Starting phenix.real_space_refine
on Fri Dec 27 16:50:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uy9_42796/12_2024/8uy9_42796.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uy9_42796/12_2024/8uy9_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_42796/12_2024/8uy9_42796.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uy9_42796/12_2024/8uy9_42796.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uy9_42796/12_2024/8uy9_42796.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uy9_42796/12_2024/8uy9_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-5532/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: 7.00, per 1000 atoms: 1.17
  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: 1.78
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.91
  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: 2.04

  Time building geometry restraints manager: 2.00 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:             7.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     21.540
  Find NCS groups from input model:        0.050
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.280
-------------------------------------------------------------------------------
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  : 0.665 
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: 0.2043
  time to fit residues: 25.4567
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  : 0.680 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
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  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8823 (m-70) cc_final: 0.8256 (m-70)
  outliers start: 12
  outliers final: 7
  residues processed: 109
  average time/residue: 0.1840
  time to fit residues: 26.8340
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  : 0.595 
-------------------------------------------------------------------------------
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 42 optimal weight:    5.9990
   chunk 23 optimal weight:   50.0000
   chunk 64 optimal weight:    0.9980
   chunk 52 optimal weight:    0.1980
   chunk 21 optimal weight:   50.0000
   chunk 77 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6094  Z= 0.239
  Angle     :  0.587  11.158   8349  Z= 0.283
  Chirality :  0.042   0.175   1029
  Planarity :  0.004   0.045   1081
  Dihedral  :  3.706  17.527    892
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.66 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.96 (0.29), residues: 857
  helix:  1.55 (0.25), residues: 455
  sheet: -0.20 (0.54), residues: 85
  loop : -0.39 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 788 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.012   0.001   PHE A 295 
 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
  110 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8803 (m-70) cc_final: 0.8248 (m-70)
REVERT: A  404 TRP cc_start: 0.7865 (t60) cc_final: 0.7515 (t-100)
REVERT: A  816 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8879 (mp)
  outliers start: 22
  outliers final: 17
  residues processed: 104
  average time/residue: 0.1640
  time to fit residues: 23.3467
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  : 0.639 
-------------------------------------------------------------------------------
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 76 optimal weight:    0.2980
   chunk 58 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 22 optimal weight:   30.0000
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6094  Z= 0.224
  Angle     :  0.572  11.621   8349  Z= 0.277
  Chirality :  0.042   0.146   1029
  Planarity :  0.004   0.045   1081
  Dihedral  :  3.688  17.345    892
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 20.79 %
    Favored  : 74.29 %
  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:  1.02 (0.29), residues: 857
  helix:  1.62 (0.25), residues: 454
  sheet: -0.17 (0.53), residues: 85
  loop : -0.39 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 788 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.012   0.001   PHE A 802 
 TYR   0.028   0.002   TYR A  97 
 ARG   0.001   0.000   ARG A 822 

*********************** 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
  113 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8809 (m-70) cc_final: 0.8292 (m-70)
REVERT: A  816 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8953 (mp)
  outliers start: 26
  outliers final: 20
  residues processed: 106
  average time/residue: 0.1609
  time to fit residues: 23.1909
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  : 0.652 
-------------------------------------------------------------------------------
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  372 THR
Chi-restraints excluded: chain A residue  384 VAL
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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 1 optimal weight:    0.4980
   chunk 61 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 56 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 41 optimal weight:    6.9990
   chunk 73 optimal weight:    0.5980
   chunk 20 optimal weight:   20.0000
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6094  Z= 0.222
  Angle     :  0.567  12.609   8349  Z= 0.273
  Chirality :  0.042   0.144   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.633  16.718    892
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 22.31 %
    Favored  : 72.97 %
  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:  1.03 (0.29), residues: 857
  helix:  1.61 (0.25), residues: 456
  sheet: -0.13 (0.54), residues: 85
  loop : -0.38 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 404 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.012   0.001   PHE A 802 
 TYR   0.011   0.001   TYR A 113 
 ARG   0.002   0.000   ARG A  98 

*********************** 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  : 0.668 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8843 (m-70) cc_final: 0.8355 (m-70)
REVERT: A  422 LEU cc_start: 0.9235 (tp) cc_final: 0.9009 (mm)
REVERT: A  816 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8951 (mp)
  outliers start: 25
  outliers final: 19
  residues processed: 105
  average time/residue: 0.1571
  time to fit residues: 22.7020
Evaluate side-chains
  104 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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  384 VAL
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  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 73 optimal weight:    0.5980
   chunk 16 optimal weight:   30.0000
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 82 optimal weight:    0.3980
   chunk 68 optimal weight:    0.0770
   chunk 38 optimal weight:    0.0060
   chunk 6 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 79 optimal weight:    0.4980
   overall best weight:    0.3154

-------------------------------------------------------------------------------
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**
A 814 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6094  Z= 0.160
  Angle     :  0.548  12.667   8349  Z= 0.261
  Chirality :  0.041   0.139   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.494  16.876    892
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 22.50 %
    Favored  : 72.97 %
  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:  1.17 (0.29), residues: 857
  helix:  1.75 (0.25), residues: 457
  sheet: -0.44 (0.52), residues: 92
  loop : -0.23 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 404 
 HIS   0.002   0.000   HIS A 401 
 PHE   0.010   0.001   PHE A 802 
 TYR   0.027   0.002   TYR A  97 
 ARG   0.002   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
  113 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8839 (m-70) cc_final: 0.8361 (m-70)
REVERT: A  422 LEU cc_start: 0.9208 (tp) cc_final: 0.8981 (mm)
REVERT: A  816 LEU cc_start: 0.9307 (mm) cc_final: 0.9039 (mp)
REVERT: A  883 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8111 (tt)
  outliers start: 24
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1725
  time to fit residues: 26.0544
Evaluate side-chains
  102 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  281 PHE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  384 VAL
Chi-restraints excluded: chain A residue  388 HIS
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  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 9 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 81 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6094  Z= 0.249
  Angle     :  0.603  12.210   8349  Z= 0.286
  Chirality :  0.043   0.234   1029
  Planarity :  0.004   0.045   1081
  Dihedral  :  3.586  16.738    892
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 22.31 %
    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:  1.08 (0.29), residues: 857
  helix:  1.63 (0.25), residues: 457
  sheet: -0.13 (0.53), residues: 87
  loop : -0.32 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 404 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.012   0.001   PHE A 802 
 TYR   0.014   0.001   TYR A 113 
 ARG   0.001   0.000   ARG A 822 

*********************** 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
  116 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8862 (m-70) cc_final: 0.8487 (m-70)
REVERT: A  422 LEU cc_start: 0.9245 (tp) cc_final: 0.9006 (mm)
REVERT: A  816 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8951 (mp)
REVERT: A  883 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8244 (tt)
  outliers start: 28
  outliers final: 19
  residues processed: 109
  average time/residue: 0.2136
  time to fit residues: 32.1011
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  : 0.679 
-------------------------------------------------------------------------------
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  384 VAL
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  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 48 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:   40.0000
   chunk 52 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 78 optimal weight:    0.3980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6094  Z= 0.238
  Angle     :  0.604  12.679   8349  Z= 0.285
  Chirality :  0.043   0.203   1029
  Planarity :  0.004   0.045   1081
  Dihedral  :  3.608  17.707    892
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 23.25 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 857
  helix:  1.61 (0.25), residues: 457
  sheet: -0.33 (0.53), residues: 92
  loop : -0.29 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 404 
 HIS   0.002   0.000   HIS A 401 
 PHE   0.012   0.001   PHE A 802 
 TYR   0.028   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
  111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8886 (m-70) cc_final: 0.8521 (m-70)
REVERT: A  422 LEU cc_start: 0.9265 (tp) cc_final: 0.9032 (mm)
REVERT: A  753 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7866 (mp10)
REVERT: A  816 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8955 (mp)
REVERT: A  883 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8226 (tt)
  outliers start: 24
  outliers final: 19
  residues processed: 104
  average time/residue: 0.1787
  time to fit residues: 25.7331
Evaluate side-chains
  107 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
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  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  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 71 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 45 optimal weight:    0.1980
   chunk 33 optimal weight:    0.6980
   chunk 59 optimal weight:    0.3980
   chunk 23 optimal weight:    9.9990
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 50 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6094  Z= 0.203
  Angle     :  0.588  12.216   8349  Z= 0.277
  Chirality :  0.042   0.193   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.555  17.324    892
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 23.44 %
    Favored  : 71.83 %
  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:  1.67 (0.25), residues: 457
  sheet: -0.35 (0.53), residues: 89
  loop : -0.27 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 404 
 HIS   0.002   0.000   HIS A 401 
 PHE   0.011   0.001   PHE A 802 
 TYR   0.019   0.002   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
  111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8895 (m-70) cc_final: 0.8549 (m-70)
REVERT: A  422 LEU cc_start: 0.9241 (tp) cc_final: 0.9008 (mm)
REVERT: A  753 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7954 (mp10)
REVERT: A  816 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8968 (mp)
REVERT: A  883 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8164 (tt)
  outliers start: 25
  outliers final: 19
  residues processed: 106
  average time/residue: 0.1541
  time to fit residues: 22.6704
Evaluate side-chains
  106 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  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  388 HIS
Chi-restraints excluded: chain A residue  471 LEU
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 49 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 84 optimal weight:    0.1980
   chunk 77 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 41 optimal weight:   20.0000
   chunk 53 optimal weight:    0.0570
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.4498

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2200

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= 0.187
  Angle     :  0.584  12.154   8349  Z= 0.273
  Chirality :  0.042   0.190   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.487  16.911    892
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 24.01 %
    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:  1.17 (0.29), residues: 857
  helix:  1.72 (0.25), residues: 457
  sheet: -0.29 (0.53), residues: 89
  loop : -0.23 (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   0.010   0.001   PHE A 802 
 TYR   0.028   0.002   TYR A  97 
 ARG   0.002   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
  110 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 HIS cc_start: 0.8895 (m-70) cc_final: 0.8557 (m-70)
REVERT: A  422 LEU cc_start: 0.9241 (tp) cc_final: 0.9011 (mm)
REVERT: A  753 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7966 (mp10)
REVERT: A  816 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8962 (mp)
REVERT: A  883 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8145 (tt)
  outliers start: 24
  outliers final: 19
  residues processed: 104
  average time/residue: 0.1539
  time to fit residues: 22.0723
Evaluate side-chains
  108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
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  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 20 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:   40.0000
   chunk 67 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:   40.0000
   chunk 59 optimal weight:    0.0870
   chunk 3 optimal weight:   40.0000
   overall best weight:    0.5360

-------------------------------------------------------------------------------
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 = 0.4066 r_free = 0.4066 target = 0.175367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.115053 restraints weight = 8293.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.117404 restraints weight = 5687.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.118509 restraints weight = 3911.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6094  Z= 0.204
  Angle     :  0.591  12.011   8349  Z= 0.277
  Chirality :  0.042   0.180   1029
  Planarity :  0.004   0.046   1081
  Dihedral  :  3.497  16.484    892
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 24.39 %
    Favored  : 71.08 %
  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:  1.17 (0.29), residues: 857
  helix:  1.69 (0.25), residues: 457
  sheet: -0.31 (0.53), residues: 89
  loop : -0.19 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 404 
 HIS   0.002   0.000   HIS A 401 
 PHE   0.010   0.001   PHE A 802 
 TYR   0.018   0.001   TYR A 113 
 ARG   0.002   0.000   ARG A 511 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1695.47 seconds
wall clock time: 32 minutes 2.58 seconds (1922.58 seconds total)