Starting phenix.real_space_refine
on Thu Feb 13 14:28:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v5d_31723/02_2025/7v5d_31723.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v5d_31723/02_2025/7v5d_31723.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v5d_31723/02_2025/7v5d_31723.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v5d_31723/02_2025/7v5d_31723.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v5d_31723/02_2025/7v5d_31723.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v5d_31723/02_2025/7v5d_31723.cif"
  }
  resolution = 3.4
  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=   0.003 sd=   0.056
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
     P       1      5.49       5
     S      40      5.16       5
     C    5652      2.51       5
     N    1491      2.21       5
     O    1638      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4392
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 15, 'TRANS': 554}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 4379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4379
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 15, 'TRANS': 554}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "A"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 51
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.44, per 1000 atoms: 0.62
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (80.51, 108.73, 137.78, 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      40     16.00
     P       1     15.00
     O    1638      8.00
     N    1491      7.00
     C    5652      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.30
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      67.8% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 170 through 176
    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 180 through 214
      Proline residue:  A 202  - end of helix
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 3.939A  pdb=" N   THR A 223 " --> pdb=" O   ASP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 264
    Processing helix  chain 'A' and resid 270 through 276
    Processing helix  chain 'A' and resid 279 through 321
      removed outlier: 4.510A  pdb=" N   LEU A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   SER A 321 " --> pdb=" O   MET A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 369
      Proline residue:  A 333  - end of helix
      removed outlier: 3.991A  pdb=" N   THR A 367 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 376
      removed outlier: 3.614A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 433
      removed outlier: 4.505A  pdb=" N   VAL A 394 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   LYS A 396 " --> pdb=" O   GLN A 392 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   LYS A 400 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLU A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 472
      removed outlier: 5.014A  pdb=" N   SER A 463 " --> pdb=" O   GLY A 459 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY A 464 " --> pdb=" O   SER A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 480
      removed outlier: 4.531A  pdb=" N   PHE A 476 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU A 477 " --> pdb=" O   GLU A 473 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   PHE A 478 " --> pdb=" O   LYS A 474 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ASP A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 549
    Processing helix  chain 'A' and resid 567 through 569
      No H-bonds generated for 'chain 'A' and resid 567 through 569'
    Processing helix  chain 'A' and resid 570 through 578
    Processing helix  chain 'A' and resid 594 through 598
      removed outlier: 3.635A  pdb=" N   TYR A 598 " --> pdb=" O   ASN A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 614
    Processing helix  chain 'A' and resid 618 through 623
      removed outlier: 3.744A  pdb=" N   MET A 622 " --> pdb=" O   HIS A 618 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLU A 623 " --> pdb=" O   GLY A 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 618 through 623'
    Processing helix  chain 'A' and resid 632 through 637
      removed outlier: 3.769A  pdb=" N   GLY A 636 " --> pdb=" O   THR A 632 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 637 " --> pdb=" O   GLY A 633 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 632 through 637'
    Processing helix  chain 'A' and resid 640 through 652
    Processing helix  chain 'A' and resid 672 through 679
    Processing helix  chain 'A' and resid 698 through 702
      removed outlier: 3.617A  pdb=" N   ARG A 702 " --> pdb=" O   THR A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 726
      removed outlier: 3.523A  pdb=" N   LEU A 723 " --> pdb=" O   THR A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 737
    Processing helix  chain 'B' and resid 170 through 174
      removed outlier: 3.502A  pdb=" N   LEU B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 170 through 174'
    Processing helix  chain 'B' and resid 177 through 179
      No H-bonds generated for 'chain 'B' and resid 177 through 179'
    Processing helix  chain 'B' and resid 180 through 214
      Proline residue:  B 202  - end of helix
    Processing helix  chain 'B' and resid 219 through 229
    Processing helix  chain 'B' and resid 229 through 264
    Processing helix  chain 'B' and resid 270 through 276
    Processing helix  chain 'B' and resid 279 through 298
      removed outlier: 4.471A  pdb=" N   LEU B 285 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   ASP B 288 " --> pdb=" O   ARG B 284 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   THR B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   VAL B 296 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 321
      removed outlier: 4.147A  pdb=" N   SER B 321 " --> pdb=" O   MET B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 370
      Proline residue:  B 333  - end of helix
      removed outlier: 4.314A  pdb=" N   THR B 363 " --> pdb=" O   ARG B 359 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ALA B 364 " --> pdb=" O   ALA B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 378
      removed outlier: 3.878A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 434
      removed outlier: 4.336A  pdb=" N   VAL B 386 " --> pdb=" O   GLU B 382 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   VAL B 394 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   LYS B 396 " --> pdb=" O   GLN B 392 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   LYS B 400 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLU B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 472
      removed outlier: 3.933A  pdb=" N   TYR B 462 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   SER B 463 " --> pdb=" O   GLY B 459 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLY B 464 " --> pdb=" O   SER B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 479
      removed outlier: 3.835A  pdb=" N   PHE B 478 " --> pdb=" O   LYS B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 549
      removed outlier: 3.908A  pdb=" N   VAL B 545 " --> pdb=" O   LYS B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 570 through 578
    Processing helix  chain 'B' and resid 591 through 596
    Processing helix  chain 'B' and resid 604 through 614
      removed outlier: 3.752A  pdb=" N   VAL B 608 " --> pdb=" O   PRO B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 622
      removed outlier: 3.731A  pdb=" N   MET B 622 " --> pdb=" O   HIS B 618 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 637
      removed outlier: 3.646A  pdb=" N   ALA B 637 " --> pdb=" O   GLY B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 654
    Processing helix  chain 'B' and resid 672 through 679
      removed outlier: 3.864A  pdb=" N   LEU B 676 " --> pdb=" O   GLU B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 700
      removed outlier: 4.140A  pdb=" N   THR B 699 " --> pdb=" O   ARG B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 726
    Processing helix  chain 'B' and resid 730 through 738
      removed outlier: 3.715A  pdb=" N   GLN B 735 " --> pdb=" O   ALA B 731 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   MET B 738 " --> pdb=" O   VAL B 734 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 522 through 524
      removed outlier: 3.816A  pdb=" N   ASP A 501 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 560 " --> pdb=" O   ASP A 501 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 659 through 660
      removed outlier: 6.790A  pdb=" N   LEU A 660 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   ILE A 693 " --> pdb=" O   LEU A 660 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE A 692 " --> pdb=" O   THR A 531 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ALA A 532 " --> pdb=" O   VAL A 707 " (cutoff:3.500A)
      removed outlier: 8.583A  pdb=" N   LEU A 709 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   VAL A 708 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG A 713 " --> pdb=" O   ASP A 710 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 518 through 521
      removed outlier: 5.729A  pdb=" N   GLN B 519 " --> pdb=" O   PHE B 507 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   PHE B 507 " --> pdb=" O   GLN B 519 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   PHE B 502 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   LEU B 560 " --> pdb=" O   PHE B 502 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   ASN B 504 " --> pdb=" O   ARG B 558 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   ARG B 558 " --> pdb=" O   ASN B 504 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 659 through 663
      removed outlier: 3.831A  pdb=" N   LEU B 660 " --> pdb=" O   THR B 689 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 692 " --> pdb=" O   THR B 531 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ALA B 532 " --> pdb=" O   VAL B 707 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   LEU B 709 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL B 534 " --> pdb=" O   LEU B 709 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   VAL B 708 " --> pdb=" O   VAL B 715 " (cutoff:3.500A)

    544 hydrogen bonds defined for protein.
    1608 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: 2.58

  Time building geometry restraints manager: 2.67 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: 2486
        1.33 -     1.45: 1498
        1.45 -     1.57: 4921
        1.57 -     1.69: 2
        1.69 -     1.81: 72
  Bond restraints: 8979
  Sorted by residual:
  bond pdb=" CA  ARG B 284 "
       pdb=" C   ARG B 284 "
    ideal  model  delta    sigma   weight residual
    1.522  1.431  0.091 1.72e-02 3.38e+03 2.81e+01
  bond pdb=" N   LEU A 729 "
       pdb=" CA  LEU A 729 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.58e+00
  bond pdb=" O4P PGT A 801 "
       pdb=" P   PGT A 801 "
    ideal  model  delta    sigma   weight residual
    1.641  1.581  0.060 2.00e-02 2.50e+03 9.11e+00
  bond pdb=" CB  ASN A 254 "
       pdb=" CG  ASN A 254 "
    ideal  model  delta    sigma   weight residual
    1.516  1.461  0.055 2.50e-02 1.60e+03 4.91e+00
  bond pdb=" CB  ASN B 254 "
       pdb=" CG  ASN B 254 "
    ideal  model  delta    sigma   weight residual
    1.516  1.463  0.053 2.50e-02 1.60e+03 4.44e+00
  ... (remaining 8974 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 11272
        1.62 -     3.24: 705
        3.24 -     4.87: 144
        4.87 -     6.49: 25
        6.49 -     8.11: 15
  Bond angle restraints: 12161
  Sorted by residual:
  angle pdb=" C   GLY A 728 "
        pdb=" N   LEU A 729 "
        pdb=" CA  LEU A 729 "
      ideal   model   delta    sigma   weight residual
     121.54  129.27   -7.73 1.91e+00 2.74e-01 1.64e+01
  angle pdb=" C   GLN A 298 "
        pdb=" N   ASN A 299 "
        pdb=" CA  ASN A 299 "
      ideal   model   delta    sigma   weight residual
     121.52  114.86    6.66 1.84e+00 2.95e-01 1.31e+01
  angle pdb=" C   VAL B 228 "
        pdb=" N   CYS B 229 "
        pdb=" CA  CYS B 229 "
      ideal   model   delta    sigma   weight residual
     121.54  115.03    6.51 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" CA  ARG B 284 "
        pdb=" C   ARG B 284 "
        pdb=" N   LEU B 285 "
      ideal   model   delta    sigma   weight residual
     118.59  123.64   -5.05 1.63e+00 3.76e-01 9.59e+00
  angle pdb=" C   PHE B 189 "
        pdb=" N   PHE B 190 "
        pdb=" CA  PHE B 190 "
      ideal   model   delta    sigma   weight residual
     120.72  115.55    5.17 1.67e+00 3.59e-01 9.57e+00
  ... (remaining 12156 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.18: 5150
       30.18 -    60.35: 197
       60.35 -    90.53: 21
       90.53 -   120.71: 0
      120.71 -   150.88: 1
  Dihedral angle restraints: 5369
    sinusoidal: 2081
      harmonic: 3288
  Sorted by residual:
  dihedral pdb=" CA  MET B 218 "
           pdb=" C   MET B 218 "
           pdb=" N   ASP B 219 "
           pdb=" CA  ASP B 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.39   26.61     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CA  MET A 218 "
           pdb=" C   MET A 218 "
           pdb=" N   ASP A 219 "
           pdb=" CA  ASP A 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.71   26.29     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  ILE A 596 "
           pdb=" C   ILE A 596 "
           pdb=" N   SER A 597 "
           pdb=" CA  SER A 597 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.74   24.26     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 5366 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 934
       0.047 -    0.094: 380
       0.094 -    0.141: 93
       0.141 -    0.188: 20
       0.188 -    0.235: 4
  Chirality restraints: 1431
  Sorted by residual:
  chirality pdb=" C5  PGT A 801 "
            pdb=" C4  PGT A 801 "
            pdb=" C6  PGT A 801 "
            pdb=" O5  PGT A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.53    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" C2  PGT A 801 "
            pdb=" C1  PGT A 801 "
            pdb=" C3  PGT A 801 "
            pdb=" O2  PGT A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.57   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  VAL B 266 "
            pdb=" CA  VAL B 266 "
            pdb=" CG1 VAL B 266 "
            pdb=" CG2 VAL B 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1428 not shown)

  Planarity restraints: 1541
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 296 "   -0.015 2.00e-02 2.50e+03   3.03e-02 9.21e+00
        pdb=" C   VAL A 296 "    0.052 2.00e-02 2.50e+03
        pdb=" O   VAL A 296 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   SER A 297 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 178 "   -0.049 5.00e-02 4.00e+02   7.33e-02 8.59e+00
        pdb=" N   PRO B 179 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 179 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 179 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 229 "    0.014 2.00e-02 2.50e+03   2.85e-02 8.10e+00
        pdb=" C   CYS B 229 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   CYS B 229 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU B 230 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1538 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1613
        2.75 -     3.29: 9019
        3.29 -     3.83: 14187
        3.83 -     4.36: 15651
        4.36 -     4.90: 27001
  Nonbonded interactions: 67471
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 651 "
            pdb=" NH1 ARG A 655 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   SER A 433 "
            pdb=" OG  SER A 433 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   PRO B 493 "
            pdb=" OH  TYR B 573 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG  SER B 640 "
            pdb=" OE1 GLN B 643 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ILE B 677 "
            pdb=" N   ILE B 681 "
     model   vdw
     2.266 3.120
  ... (remaining 67466 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 169 through 669 or (resid 670 through 672 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 673 through 677 or (resid 678  \ 
and (name N or name CA or name C or name O or name CB )) or resid 679 through 68 \ 
3 or (resid 684 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 685 through 686 or (resid 687 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 688 through 695 or (resid 696 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 697 through 735 or (resid 736 through 737 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 738))
  selection = (chain 'B' and (resid 169 through 171 or (resid 172 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 173 through 634 or (resid 635 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 636 through 665 or (resid  \ 
666 through 672 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 673 through 734 or (resid 735 through 737 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 738))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.440
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
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      :  0.010   0.091   8979  Z= 0.667
  Angle     :  0.937   8.109  12161  Z= 0.508
  Chirality :  0.054   0.235   1431
  Planarity :  0.006   0.073   1541
  Dihedral  : 16.059 150.884   3261
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 13.28 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.23), residues: 1136
  helix: -0.95 (0.17), residues: 724
  sheet: -4.49 (0.49), residues: 34
  loop : -3.20 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 322 
 HIS   0.007   0.001   HIS A 429 
 PHE   0.027   0.003   PHE B 272 
 TYR   0.018   0.002   TYR A 509 
 ARG   0.023   0.001   ARG A 263 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.973 
Fit side-chains
REVERT: A  607 MET cc_start: 0.6627 (mmm) cc_final: 0.6316 (mmm)
REVERT: A  616 ASN cc_start: 0.9056 (m-40) cc_final: 0.8619 (t0)
REVERT: A  664 GLU cc_start: 0.7539 (pp20) cc_final: 0.7283 (pp20)
REVERT: A  721 GLN cc_start: 0.8008 (pp30) cc_final: 0.7740 (pm20)
REVERT: B  375 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8375 (mmt180)
REVERT: B  456 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8492 (tm-30)
REVERT: B  462 TYR cc_start: 0.8218 (t80) cc_final: 0.7853 (t80)
REVERT: B  607 MET cc_start: 0.8628 (mpp) cc_final: 0.8390 (mpp)
REVERT: B  713 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7310 (ptp-110)
  outliers start: 6
  outliers final: 4
  residues processed: 126
  average time/residue: 0.2016
  time to fit residues: 36.0585
Evaluate side-chains
  94 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  353 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 89 optimal weight:    9.9990
   chunk 34 optimal weight:    8.9990
   chunk 54 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 520 ASN
A 618 HIS
A 625 GLN
** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 688 HIS
A 726 GLN
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 679 GLN
B 695 HIS
B 716 GLN
B 720 HIS
B 721 GLN
B 722 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.143395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.099311 restraints weight = 14165.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 3.98
r_work: 0.3140 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   8979  Z= 0.369
  Angle     :  0.666   7.766  12161  Z= 0.355
  Chirality :  0.043   0.150   1431
  Planarity :  0.004   0.054   1541
  Dihedral  :  8.514 137.090   1288
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 19.28 %
    Favored  : 77.13 %
  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: -1.24 (0.25), residues: 1136
  helix:  0.33 (0.19), residues: 730
  sheet: -4.26 (0.47), residues: 50
  loop : -2.70 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 322 
 HIS   0.005   0.001   HIS A 429 
 PHE   0.018   0.002   PHE B 272 
 TYR   0.018   0.001   TYR A 730 
 ARG   0.005   0.000   ARG A 651 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  448 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: A  466 MET cc_start: 0.8178 (tpp) cc_final: 0.7443 (tpp)
REVERT: A  616 ASN cc_start: 0.9011 (m-40) cc_final: 0.8419 (t0)
REVERT: A  664 GLU cc_start: 0.7720 (pp20) cc_final: 0.7498 (pp20)
REVERT: A  721 GLN cc_start: 0.7907 (pp30) cc_final: 0.7694 (pm20)
REVERT: B  375 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8318 (mmt180)
REVERT: B  607 MET cc_start: 0.8691 (mpp) cc_final: 0.8393 (mpp)
REVERT: B  713 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7437 (ptp-110)
  outliers start: 34
  outliers final: 25
  residues processed: 129
  average time/residue: 0.1881
  time to fit residues: 35.3825
Evaluate side-chains
  118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  692 ILE
Chi-restraints excluded: chain A residue  722 GLN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  707 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.149245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.105656 restraints weight = 14196.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 3.60
r_work: 0.3255 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8979  Z= 0.178
  Angle     :  0.544   8.711  12161  Z= 0.284
  Chirality :  0.039   0.156   1431
  Planarity :  0.004   0.048   1541
  Dihedral  :  8.015 133.294   1288
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.44 %
    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: -0.25 (0.26), residues: 1136
  helix:  1.21 (0.20), residues: 724
  sheet: -3.92 (0.50), residues: 50
  loop : -2.52 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 322 
 HIS   0.003   0.001   HIS B 487 
 PHE   0.016   0.001   PHE B 250 
 TYR   0.020   0.001   TYR A 730 
 ARG   0.004   0.000   ARG A 277 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 MET cc_start: 0.7100 (ttm) cc_final: 0.6818 (ttp)
REVERT: A  448 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7487 (tm-30)
REVERT: A  466 MET cc_start: 0.8050 (tpp) cc_final: 0.7403 (tpp)
REVERT: A  607 MET cc_start: 0.6631 (mmp) cc_final: 0.6062 (mmm)
REVERT: A  616 ASN cc_start: 0.8971 (m-40) cc_final: 0.8355 (t0)
REVERT: A  721 GLN cc_start: 0.7923 (pp30) cc_final: 0.7721 (pm20)
REVERT: B  607 MET cc_start: 0.8716 (mpp) cc_final: 0.8492 (mpp)
REVERT: B  713 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7417 (ptp-110)
  outliers start: 31
  outliers final: 19
  residues processed: 141
  average time/residue: 0.1859
  time to fit residues: 37.6025
Evaluate side-chains
  120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  692 ILE
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  621 ILE
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 40 optimal weight:    8.9990
   chunk 16 optimal weight:    0.6980
   chunk 93 optimal weight:   20.0000
   chunk 109 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 678 GLN
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.158228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.116622 restraints weight = 13940.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 3.16
r_work: 0.3483 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8979  Z= 0.161
  Angle     :  0.542   8.960  12161  Z= 0.276
  Chirality :  0.039   0.157   1431
  Planarity :  0.003   0.043   1541
  Dihedral  :  7.777 131.925   1287
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.55 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.21 (0.26), residues: 1136
  helix:  1.57 (0.20), residues: 724
  sheet: -3.49 (0.55), residues: 50
  loop : -2.38 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 322 
 HIS   0.004   0.001   HIS B 618 
 PHE   0.015   0.001   PHE B 250 
 TYR   0.012   0.001   TYR A 730 
 ARG   0.004   0.000   ARG A 277 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 MET cc_start: 0.7708 (ttm) cc_final: 0.7420 (ttp)
REVERT: A  448 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7749 (tm-30)
REVERT: A  607 MET cc_start: 0.6586 (mmp) cc_final: 0.6304 (mmm)
REVERT: A  616 ASN cc_start: 0.8996 (m-40) cc_final: 0.8450 (t0)
REVERT: A  721 GLN cc_start: 0.8010 (pp30) cc_final: 0.7513 (pm20)
REVERT: B  466 MET cc_start: 0.8507 (mmm) cc_final: 0.8262 (mtt)
REVERT: B  713 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7494 (ptp-110)
  outliers start: 35
  outliers final: 25
  residues processed: 136
  average time/residue: 0.1645
  time to fit residues: 33.8011
Evaluate side-chains
  125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  621 ILE
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:   20.0000
   chunk 90 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 379 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.154967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.113076 restraints weight = 13676.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 3.20
r_work: 0.3431 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8979  Z= 0.205
  Angle     :  0.556   9.001  12161  Z= 0.284
  Chirality :  0.040   0.155   1431
  Planarity :  0.003   0.037   1541
  Dihedral  :  7.711 131.142   1285
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 22.87 %
    Favored  : 72.39 %
  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:  0.23 (0.26), residues: 1136
  helix:  1.60 (0.20), residues: 724
  sheet: -3.46 (0.49), residues: 68
  loop : -2.28 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 322 
 HIS   0.003   0.001   HIS A 429 
 PHE   0.015   0.001   PHE B 250 
 TYR   0.027   0.001   TYR B 573 
 ARG   0.004   0.000   ARG A 277 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 105
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 MET cc_start: 0.7703 (ttm) cc_final: 0.7430 (ttp)
REVERT: A  448 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: A  466 MET cc_start: 0.7989 (tpp) cc_final: 0.7253 (tpp)
REVERT: A  607 MET cc_start: 0.6641 (mmp) cc_final: 0.6382 (mmm)
REVERT: A  616 ASN cc_start: 0.8982 (m-40) cc_final: 0.8499 (t0)
REVERT: A  721 GLN cc_start: 0.7832 (pp30) cc_final: 0.7591 (pm20)
REVERT: B  198 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7922 (mm-30)
REVERT: B  662 LEU cc_start: 0.8343 (tt) cc_final: 0.8142 (mt)
REVERT: B  713 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7510 (ptp-110)
  outliers start: 45
  outliers final: 39
  residues processed: 137
  average time/residue: 0.1635
  time to fit residues: 33.9336
Evaluate side-chains
  141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 102
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  692 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  621 ILE
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    0.3980
   chunk 87 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 56 optimal weight:    0.0670
   chunk 33 optimal weight:    9.9990
   chunk 21 optimal weight:    0.5980
   chunk 103 optimal weight:    8.9990
   chunk 108 optimal weight:   20.0000
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.0120

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

Flipped N/Q/H residues before XYZ refinement:
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.158288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.115488 restraints weight = 13559.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 3.14
r_work: 0.3484 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8979  Z= 0.164
  Angle     :  0.534   9.141  12161  Z= 0.271
  Chirality :  0.039   0.158   1431
  Planarity :  0.003   0.036   1541
  Dihedral  :  7.620 129.975   1285
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 23.08 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.27), residues: 1136
  helix:  1.74 (0.20), residues: 726
  sheet: -3.17 (0.51), residues: 68
  loop : -2.18 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 322 
 HIS   0.002   0.001   HIS A 618 
 PHE   0.016   0.001   PHE B 250 
 TYR   0.020   0.001   TYR B 573 
 ARG   0.003   0.000   ARG A 277 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 107
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 MET cc_start: 0.7703 (ttm) cc_final: 0.7439 (ttp)
REVERT: A  448 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: A  607 MET cc_start: 0.6612 (mmp) cc_final: 0.6349 (mmm)
REVERT: A  616 ASN cc_start: 0.8945 (m-40) cc_final: 0.8505 (t0)
REVERT: B  198 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7913 (mm-30)
REVERT: B  210 ASP cc_start: 0.8788 (t70) cc_final: 0.8579 (t0)
REVERT: B  466 MET cc_start: 0.8358 (mtt) cc_final: 0.8140 (mmm)
REVERT: B  713 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7517 (ptp-110)
  outliers start: 42
  outliers final: 38
  residues processed: 138
  average time/residue: 0.1647
  time to fit residues: 33.7739
Evaluate side-chains
  138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  692 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  621 ILE
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0770
   chunk 31 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9940

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

Flipped N/Q/H residues before XYZ refinement:
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.159045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.118010 restraints weight = 13710.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 3.12
r_work: 0.3486 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8979  Z= 0.166
  Angle     :  0.533   8.569  12161  Z= 0.272
  Chirality :  0.039   0.156   1431
  Planarity :  0.003   0.036   1541
  Dihedral  :  7.574 129.978   1285
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 24.03 %
    Favored  : 71.13 %
  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:  0.58 (0.27), residues: 1136
  helix:  1.74 (0.20), residues: 740
  sheet: -2.52 (0.67), residues: 50
  loop : -2.25 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 322 
 HIS   0.002   0.001   HIS A 429 
 PHE   0.016   0.001   PHE B 250 
 TYR   0.018   0.001   TYR B 598 
 ARG   0.004   0.000   ARG B 389 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 103
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: A  330 MET cc_start: 0.7684 (ttm) cc_final: 0.7325 (ttp)
REVERT: A  448 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: A  466 MET cc_start: 0.7898 (tpp) cc_final: 0.7124 (tpp)
REVERT: A  607 MET cc_start: 0.6599 (mmp) cc_final: 0.6336 (mmm)
REVERT: A  616 ASN cc_start: 0.8962 (m-40) cc_final: 0.8549 (t0)
REVERT: B  198 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7948 (mm-30)
REVERT: B  210 ASP cc_start: 0.8794 (t70) cc_final: 0.8585 (t0)
REVERT: B  401 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: B  466 MET cc_start: 0.8349 (mtt) cc_final: 0.8130 (mmm)
REVERT: B  662 LEU cc_start: 0.7935 (mt) cc_final: 0.7697 (mt)
REVERT: B  713 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7542 (ptp-110)
  outliers start: 46
  outliers final: 42
  residues processed: 137
  average time/residue: 0.1654
  time to fit residues: 34.1147
Evaluate side-chains
  142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 100
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  246 PHE
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  692 ILE
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  621 ILE
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 98 optimal weight:    0.0030
   chunk 52 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.7998

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

Flipped N/Q/H residues before XYZ refinement:
A 379 ASN
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.155025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.113629 restraints weight = 14074.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 3.47
r_work: 0.3404 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8979  Z= 0.236
  Angle     :  0.581   8.168  12161  Z= 0.295
  Chirality :  0.040   0.155   1431
  Planarity :  0.003   0.035   1541
  Dihedral  :  7.642 130.093   1285
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.60 %
    Favored  : 71.02 %
  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:  0.45 (0.26), residues: 1136
  helix:  1.65 (0.20), residues: 728
  sheet: -2.85 (0.57), residues: 68
  loop : -2.08 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 322 
 HIS   0.004   0.001   HIS A 429 
 PHE   0.015   0.001   PHE B 250 
 TYR   0.018   0.001   TYR B 573 
 ARG   0.006   0.000   ARG A 277 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 91
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 MET cc_start: 0.7623 (ttm) cc_final: 0.7368 (ttp)
REVERT: A  448 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: A  466 MET cc_start: 0.7964 (tpp) cc_final: 0.7191 (tpp)
REVERT: A  607 MET cc_start: 0.6616 (mmp) cc_final: 0.6089 (mmm)
REVERT: A  616 ASN cc_start: 0.8980 (m-40) cc_final: 0.8563 (t0)
REVERT: B  198 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7902 (mm-30)
REVERT: B  466 MET cc_start: 0.8433 (mtt) cc_final: 0.8201 (mmm)
REVERT: B  475 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8163 (m)
REVERT: B  713 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7703 (ptp-110)
  outliers start: 51
  outliers final: 47
  residues processed: 133
  average time/residue: 0.1609
  time to fit residues: 32.6922
Evaluate side-chains
  138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 90
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  692 ILE
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  621 ILE
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.158397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.116927 restraints weight = 13937.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 3.36
r_work: 0.3469 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8979  Z= 0.172
  Angle     :  0.556   8.601  12161  Z= 0.280
  Chirality :  0.039   0.155   1431
  Planarity :  0.003   0.037   1541
  Dihedral  :  7.557 129.117   1285
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 24.76 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.27), residues: 1136
  helix:  1.82 (0.20), residues: 726
  sheet: -2.74 (0.57), residues: 68
  loop : -2.06 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 322 
 HIS   0.002   0.001   HIS A 618 
 PHE   0.016   0.001   PHE B 250 
 TYR   0.016   0.001   TYR B 573 
 ARG   0.005   0.000   ARG A 277 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 101
  time to evaluate  : 2.948 
Fit side-chains
REVERT: A  448 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: A  607 MET cc_start: 0.6615 (mmp) cc_final: 0.6333 (mmm)
REVERT: A  616 ASN cc_start: 0.8963 (m-40) cc_final: 0.8564 (t0)
REVERT: B  198 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7918 (mm-30)
REVERT: B  347 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8573 (mttm)
REVERT: B  401 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7886 (tm-30)
REVERT: B  475 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8209 (m)
REVERT: B  713 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7694 (ptp-110)
  outliers start: 43
  outliers final: 39
  residues processed: 135
  average time/residue: 0.1739
  time to fit residues: 35.1114
Evaluate side-chains
  136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 96
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  236 SER
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  332 PHE
Chi-restraints excluded: chain A residue  340 ASN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  394 VAL
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 88 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0370
   chunk 102 optimal weight:    4.9990
   overall best weight:    0.6060

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

Flipped N/Q/H residues before XYZ refinement:
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.160864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.118655 restraints weight = 13820.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 3.63
r_work: 0.3504 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8979  Z= 0.154
  Angle     :  0.580  10.581  12161  Z= 0.285
  Chirality :  0.039   0.158   1431
  Planarity :  0.003   0.034   1541
  Dihedral  :  7.498 129.403   1285
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 26.24 %
    Favored  : 70.39 %
  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:  0.77 (0.27), residues: 1136
  helix:  1.92 (0.20), residues: 736
  sheet: -2.36 (0.58), residues: 72
  loop : -2.18 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 322 
 HIS   0.002   0.000   HIS A 618 
 PHE   0.017   0.001   PHE B 250 
 TYR   0.016   0.001   TYR B 573 
 ARG   0.005   0.000   ARG A 277 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.995 
Fit side-chains
REVERT: A  448 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7668 (tm-30)
REVERT: A  518 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6494 (tp)
REVERT: A  607 MET cc_start: 0.6588 (mmp) cc_final: 0.6303 (mmm)
REVERT: A  616 ASN cc_start: 0.8930 (m-40) cc_final: 0.8529 (t0)
REVERT: B  218 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7246 (mmp)
REVERT: B  347 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8538 (mttm)
REVERT: B  401 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: B  466 MET cc_start: 0.8515 (mmm) cc_final: 0.8050 (mmm)
REVERT: B  475 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8189 (m)
REVERT: B  518 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8141 (tp)
REVERT: B  713 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7713 (ptp-110)
  outliers start: 32
  outliers final: 24
  residues processed: 132
  average time/residue: 0.1821
  time to fit residues: 35.2475
Evaluate side-chains
  127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ASP
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  594 ASP
Chi-restraints excluded: chain B residue  603 VAL
Chi-restraints excluded: chain B residue  621 ILE
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  714 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 12 optimal weight:    0.3980
   chunk 41 optimal weight:    5.9990
   chunk 54 optimal weight:   20.0000
   chunk 88 optimal weight:   10.0000
   chunk 113 optimal weight:    0.0470
   chunk 104 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0980
   overall best weight:    0.4078

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

Flipped N/Q/H residues before XYZ refinement:
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.163304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.121856 restraints weight = 13662.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 3.47
r_work: 0.3562 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056   8979  Z= 0.152
  Angle     :  0.574  10.570  12161  Z= 0.282
  Chirality :  0.038   0.158   1431
  Planarity :  0.003   0.037   1541
  Dihedral  :  7.420 128.777   1285
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 27.19 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.88 (0.27), residues: 1136
  helix:  2.01 (0.20), residues: 738
  sheet: -2.42 (0.58), residues: 76
  loop : -2.14 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 322 
 HIS   0.002   0.000   HIS B 695 
 PHE   0.017   0.001   PHE B 250 
 TYR   0.016   0.001   TYR B 573 
 ARG   0.005   0.000   ARG A 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4111.04 seconds
wall clock time: 73 minutes 41.02 seconds (4421.02 seconds total)