHE   0.013   0.001   PHE A 802 
 TYR   0.020   0.001   TYR A 113 
 ARG   0.002   0.000   ARG A 511 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8846 (m-70) cc_final: 0.8518 (m-70)
REVERT: A  753 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7854 (mp10)
REVERT: A  816 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8958 (mp)
REVERT: A  883 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8249 (tt)
  outliers start: 26
  outliers final: 22
  residues processed: 102
  average time/residue: 0.1451
  time to fit residues: 20.6484
Evaluate side-chains
  106 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  281 PHE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  739 VAL
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  883 LEU
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   chunk 55 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   chunk 26 optimal weight:    0.4980
   chunk 19 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 70 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 HIS ** 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 = 0.4057 r_free = 0.4057 target = 0.174557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.112528 restraints weight = 8387.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.115319 restraints weight = 5353.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.117101 restraints weight = 3990.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6094  Z= 0.222
  Angle     :  0.594  12.477   8349  Z= 0.280
  Chirality :  0.042   0.230   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.595  16.518    892
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 24.20 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.29), residues: 857
  helix:  1.59 (0.25), residues: 457
  sheet: -0.40 (0.53), residues: 89
  loop : -0.22 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 404 
 HIS   0.002   0.000   HIS A 401 
 PHE   0.012   0.001   PHE A 802 
 TYR   0.026   0.002   TYR A  97 
 ARG   0.001   0.000   ARG A  98 

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8857 (m-70) cc_final: 0.8540 (m-70)
REVERT: A  422 LEU cc_start: 0.9226 (tp) cc_final: 0.9004 (mm)
REVERT: A  753 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7939 (mp10)
REVERT: A  816 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8963 (mp)
REVERT: A  883 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8183 (tt)
  outliers start: 26
  outliers final: 22
  residues processed: 105
  average time/residue: 0.1491
  time to fit residues: 21.8546
Evaluate side-chains
  107 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  281 PHE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  388 HIS
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  572 SER
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  589 GLU
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  883 LEU
Chi-restraints excluded: chain A residue  884 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:   50.0000
   chunk 57 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 80 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 HIS ** 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 = 0.4053 r_free = 0.4053 target = 0.174173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.111683 restraints weight = 8509.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.114778 restraints weight = 5414.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.116495 restraints weight = 3960.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6094  Z= 0.232
  Angle     :  0.603  12.302   8349  Z= 0.285
  Chirality :  0.043   0.223   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.595  16.086    892
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.33 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 24.01 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.29), residues: 857
  helix:  1.59 (0.25), residues: 457
  sheet: -0.40 (0.53), residues: 89
  loop : -0.19 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 404 
 HIS   0.002   0.001   HIS A 401 
 PHE   0.012   0.001   PHE A 802 
 TYR   0.006   0.001   TYR A 891 
 ARG   0.001   0.000   ARG A 511 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2258.09 seconds
wall clock time: 39 minutes 37.11 seconds (2377.11 seconds total)