Starting phenix.real_space_refine
on Tue Feb  3 18:45:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gw9_51644/02_2026/9gw9_51644.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gw9_51644/02_2026/9gw9_51644.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gw9_51644/02_2026/9gw9_51644.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gw9_51644/02_2026/9gw9_51644.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gw9_51644/02_2026/9gw9_51644.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gw9_51644/02_2026/9gw9_51644.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.085
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    3846      2.51       5
     N    1072      2.21       5
     O    1151      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6105
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3058
          Classifications: {'peptide': 410}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 379}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 39
    Chain: "B"
      Number of atoms: 2455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2455
          Classifications: {'peptide': 322}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 592
          Classifications: {'peptide': 87}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 6, 'TRANS': 80}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   PHE B 600 " occ=0.82
      ... (9 atoms not shown)
      pdb=" CZ  PHE B 600 " occ=0.82
  Time building chain proxies: 1.14, per 1000 atoms: 0.19
  Number of scatterers: 6105
  At special positions: 0
  Unit cell: (78.442, 81.028, 119.818, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1151      8.00
     N    1072      7.00
     C    3846      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 460.0 milliseconds
  

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 11 sheets defined
      18.2% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 327 through 334
      removed outlier: 3.644A  pdb=" N   ILE A 331 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 489
      removed outlier: 3.864A  pdb=" N   ILE A 482 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLY A 483 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 532
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 4.369A  pdb=" N   HIS A 537 " --> pdb=" O   THR A 533 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLY A 538 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 533 through 538'
    Processing helix  chain 'A' and resid 552 through 562
      removed outlier: 3.655A  pdb=" N   ASN A 556 " --> pdb=" O   ASP A 552 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   GLU A 560 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 588
      removed outlier: 3.698A  pdb=" N   GLN A 584 " --> pdb=" O   ASP A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 635
      removed outlier: 4.373A  pdb=" N   VAL A 632 " --> pdb=" O   PRO A 628 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL A 633 " --> pdb=" O   VAL A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 648
      removed outlier: 3.802A  pdb=" N   ARG A 644 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   LYS A 645 " --> pdb=" O   PRO A 641 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   MET A 646 " --> pdb=" O   ALA A 642 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLN A 647 " --> pdb=" O   LEU A 643 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY A 648 " --> pdb=" O   ARG A 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 335
    Processing helix  chain 'B' and resid 480 through 488
      removed outlier: 4.061A  pdb=" N   LEU B 484 " --> pdb=" O   SER B 480 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU B 485 " --> pdb=" O   GLU B 481 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ALA B 486 " --> pdb=" O   ILE B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 538
      removed outlier: 3.827A  pdb=" N   HIS B 537 " --> pdb=" O   THR B 533 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY B 538 " --> pdb=" O   ILE B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 550 through 565
    Processing helix  chain 'B' and resid 576 through 579
    Processing helix  chain 'B' and resid 580 through 586
      removed outlier: 3.672A  pdb=" N   GLN B 584 " --> pdb=" O   ASP B 580 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 586 " --> pdb=" O   LEU B 582 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 638
      removed outlier: 4.493A  pdb=" N   VAL B 632 " --> pdb=" O   PRO B 628 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   VAL B 633 " --> pdb=" O   VAL B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 639 through 648
      removed outlier: 3.852A  pdb=" N   ARG B 644 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   LYS B 645 " --> pdb=" O   PRO B 641 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   MET B 646 " --> pdb=" O   ALA B 642 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 342 through 345
    Processing sheet with id=AA2, first strand: chain 'A' and resid 388 through 389
      removed outlier: 6.558A  pdb=" N   PHE A 388 " --> pdb=" O   VAL A 408 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 547
      removed outlier: 6.412A  pdb=" N   VAL A 501 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   LEU A 544 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   VAL A 503 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ILE A 546 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   SER A 505 " --> pdb=" O   ILE A 546 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR A 506 " --> pdb=" O   SER A 571 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ILE A 568 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   LEU A 624 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   THR A 570 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE A 614 " --> pdb=" O   VAL A 617 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   THR A 607 " --> pdb=" O   ARG A 598 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   PHE A 596 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   THR A 611 " --> pdb=" O   ILE A 594 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   ILE A 594 " --> pdb=" O   THR A 611 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 511
      removed outlier: 3.563A  pdb=" N   LEU A 511 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 656 through 661
      removed outlier: 8.163A  pdb=" N   ALA A 689 " --> pdb=" O   LYS A 658 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ARG A 660 " --> pdb=" O   ALA A 689 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   SER A 691 " --> pdb=" O   ARG A 660 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A 709 " --> pdb=" O   MET A 731 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ASP A 729 " --> pdb=" O   MET A 711 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   GLU A 726 " --> pdb=" O   LEU A 661 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   LEU A 661 " --> pdb=" O   GLU A 726 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 665 through 666
      removed outlier: 3.747A  pdb=" N   VAL A 665 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A 722 " --> pdb=" O   VAL A 665 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 342 through 346
    Processing sheet with id=AA8, first strand: chain 'B' and resid 541 through 546
      removed outlier: 6.402A  pdb=" N   VAL B 501 " --> pdb=" O   THR B 541 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   ASN B 543 " --> pdb=" O   VAL B 501 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL B 503 " --> pdb=" O   ASN B 543 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   GLY B 545 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE B 568 " --> pdb=" O   PHE B 622 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   LEU B 624 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR B 570 " --> pdb=" O   LEU B 624 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   PHE B 609 " --> pdb=" O   HIS B 595 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 510 through 511
    Processing sheet with id=AB1, first strand: chain 'B' and resid 656 through 661
      removed outlier: 8.049A  pdb=" N   ALA B 689 " --> pdb=" O   LYS B 658 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ARG B 660 " --> pdb=" O   ALA B 689 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   SER B 691 " --> pdb=" O   ARG B 660 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   MET B 731 " --> pdb=" O   LEU B 709 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   MET B 711 " --> pdb=" O   ASP B 729 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   ASP B 729 " --> pdb=" O   MET B 711 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 388 through 391
      removed outlier: 5.343A  pdb=" N   ILE C 389 " --> pdb=" O   VAL C 408 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   ARG C 410 " --> pdb=" O   ILE C 389 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   GLY C 391 " --> pdb=" O   ARG C 410 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA C 423 " --> pdb=" O   VAL C 378 " (cutoff:3.500A)

    123 hydrogen bonds defined for protein.
    345 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: 0.66

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2086
        1.34 -     1.46: 961
        1.46 -     1.57: 3110
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6219
  Sorted by residual:
  bond pdb=" N   PRO A 366 "
       pdb=" CD  PRO A 366 "
    ideal  model  delta    sigma   weight residual
    1.474  1.541 -0.067 1.40e-02 5.10e+03 2.28e+01
  bond pdb=" N   ASP B 668 "
       pdb=" CA  ASP B 668 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.036 1.18e-02 7.18e+03 9.41e+00
  bond pdb=" N   TYR B 719 "
       pdb=" CA  TYR B 719 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.10e-02 8.26e+03 7.91e+00
  bond pdb=" N   VAL B 599 "
       pdb=" CA  VAL B 599 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.28e-02 6.10e+03 7.86e+00
  bond pdb=" N   VAL B 720 "
       pdb=" CA  VAL B 720 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.48e+00
  ... (remaining 6214 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 8231
        1.98 -     3.95: 215
        3.95 -     5.93: 18
        5.93 -     7.91: 2
        7.91 -     9.88: 3
  Bond angle restraints: 8469
  Sorted by residual:
  angle pdb=" C   LYS B 497 "
        pdb=" N   PHE B 498 "
        pdb=" CA  PHE B 498 "
      ideal   model   delta    sigma   weight residual
     120.68  129.73   -9.05 1.52e+00 4.33e-01 3.54e+01
  angle pdb=" N   VAL A 425 "
        pdb=" CA  VAL A 425 "
        pdb=" C   VAL A 425 "
      ideal   model   delta    sigma   weight residual
     112.29  107.64    4.65 9.40e-01 1.13e+00 2.45e+01
  angle pdb=" N   VAL A 720 "
        pdb=" CA  VAL A 720 "
        pdb=" C   VAL A 720 "
      ideal   model   delta    sigma   weight residual
     113.20  108.54    4.66 9.60e-01 1.09e+00 2.35e+01
  angle pdb=" C   SER B 698 "
        pdb=" CA  SER B 698 "
        pdb=" CB  SER B 698 "
      ideal   model   delta    sigma   weight residual
     115.89  110.30    5.59 1.32e+00 5.74e-01 1.80e+01
  angle pdb=" N   VAL B 720 "
        pdb=" CA  VAL B 720 "
        pdb=" C   VAL B 720 "
      ideal   model   delta    sigma   weight residual
     110.62  106.31    4.31 1.02e+00 9.61e-01 1.79e+01
  ... (remaining 8464 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.85: 3389
       12.85 -    25.71: 274
       25.71 -    38.56: 111
       38.56 -    51.41: 12
       51.41 -    64.26: 12
  Dihedral angle restraints: 3798
    sinusoidal: 1479
      harmonic: 2319
  Sorted by residual:
  dihedral pdb=" CA  LEU A 605 "
           pdb=" C   LEU A 605 "
           pdb=" N   PRO A 606 "
           pdb=" CA  PRO A 606 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.02  -26.98     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  GLU A 392 "
           pdb=" C   GLU A 392 "
           pdb=" N   SER A 393 "
           pdb=" CA  SER A 393 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.94   17.06     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  MET B 601 "
           pdb=" CG  MET B 601 "
           pdb=" SD  MET B 601 "
           pdb=" CE  MET B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.29  -58.71     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 3795 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 682
       0.040 -    0.081: 204
       0.081 -    0.121: 94
       0.121 -    0.161: 11
       0.161 -    0.201: 4
  Chirality restraints: 995
  Sorted by residual:
  chirality pdb=" CA  VAL B 720 "
            pdb=" N   VAL B 720 "
            pdb=" C   VAL B 720 "
            pdb=" CB  VAL B 720 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  PHE B 600 "
            pdb=" N   PHE B 600 "
            pdb=" C   PHE B 600 "
            pdb=" CB  PHE B 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  VAL B 599 "
            pdb=" N   VAL B 599 "
            pdb=" C   VAL B 599 "
            pdb=" CB  VAL B 599 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.93e-01
  ... (remaining 992 not shown)

  Planarity restraints: 1119
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 365 "    0.051 5.00e-02 4.00e+02   7.56e-02 9.15e+00
        pdb=" N   PRO A 366 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 366 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 366 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 688 "   -0.010 2.00e-02 2.50e+03   1.02e-02 2.59e+00
        pdb=" CG  TRP B 688 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 688 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 688 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 688 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 688 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 688 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 688 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 688 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 688 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 680 "    0.011 2.00e-02 2.50e+03   9.76e-03 2.38e+00
        pdb=" CG  TRP A 680 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 680 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 680 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 680 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 680 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 680 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 680 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 680 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 680 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1116 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 951
        2.76 -     3.30: 5392
        3.30 -     3.83: 8736
        3.83 -     4.37: 9651
        4.37 -     4.90: 17265
  Nonbonded interactions: 41995
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 675 "
            pdb=" OG1 THR A 692 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER C 393 "
            pdb=" O   ARG C 410 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" NE2 GLN A 401 "
            pdb=" O   THR A 402 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" OE1 GLU A 672 "
            pdb=" ND2 ASN A 694 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" O   VAL C 427 "
            pdb=" OG1 THR C 430 "
     model   vdw
     2.355 3.040
  ... (remaining 41990 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.82 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.330
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.590
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6219  Z= 0.239
  Angle     :  0.713   9.884   8469  Z= 0.416
  Chirality :  0.047   0.201    995
  Planarity :  0.005   0.076   1119
  Dihedral  : 11.656  64.263   2308
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  : 12.70 %
    Favored  : 86.44 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  0.61 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.28), residues: 811
  helix: -1.11 (0.46), residues: 125
  sheet: -0.16 (0.45), residues: 139
  loop : -2.36 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 379 
 TYR   0.007   0.001   TYR A 347 
 PHE   0.016   0.002   PHE A 622 
 TRP   0.027   0.004   TRP B 688 
 HIS   0.005   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 6219)
  covalent geometry    : angle       0.71339 ( 8469)
  hydrogen bonds       : bond        0.31748 (  123)
  hydrogen bonds       : angle       8.47638 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 218
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  328 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7768 (mmtm)
REVERT: A  410 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7580 (ttt-90)
REVERT: A  583 LYS cc_start: 0.8883 (mttt) cc_final: 0.8496 (tttp)
REVERT: A  703 MET cc_start: 0.8476 (mmp) cc_final: 0.7692 (mmt)
REVERT: A  735 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7430 (ttm-80)
REVERT: B  599 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.5177 (m)
REVERT: B  664 ASP cc_start: 0.7233 (p0) cc_final: 0.6840 (p0)
REVERT: C  387 ARG cc_start: 0.7181 (mtt90) cc_final: 0.6906 (mmt90)
REVERT: C  404 MET cc_start: 0.6934 (mmm) cc_final: 0.6604 (mpp)
  outliers start: 4
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0718
  time to fit residues: 20.1256
Evaluate side-chains
  125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  599 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0000
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 682 HIS
B 496 ASN
B 681 HIS
** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.199729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.148130 restraints weight = 7417.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.153392 restraints weight = 4334.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.156761 restraints weight = 3123.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.158930 restraints weight = 2556.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.159850 restraints weight = 2256.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3998 r_free = 0.3998    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3998 r_free = 0.3998    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6219  Z= 0.132
  Angle     :  0.660   8.187   8469  Z= 0.337
  Chirality :  0.046   0.241    995
  Planarity :  0.005   0.049   1119
  Dihedral  :  4.333  22.954    871
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 11.10 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.14 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.28), residues: 811
  helix: -0.56 (0.47), residues: 125
  sheet:  0.19 (0.49), residues: 117
  loop : -2.34 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 670 
 TYR   0.004   0.001   TYR C 376 
 PHE   0.011   0.002   PHE B 609 
 TRP   0.007   0.001   TRP A 680 
 HIS   0.006   0.001   HIS B 674 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6219)
  covalent geometry    : angle       0.65980 ( 8469)
  hydrogen bonds       : bond        0.04135 (  123)
  hydrogen bonds       : angle       6.04328 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  471 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6803 (mp)
REVERT: A  559 ASN cc_start: 0.8111 (t0) cc_final: 0.7713 (m-40)
REVERT: A  583 LYS cc_start: 0.8574 (mttt) cc_final: 0.8304 (tttp)
REVERT: A  703 MET cc_start: 0.8549 (mmp) cc_final: 0.7920 (mmt)
REVERT: B  596 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6680 (p90)
REVERT: B  664 ASP cc_start: 0.6698 (p0) cc_final: 0.6307 (p0)
REVERT: B  670 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6629 (ptm-80)
REVERT: C  404 MET cc_start: 0.6460 (mmm) cc_final: 0.6140 (mpp)
  outliers start: 19
  outliers final: 7
  residues processed: 147
  average time/residue: 0.0640
  time to fit residues: 12.4292
Evaluate side-chains
  127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain B residue  596 PHE
Chi-restraints excluded: chain B residue  670 ARG
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain C residue  427 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0470
   overall best weight:    0.5680

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

Flipped N/Q/H residues before XYZ refinement:
A 681 HIS
** B 695 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 = 0.4415 r_free = 0.4415 target = 0.205729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.154941 restraints weight = 7469.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.160427 restraints weight = 4364.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.164015 restraints weight = 3137.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.165994 restraints weight = 2554.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.167548 restraints weight = 2260.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4071 r_free = 0.4071    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4071 r_free = 0.4071    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6219  Z= 0.121
  Angle     :  0.637   7.921   8469  Z= 0.319
  Chirality :  0.045   0.246    995
  Planarity :  0.005   0.078   1119
  Dihedral  :  4.242  22.538    870
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.74 %
    Allowed  : 10.23 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.44 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.28), residues: 811
  helix: -0.29 (0.49), residues: 130
  sheet:  0.28 (0.47), residues: 126
  loop : -2.34 (0.24), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 670 
 TYR   0.003   0.001   TYR A 539 
 PHE   0.014   0.001   PHE B 596 
 TRP   0.011   0.002   TRP A 680 
 HIS   0.003   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6219)
  covalent geometry    : angle       0.63683 ( 8469)
  hydrogen bonds       : bond        0.03498 (  123)
  hydrogen bonds       : angle       5.56138 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A  408 VAL cc_start: 0.8445 (t) cc_final: 0.8206 (t)
REVERT: A  559 ASN cc_start: 0.8179 (t0) cc_final: 0.7842 (m-40)
REVERT: A  583 LYS cc_start: 0.8529 (mttt) cc_final: 0.8286 (tttp)
REVERT: B  563 SER cc_start: 0.9166 (t) cc_final: 0.8940 (t)
REVERT: B  571 SER cc_start: 0.9072 (t) cc_final: 0.8579 (p)
REVERT: B  664 ASP cc_start: 0.6700 (p0) cc_final: 0.6341 (p0)
REVERT: B  701 MET cc_start: 0.7328 (tpp) cc_final: 0.7098 (tpt)
REVERT: C  404 MET cc_start: 0.6395 (mmm) cc_final: 0.6070 (mpp)
  outliers start: 16
  outliers final: 12
  residues processed: 131
  average time/residue: 0.0556
  time to fit residues: 9.6070
Evaluate side-chains
  120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain C residue  409 MET
Chi-restraints excluded: chain C residue  427 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0020
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0670
   chunk 53 optimal weight:    0.4980
   chunk 69 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   chunk 80 optimal weight:    9.9990
   overall best weight:    0.7128

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

Flipped N/Q/H residues before XYZ refinement:
** B 695 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 = 0.4395 r_free = 0.4395 target = 0.203869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.152893 restraints weight = 7598.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.158280 restraints weight = 4453.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.161796 restraints weight = 3200.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.163798 restraints weight = 2604.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.165382 restraints weight = 2307.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6219  Z= 0.128
  Angle     :  0.651   8.665   8469  Z= 0.325
  Chirality :  0.045   0.270    995
  Planarity :  0.005   0.069   1119
  Dihedral  :  4.195  20.361    870
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.74 %
    Allowed  : 10.48 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.97 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.28), residues: 811
  helix: -0.14 (0.49), residues: 132
  sheet:  0.22 (0.47), residues: 124
  loop : -2.31 (0.24), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 410 
 TYR   0.008   0.001   TYR A 376 
 PHE   0.014   0.002   PHE B 596 
 TRP   0.006   0.001   TRP A 680 
 HIS   0.003   0.000   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6219)
  covalent geometry    : angle       0.65144 ( 8469)
  hydrogen bonds       : bond        0.03136 (  123)
  hydrogen bonds       : angle       5.32857 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  328 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7261 (mmtm)
REVERT: A  559 ASN cc_start: 0.8199 (t0) cc_final: 0.7804 (m-40)
REVERT: A  583 LYS cc_start: 0.8531 (mttt) cc_final: 0.8290 (tttp)
REVERT: A  703 MET cc_start: 0.8335 (mmm) cc_final: 0.7913 (mmm)
REVERT: B  563 SER cc_start: 0.9248 (t) cc_final: 0.9044 (t)
REVERT: B  571 SER cc_start: 0.9074 (t) cc_final: 0.8573 (p)
REVERT: C  387 ARG cc_start: 0.7603 (mtt90) cc_final: 0.6899 (mpt180)
REVERT: C  404 MET cc_start: 0.6373 (mmm) cc_final: 0.6046 (mpp)
  outliers start: 18
  outliers final: 12
  residues processed: 118
  average time/residue: 0.0585
  time to fit residues: 9.4103
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain C residue  409 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0270
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    1.4044

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

Flipped N/Q/H residues before XYZ refinement:
B 647 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.191971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.140398 restraints weight = 7837.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.145476 restraints weight = 4615.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.148811 restraints weight = 3346.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.150970 restraints weight = 2747.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.152040 restraints weight = 2424.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6219  Z= 0.185
  Angle     :  0.707  11.211   8469  Z= 0.356
  Chirality :  0.047   0.291    995
  Planarity :  0.005   0.080   1119
  Dihedral  :  4.545  21.437    870
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.74 %
    Allowed  : 11.10 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.74 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.28), residues: 811
  helix: -0.14 (0.48), residues: 130
  sheet: -0.32 (0.43), residues: 141
  loop : -2.45 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 410 
 TYR   0.008   0.001   TYR A 539 
 PHE   0.016   0.002   PHE A 609 
 TRP   0.008   0.002   TRP B 688 
 HIS   0.006   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 6219)
  covalent geometry    : angle       0.70745 ( 8469)
  hydrogen bonds       : bond        0.03618 (  123)
  hydrogen bonds       : angle       5.54604 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  328 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7346 (mmtm)
REVERT: A  583 LYS cc_start: 0.8602 (mttt) cc_final: 0.8333 (tttp)
REVERT: A  703 MET cc_start: 0.8259 (mmm) cc_final: 0.7859 (mmm)
REVERT: B  482 ILE cc_start: 0.8532 (tt) cc_final: 0.8330 (tt)
REVERT: B  493 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8260 (p)
REVERT: B  571 SER cc_start: 0.9121 (t) cc_final: 0.8648 (p)
REVERT: C  387 ARG cc_start: 0.7675 (mtt90) cc_final: 0.7057 (mpt180)
REVERT: C  404 MET cc_start: 0.6482 (mmm) cc_final: 0.6153 (mpp)
  outliers start: 17
  outliers final: 12
  residues processed: 108
  average time/residue: 0.0551
  time to fit residues: 8.1308
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  404 MET
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  703 MET
Chi-restraints excluded: chain C residue  409 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0870
   chunk 29 optimal weight:    0.5980
   chunk 69 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.194679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.144072 restraints weight = 7698.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.149307 restraints weight = 4480.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.152708 restraints weight = 3220.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.154852 restraints weight = 2627.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.155744 restraints weight = 2320.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.4265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6219  Z= 0.117
  Angle     :  0.636  10.202   8469  Z= 0.316
  Chirality :  0.045   0.343    995
  Planarity :  0.005   0.066   1119
  Dihedral  :  4.198  20.737    870
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  :  9.74 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.58 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.28), residues: 811
  helix:  0.09 (0.49), residues: 130
  sheet: -0.20 (0.43), residues: 141
  loop : -2.40 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 410 
 TYR   0.004   0.001   TYR A 347 
 PHE   0.017   0.001   PHE B 596 
 TRP   0.008   0.001   TRP B 688 
 HIS   0.003   0.000   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6219)
  covalent geometry    : angle       0.63573 ( 8469)
  hydrogen bonds       : bond        0.02791 (  123)
  hydrogen bonds       : angle       5.17451 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  328 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7303 (mmtm)
REVERT: A  498 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8385 (m-10)
REVERT: A  583 LYS cc_start: 0.8597 (mttt) cc_final: 0.8332 (tttp)
REVERT: A  703 MET cc_start: 0.8193 (mmm) cc_final: 0.7889 (mmm)
REVERT: B  571 SER cc_start: 0.9022 (t) cc_final: 0.8566 (p)
REVERT: C  387 ARG cc_start: 0.7675 (mtt90) cc_final: 0.7121 (mpt180)
REVERT: C  404 MET cc_start: 0.6365 (mmm) cc_final: 0.6043 (mpp)
  outliers start: 16
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0655
  time to fit residues: 9.4590
Evaluate side-chains
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  404 MET
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain C residue  409 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 28 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.193879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.143070 restraints weight = 7713.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.148215 restraints weight = 4527.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.151626 restraints weight = 3271.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.153698 restraints weight = 2673.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.154766 restraints weight = 2368.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3927 r_free = 0.3927    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3927 r_free = 0.3927    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6219  Z= 0.129
  Angle     :  0.641  11.269   8469  Z= 0.317
  Chirality :  0.045   0.291    995
  Planarity :  0.005   0.058   1119
  Dihedral  :  4.192  20.799    870
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 10.23 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.12 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.28 (0.28), residues: 811
  helix: -0.02 (0.48), residues: 134
  sheet: -0.26 (0.42), residues: 141
  loop : -2.44 (0.24), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 410 
 TYR   0.004   0.001   TYR A 347 
 PHE   0.014   0.001   PHE B 596 
 TRP   0.007   0.001   TRP B 688 
 HIS   0.003   0.000   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6219)
  covalent geometry    : angle       0.64080 ( 8469)
  hydrogen bonds       : bond        0.02900 (  123)
  hydrogen bonds       : angle       5.11573 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  328 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7271 (mmtm)
REVERT: A  498 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8329 (m-10)
REVERT: A  583 LYS cc_start: 0.8573 (mttt) cc_final: 0.8306 (tttp)
REVERT: A  703 MET cc_start: 0.8181 (mmm) cc_final: 0.7885 (mmm)
REVERT: B  493 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8225 (p)
REVERT: B  571 SER cc_start: 0.9060 (t) cc_final: 0.8620 (p)
REVERT: C  387 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7351 (mmt90)
REVERT: C  404 MET cc_start: 0.6356 (mmm) cc_final: 0.6023 (mpp)
  outliers start: 23
  outliers final: 11
  residues processed: 117
  average time/residue: 0.0595
  time to fit residues: 9.3430
Evaluate side-chains
  113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  404 MET
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain C residue  409 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0030
   chunk 11 optimal weight:   30.0000
   chunk 31 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.8792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.193248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142257 restraints weight = 7722.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.147342 restraints weight = 4557.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.150697 restraints weight = 3307.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.152833 restraints weight = 2708.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.153762 restraints weight = 2392.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3920 r_free = 0.3920    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3920 r_free = 0.3920    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.4492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6219  Z= 0.134
  Angle     :  0.660  11.811   8469  Z= 0.326
  Chirality :  0.046   0.373    995
  Planarity :  0.005   0.053   1119
  Dihedral  :  4.261  21.795    870
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 10.73 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.66 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.28), residues: 811
  helix:  0.07 (0.49), residues: 134
  sheet: -0.36 (0.42), residues: 140
  loop : -2.40 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 598 
 TYR   0.004   0.001   TYR A 673 
 PHE   0.014   0.002   PHE B 596 
 TRP   0.008   0.001   TRP B 688 
 HIS   0.003   0.000   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6219)
  covalent geometry    : angle       0.65987 ( 8469)
  hydrogen bonds       : bond        0.02864 (  123)
  hydrogen bonds       : angle       5.05297 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  328 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7258 (mmtm)
REVERT: A  498 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8374 (m-10)
REVERT: A  583 LYS cc_start: 0.8581 (mttt) cc_final: 0.8313 (tttp)
REVERT: A  703 MET cc_start: 0.8162 (mmm) cc_final: 0.7864 (mmm)
REVERT: B  493 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8235 (p)
REVERT: B  571 SER cc_start: 0.9084 (t) cc_final: 0.8609 (p)
REVERT: B  695 GLN cc_start: 0.6419 (mp10) cc_final: 0.6085 (pp30)
REVERT: C  387 ARG cc_start: 0.7682 (mtt90) cc_final: 0.7328 (mmt90)
REVERT: C  404 MET cc_start: 0.6310 (mmm) cc_final: 0.5987 (mpp)
  outliers start: 15
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0673
  time to fit residues: 9.6184
Evaluate side-chains
  111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  404 MET
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain C residue  409 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 21 optimal weight:    0.0970
   chunk 23 optimal weight:    0.8980
   chunk 12 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.193768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.142750 restraints weight = 7759.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.147890 restraints weight = 4559.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.151257 restraints weight = 3304.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.153447 restraints weight = 2699.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154659 restraints weight = 2375.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3929 r_free = 0.3929    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3929 r_free = 0.3929    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6219  Z= 0.126
  Angle     :  0.668  12.764   8469  Z= 0.328
  Chirality :  0.046   0.359    995
  Planarity :  0.005   0.080   1119
  Dihedral  :  4.230  19.985    870
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 10.48 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.81 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.28), residues: 811
  helix: -0.02 (0.49), residues: 134
  sheet: -0.35 (0.42), residues: 140
  loop : -2.39 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A 598 
 TYR   0.004   0.001   TYR A 347 
 PHE   0.014   0.001   PHE B 596 
 TRP   0.007   0.001   TRP B 688 
 HIS   0.003   0.000   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6219)
  covalent geometry    : angle       0.66786 ( 8469)
  hydrogen bonds       : bond        0.02752 (  123)
  hydrogen bonds       : angle       4.95187 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  328 LYS cc_start: 0.7512 (mmtt) cc_final: 0.7275 (mmtm)
REVERT: A  498 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8385 (m-10)
REVERT: A  583 LYS cc_start: 0.8550 (mttt) cc_final: 0.8274 (tttp)
REVERT: A  703 MET cc_start: 0.8123 (mmm) cc_final: 0.7825 (mmm)
REVERT: B  493 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8217 (p)
REVERT: B  571 SER cc_start: 0.9059 (t) cc_final: 0.8563 (p)
REVERT: B  695 GLN cc_start: 0.6418 (mp10) cc_final: 0.6166 (pp30)
REVERT: C  387 ARG cc_start: 0.7669 (mtt90) cc_final: 0.7320 (mmt90)
REVERT: C  404 MET cc_start: 0.6311 (mmm) cc_final: 0.5985 (mpp)
  outliers start: 16
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0581
  time to fit residues: 8.6920
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  404 MET
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain C residue  409 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 61 optimal weight:    0.1980
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 543 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.188577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.137700 restraints weight = 7859.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.142446 restraints weight = 4747.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.145633 restraints weight = 3501.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.147673 restraints weight = 2886.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.148873 restraints weight = 2559.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3856 r_free = 0.3856    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3856 r_free = 0.3856    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.4738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   6219  Z= 0.218
  Angle     :  0.761  13.460   8469  Z= 0.379
  Chirality :  0.049   0.356    995
  Planarity :  0.006   0.090   1119
  Dihedral  :  4.836  21.251    870
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 12.21 %
    Favored  : 87.18 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.97 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.27), residues: 811
  helix: -0.38 (0.48), residues: 132
  sheet: -0.59 (0.40), residues: 147
  loop : -2.60 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 598 
 TYR   0.008   0.001   TYR A 539 
 PHE   0.018   0.002   PHE A 609 
 TRP   0.010   0.002   TRP B 688 
 HIS   0.006   0.001   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 6219)
  covalent geometry    : angle       0.76132 ( 8469)
  hydrogen bonds       : bond        0.03730 (  123)
  hydrogen bonds       : angle       5.36190 (  345)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  498 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8551 (m-10)
REVERT: A  583 LYS cc_start: 0.8618 (mttt) cc_final: 0.8351 (tttp)
REVERT: A  703 MET cc_start: 0.8089 (mmm) cc_final: 0.7750 (mmm)
REVERT: B  493 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8224 (p)
REVERT: B  571 SER cc_start: 0.9085 (t) cc_final: 0.8634 (p)
REVERT: B  695 GLN cc_start: 0.6573 (mp10) cc_final: 0.6350 (pp30)
REVERT: C  387 ARG cc_start: 0.7712 (mtt90) cc_final: 0.7308 (mmt90)
REVERT: C  404 MET cc_start: 0.6455 (mmm) cc_final: 0.6105 (mpp)
  outliers start: 15
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0686
  time to fit residues: 9.4886
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ASP
Chi-restraints excluded: chain A residue  404 MET
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain A residue  456 ASP
Chi-restraints excluded: chain A residue  477 MET
Chi-restraints excluded: chain A residue  498 PHE
Chi-restraints excluded: chain A residue  529 THR
Chi-restraints excluded: chain A residue  543 ASN
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  701 MET
Chi-restraints excluded: chain C residue  409 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0670
   chunk 8 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 543 ASN
A 595 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.191486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.140669 restraints weight = 7770.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.145704 restraints weight = 4608.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.148971 restraints weight = 3356.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.151060 restraints weight = 2756.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.151980 restraints weight = 2436.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3888 r_free = 0.3888    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3888 r_free = 0.3888    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6219  Z= 0.131
  Angle     :  0.706  13.830   8469  Z= 0.349
  Chirality :  0.047   0.394    995
  Planarity :  0.005   0.054   1119
  Dihedral  :  4.560  21.577    870
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 10.73 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 22.12 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.39 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.47 (0.28), residues: 811
  helix: -0.16 (0.48), residues: 132
  sheet: -0.53 (0.41), residues: 141
  loop : -2.52 (0.24), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 598 
 TYR   0.005   0.001   TYR A 673 
 PHE   0.017   0.002   PHE B 596 
 TRP   0.009   0.001   TRP B 688 
 HIS   0.003   0.001   HIS A 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6219)
  covalent geometry    : angle       0.70648 ( 8469)
  hydrogen bonds       : bond        0.02961 (  123)
  hydrogen bonds       : angle       5.14808 (  345)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1052.43 seconds
wall clock time: 18 minutes 40.62 seconds (1120.62 seconds total)