Starting phenix.real_space_refine
on Tue Feb  3 22:57:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jh5_36254/02_2026/8jh5_36254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jh5_36254/02_2026/8jh5_36254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jh5_36254/02_2026/8jh5_36254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jh5_36254/02_2026/8jh5_36254.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jh5_36254/02_2026/8jh5_36254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jh5_36254/02_2026/8jh5_36254.map"
  }
  resolution = 3.7
  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=   0.003 sd=   0.079
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      56      5.16       5
     C    5070      2.51       5
     N    1266      2.21       5
     O    1342      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 7734
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 2957
          Classifications: {'peptide': 379}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 360}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 893
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 3, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'NPS': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 1.53, per 1000 atoms: 0.20
  Number of scatterers: 7734
  At special positions: 0
  Unit cell: (106.7, 121, 96.8, 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      56     16.00
     O    1342      8.00
     N    1266      7.00
     C    5070      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  26 " - pdb=" SG  CYS C 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D 100 " distance=2.03

  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: 0.51
  Conformation dependent library (CDL) restraints added in 182.0 milliseconds
  

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1840

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 8 sheets defined
      48.6% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 13
      removed outlier: 4.149A  pdb=" N   PHE A   7 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET A  11 " --> pdb=" O   PHE A   7 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA A  13 " --> pdb=" O   HIS A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 30
      removed outlier: 3.532A  pdb=" N   TYR A  18 " --> pdb=" O   MET A  14 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ALA A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   VAL A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS A  29 " --> pdb=" O   TYR A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 49
      removed outlier: 4.120A  pdb=" N   ILE A  42 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASN A  43 " --> pdb=" O   CYS A  39 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA A  47 " --> pdb=" O   ASN A  43 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A  48 " --> pdb=" O   ARG A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 60
      removed outlier: 3.597A  pdb=" N   LEU A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   HIS A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 90
      removed outlier: 4.010A  pdb=" N   LEU A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 116 through 123
      removed outlier: 3.505A  pdb=" N   LEU A 120 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 133
    Processing helix  chain 'A' and resid 133 through 141
      removed outlier: 3.764A  pdb=" N   VAL A 137 " --> pdb=" O   MET A 133 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 165
      removed outlier: 3.557A  pdb=" N   GLU A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU A 159 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 474
      removed outlier: 3.565A  pdb=" N   THR A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ARG A 463 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU A 466 " --> pdb=" O   THR A 462 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TRP A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   LYS A 472 " --> pdb=" O   MET A 468 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE A 474 " --> pdb=" O   TRP A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.929A  pdb=" N   PHE A 484 " --> pdb=" O   TYR A 480 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE A 486 " --> pdb=" O   SER A 482 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE A 493 " --> pdb=" O   SER A 489 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   LYS A 494 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TRP A 495 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 508
      removed outlier: 3.589A  pdb=" N   SER A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 529
      removed outlier: 3.556A  pdb=" N   MET A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A 524 " --> pdb=" O   PHE A 520 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA A 527 " --> pdb=" O   GLY A 523 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASN A 529 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 544
      removed outlier: 3.657A  pdb=" N   ALA A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 556
      removed outlier: 3.690A  pdb=" N   VAL A 554 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 575
    Processing helix  chain 'A' and resid 582 through 591
      removed outlier: 3.636A  pdb=" N   ALA A 588 " --> pdb=" O   PRO A 584 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU A 590 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 608
      removed outlier: 4.022A  pdb=" N   LEU A 598 " --> pdb=" O   HIS A 594 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE A 603 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A 607 " --> pdb=" O   ILE A 603 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 621
      removed outlier: 4.348A  pdb=" N   LEU A 615 " --> pdb=" O   PRO A 611 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY A 621 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 13
      removed outlier: 4.148A  pdb=" N   PHE B   7 " --> pdb=" O   THR B   3 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET B  11 " --> pdb=" O   PHE B   7 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ALA B  13 " --> pdb=" O   HIS B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 through 30
      removed outlier: 3.533A  pdb=" N   TYR B  18 " --> pdb=" O   MET B  14 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA B  20 " --> pdb=" O   PRO B  16 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ALA B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS B  29 " --> pdb=" O   TYR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 49
      removed outlier: 4.120A  pdb=" N   ILE B  42 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASN B  43 " --> pdb=" O   CYS B  39 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA B  47 " --> pdb=" O   ASN B  43 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU B  48 " --> pdb=" O   ARG B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 60
      removed outlier: 3.597A  pdb=" N   LEU B  53 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B  56 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   HIS B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 90
      removed outlier: 4.009A  pdb=" N   LEU B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 116 through 123
      removed outlier: 3.505A  pdb=" N   LEU B 120 " --> pdb=" O   MET B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 133
    Processing helix  chain 'B' and resid 133 through 141
      removed outlier: 3.764A  pdb=" N   VAL B 137 " --> pdb=" O   MET B 133 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 165
      removed outlier: 3.558A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU B 159 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ILE B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   GLN B 164 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 474
      removed outlier: 3.566A  pdb=" N   THR B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   ARG B 463 " --> pdb=" O   SER B 459 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   LEU B 466 " --> pdb=" O   THR B 462 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TRP B 470 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   LYS B 472 " --> pdb=" O   MET B 468 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 474 " --> pdb=" O   TRP B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 479
    Processing helix  chain 'B' and resid 480 through 496
      removed outlier: 3.929A  pdb=" N   PHE B 484 " --> pdb=" O   TYR B 480 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 486 " --> pdb=" O   SER B 482 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE B 493 " --> pdb=" O   SER B 489 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   LYS B 494 " --> pdb=" O   LEU B 490 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TRP B 495 " --> pdb=" O   ILE B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 508
      removed outlier: 3.589A  pdb=" N   SER B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 529
      removed outlier: 3.556A  pdb=" N   MET B 519 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 524 " --> pdb=" O   PHE B 520 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE B 525 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   MET B 526 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ALA B 527 " --> pdb=" O   GLY B 523 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU B 528 " --> pdb=" O   LEU B 524 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASN B 529 " --> pdb=" O   PHE B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 544
      removed outlier: 3.657A  pdb=" N   ALA B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 556
      removed outlier: 3.689A  pdb=" N   VAL B 554 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   MET B 555 " --> pdb=" O   GLY B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 575
    Processing helix  chain 'B' and resid 582 through 591
      removed outlier: 3.636A  pdb=" N   ALA B 588 " --> pdb=" O   PRO B 584 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU B 590 " --> pdb=" O   VAL B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 608
      removed outlier: 4.022A  pdb=" N   LEU B 598 " --> pdb=" O   HIS B 594 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE B 603 " --> pdb=" O   SER B 599 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU B 607 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE B 608 " --> pdb=" O   PHE B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 621
      removed outlier: 4.348A  pdb=" N   LEU B 615 " --> pdb=" O   PRO B 611 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B 621 " --> pdb=" O   TYR B 617 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 11
      removed outlier: 3.563A  pdb=" N   GLN C   7 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 16
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 56
      removed outlier: 6.623A  pdb=" N   TRP C  40 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   ALA C  54 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   MET C  38 " --> pdb=" O   ALA C  54 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TYR C  41 " --> pdb=" O   TYR C  99 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR C  99 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 11
      removed outlier: 3.563A  pdb=" N   GLN D   7 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 15 through 16
    Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 56
      removed outlier: 6.623A  pdb=" N   TRP D  40 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   ALA D  54 " --> pdb=" O   MET D  38 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   MET D  38 " --> pdb=" O   ALA D  54 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR D  41 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR D  99 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 109
      removed outlier: 6.534A  pdb=" N   TRP D 107 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)

    257 hydrogen bonds defined for protein.
    750 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: 0.95

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1178
        1.30 -     1.43: 2126
        1.43 -     1.55: 4515
        1.55 -     1.68: 3
        1.68 -     1.81: 100
  Bond restraints: 7922
  Sorted by residual:
  bond pdb=" CA  ASN A 112 "
       pdb=" C   ASN A 112 "
    ideal  model  delta    sigma   weight residual
    1.526  1.438  0.087 1.30e-02 5.92e+03 4.52e+01
  bond pdb=" CA  ASN B 112 "
       pdb=" C   ASN B 112 "
    ideal  model  delta    sigma   weight residual
    1.526  1.438  0.087 1.30e-02 5.92e+03 4.52e+01
  bond pdb=" CA  PHE A 585 "
       pdb=" C   PHE A 585 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.082 1.37e-02 5.33e+03 3.55e+01
  bond pdb=" CA  PHE B 585 "
       pdb=" C   PHE B 585 "
    ideal  model  delta    sigma   weight residual
    1.524  1.443  0.081 1.37e-02 5.33e+03 3.46e+01
  bond pdb=" C   PHE B 585 "
       pdb=" O   PHE B 585 "
    ideal  model  delta    sigma   weight residual
    1.236  1.168  0.068 1.28e-02 6.10e+03 2.82e+01
  ... (remaining 7917 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.60: 10722
        4.60 -     9.21: 44
        9.21 -    13.81: 2
       13.81 -    18.41: 0
       18.41 -    23.02: 4
  Bond angle restraints: 10772
  Sorted by residual:
  angle pdb=" O   NPS A 701 "
        pdb=" C15 NPS A 701 "
        pdb=" OXT NPS A 701 "
      ideal   model   delta    sigma   weight residual
     126.82  103.80   23.02 3.00e+00 1.11e-01 5.89e+01
  angle pdb=" O   NPS B 701 "
        pdb=" C15 NPS B 701 "
        pdb=" OXT NPS B 701 "
      ideal   model   delta    sigma   weight residual
     126.82  103.82   23.00 3.00e+00 1.11e-01 5.88e+01
  angle pdb=" O   NPS B 701 "
        pdb=" C15 NPS B 701 "
        pdb=" C14 NPS B 701 "
      ideal   model   delta    sigma   weight residual
     116.41  138.94  -22.53 3.00e+00 1.11e-01 5.64e+01
  angle pdb=" O   NPS A 701 "
        pdb=" C15 NPS A 701 "
        pdb=" C14 NPS A 701 "
      ideal   model   delta    sigma   weight residual
     116.41  138.92  -22.51 3.00e+00 1.11e-01 5.63e+01
  angle pdb=" N   PHE A 585 "
        pdb=" CA  PHE A 585 "
        pdb=" C   PHE A 585 "
      ideal   model   delta    sigma   weight residual
     112.45  104.66    7.79 1.39e+00 5.18e-01 3.14e+01
  ... (remaining 10767 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.88: 4440
       14.88 -    29.76: 147
       29.76 -    44.64: 71
       44.64 -    59.51: 6
       59.51 -    74.39: 2
  Dihedral angle restraints: 4666
    sinusoidal: 1806
      harmonic: 2860
  Sorted by residual:
  dihedral pdb=" CA  ILE D  35 "
           pdb=" C   ILE D  35 "
           pdb=" N   THR D  36 "
           pdb=" CA  THR D  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.45  -38.55     0      5.00e+00 4.00e-02 5.95e+01
  dihedral pdb=" CA  ILE C  35 "
           pdb=" C   ILE C  35 "
           pdb=" N   THR C  36 "
           pdb=" CA  THR C  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.46  -38.54     0      5.00e+00 4.00e-02 5.94e+01
  dihedral pdb=" C   ASN B 112 "
           pdb=" N   ASN B 112 "
           pdb=" CA  ASN B 112 "
           pdb=" CB  ASN B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.35  -10.25     0      2.50e+00 1.60e-01 1.68e+01
  ... (remaining 4663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 614
       0.035 -    0.070: 446
       0.070 -    0.106: 123
       0.106 -    0.141: 43
       0.141 -    0.176: 20
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CB  VAL B 557 "
            pdb=" CA  VAL B 557 "
            pdb=" CG1 VAL B 557 "
            pdb=" CG2 VAL B 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CB  VAL A 557 "
            pdb=" CA  VAL A 557 "
            pdb=" CG1 VAL A 557 "
            pdb=" CG2 VAL A 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.17 2.00e-01 2.50e+01 7.63e-01
  chirality pdb=" CB  VAL D   6 "
            pdb=" CA  VAL D   6 "
            pdb=" CG1 VAL D   6 "
            pdb=" CG2 VAL D   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.17 2.00e-01 2.50e+01 7.62e-01
  ... (remaining 1243 not shown)

  Planarity restraints: 1320
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 584 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.94e+00
        pdb=" C   PRO B 584 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   PRO B 584 "    0.017 2.00e-02 2.50e+03
        pdb=" N   PHE B 585 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 584 "   -0.014 2.00e-02 2.50e+03   2.82e-02 7.93e+00
        pdb=" C   PRO A 584 "    0.049 2.00e-02 2.50e+03
        pdb=" O   PRO A 584 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PHE A 585 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 551 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO B 552 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 552 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 552 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1317 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2388
        2.84 -     3.35: 6505
        3.35 -     3.87: 11808
        3.87 -     4.38: 13316
        4.38 -     4.90: 23069
  Nonbonded interactions: 57086
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 547 "
            pdb=" O   ALA A 576 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" NH2 ARG B 547 "
            pdb=" O   ALA B 576 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" NH2 ARG D 101 "
            pdb=" OE2 GLU B 191 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" ND2 ASN B  43 "
            pdb=" OG  SER B 521 "
     model   vdw
     2.371 3.120
  nonbonded pdb=" ND2 ASN A  43 "
            pdb=" OG  SER A 521 "
     model   vdw
     2.371 3.120
  ... (remaining 57081 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.330
  Find NCS groups from input model:        0.040
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
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      :  0.006   0.090   7924  Z= 0.323
  Angle     :  0.965  23.015  10776  Z= 0.481
  Chirality :  0.053   0.176   1246
  Planarity :  0.007   0.053   1320
  Dihedral  :  9.929  74.392   2820
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -5.76 (0.20), residues: 976
  helix: -4.77 (0.08), residues: 512
  sheet: -1.41 (0.42), residues: 166
  loop : -2.85 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 547 
 TYR   0.022   0.002   TYR C  56 
 PHE   0.022   0.002   PHE B 585 
 TRP   0.030   0.002   TRP C  37 
 HIS   0.004   0.001   HIS A   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 ( 7922)
  covalent geometry    : angle       0.96470 (10772)
  SS BOND              : bond        0.00078 (    2)
  SS BOND              : angle       0.47807 (    4)
  hydrogen bonds       : bond        0.33194 (  257)
  hydrogen bonds       : angle      10.43112 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8810 (t0) cc_final: 0.8566 (t0)
REVERT: A  196 ILE cc_start: 0.8605 (mt) cc_final: 0.8128 (mt)
REVERT: A  468 MET cc_start: 0.8521 (mmm) cc_final: 0.8304 (mmm)
REVERT: A  499 MET cc_start: 0.8561 (ttp) cc_final: 0.8353 (ttp)
REVERT: A  519 MET cc_start: 0.8565 (mmt) cc_final: 0.8362 (mmm)
REVERT: A  538 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7327 (tmt170)
REVERT: A  575 GLN cc_start: 0.8996 (pp30) cc_final: 0.8721 (pp30)
REVERT: A  615 LEU cc_start: 0.8924 (tp) cc_final: 0.8673 (tp)
REVERT: C   51 TRP cc_start: 0.7421 (m-10) cc_final: 0.7027 (m100)
REVERT: C   76 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6817 (ttp-110)
REVERT: D   42 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8425 (ptm160)
REVERT: D   76 ARG cc_start: 0.7232 (ttp-170) cc_final: 0.6552 (ttp-170)
REVERT: B   62 ASN cc_start: 0.8811 (t0) cc_final: 0.8568 (t0)
REVERT: B  196 ILE cc_start: 0.8627 (mt) cc_final: 0.8157 (mt)
REVERT: B  468 MET cc_start: 0.8522 (mmm) cc_final: 0.8290 (mmm)
REVERT: B  499 MET cc_start: 0.8558 (ttp) cc_final: 0.8352 (ttp)
REVERT: B  519 MET cc_start: 0.8553 (mmt) cc_final: 0.8293 (mmm)
REVERT: B  615 LEU cc_start: 0.8936 (tp) cc_final: 0.8690 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.0890
  time to fit residues: 26.0034
Evaluate side-chains
  156 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:   40.0000
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:   50.0000
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A   9 HIS
A  43 ASN
A 570 HIS
C   7 GLN
B   9 HIS
B  43 ASN
B 127 ASN
B 570 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.148812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.100607 restraints weight = 12473.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.103721 restraints weight = 6551.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.105758 restraints weight = 4398.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.106971 restraints weight = 3459.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.107717 restraints weight = 3009.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7924  Z= 0.185
  Angle     :  0.657   6.400  10776  Z= 0.340
  Chirality :  0.044   0.120   1246
  Planarity :  0.006   0.045   1320
  Dihedral  :  5.535  33.860   1084
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 10.99 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -4.45 (0.22), residues: 976
  helix: -3.39 (0.15), residues: 488
  sheet: -0.89 (0.43), residues: 166
  loop : -2.98 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 463 
 TYR   0.025   0.001   TYR C  56 
 PHE   0.026   0.002   PHE A 128 
 TRP   0.016   0.001   TRP B 144 
 HIS   0.004   0.001   HIS A   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 7922)
  covalent geometry    : angle       0.65477 (10772)
  SS BOND              : bond        0.01153 (    2)
  SS BOND              : angle       2.57720 (    4)
  hydrogen bonds       : bond        0.04999 (  257)
  hydrogen bonds       : angle       5.76100 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 ILE cc_start: 0.8473 (mt) cc_final: 0.8117 (mt)
REVERT: A  468 MET cc_start: 0.8814 (mmm) cc_final: 0.8412 (mmm)
REVERT: A  499 MET cc_start: 0.8531 (ttp) cc_final: 0.8326 (ttp)
REVERT: A  519 MET cc_start: 0.8730 (mmt) cc_final: 0.8522 (mmm)
REVERT: A  538 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7351 (tmt170)
REVERT: C   51 TRP cc_start: 0.7321 (m-10) cc_final: 0.6941 (m100)
REVERT: C   76 ARG cc_start: 0.7272 (ttp-170) cc_final: 0.6568 (ttm110)
REVERT: D   42 ARG cc_start: 0.8657 (ptp-110) cc_final: 0.8363 (ptp-110)
REVERT: D   76 ARG cc_start: 0.7250 (ttp-170) cc_final: 0.6357 (ttp-170)
REVERT: D   87 MET cc_start: 0.8427 (mtp) cc_final: 0.8198 (mtt)
REVERT: B  195 GLU cc_start: 0.7270 (tp30) cc_final: 0.7049 (tm-30)
REVERT: B  196 ILE cc_start: 0.8522 (mt) cc_final: 0.8045 (mt)
REVERT: B  468 MET cc_start: 0.8818 (mmm) cc_final: 0.8409 (mmm)
REVERT: B  538 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7240 (tmt170)
REVERT: B  604 PHE cc_start: 0.8632 (t80) cc_final: 0.8384 (t80)
  outliers start: 30
  outliers final: 21
  residues processed: 204
  average time/residue: 0.0652
  time to fit residues: 18.0506
Evaluate side-chains
  173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue  127 ASN
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  562 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 85 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 95 optimal weight:    0.0980
   chunk 79 optimal weight:    0.9990
   chunk 50 optimal weight:   20.0000
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.151677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.104673 restraints weight = 12197.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.107771 restraints weight = 6384.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.109691 restraints weight = 4257.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.111146 restraints weight = 3340.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.111849 restraints weight = 2873.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7924  Z= 0.115
  Angle     :  0.591   7.467  10776  Z= 0.296
  Chirality :  0.042   0.164   1246
  Planarity :  0.005   0.034   1320
  Dihedral  :  5.087  32.064   1084
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.80 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.31 (0.23), residues: 976
  helix: -2.28 (0.19), residues: 496
  sheet:  0.65 (0.52), residues: 104
  loop : -2.77 (0.28), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  71 
 TYR   0.023   0.001   TYR C  56 
 PHE   0.020   0.001   PHE A 128 
 TRP   0.011   0.001   TRP C  37 
 HIS   0.002   0.000   HIS B 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7922)
  covalent geometry    : angle       0.59005 (10772)
  SS BOND              : bond        0.00337 (    2)
  SS BOND              : angle       1.33842 (    4)
  hydrogen bonds       : bond        0.04003 (  257)
  hydrogen bonds       : angle       5.08749 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8716 (p)
REVERT: A  468 MET cc_start: 0.8783 (mmm) cc_final: 0.8240 (mmm)
REVERT: A  538 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7283 (tmt170)
REVERT: A  610 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8593 (mp)
REVERT: A  616 TYR cc_start: 0.8397 (m-80) cc_final: 0.8081 (m-80)
REVERT: C   51 TRP cc_start: 0.7386 (m-10) cc_final: 0.6918 (m-90)
REVERT: C   76 ARG cc_start: 0.6819 (ttp-170) cc_final: 0.6482 (ttm170)
REVERT: D   76 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.5975 (ttp-110)
REVERT: B  168 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8707 (p)
REVERT: B  196 ILE cc_start: 0.8569 (mt) cc_final: 0.8071 (mt)
REVERT: B  468 MET cc_start: 0.8802 (mmm) cc_final: 0.8317 (mmm)
REVERT: B  616 TYR cc_start: 0.8229 (m-80) cc_final: 0.7772 (m-80)
  outliers start: 27
  outliers final: 14
  residues processed: 169
  average time/residue: 0.0738
  time to fit residues: 16.7979
Evaluate side-chains
  164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  610 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 67 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.151166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.106025 restraints weight = 12317.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.109075 restraints weight = 6387.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.110143 restraints weight = 4007.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.110071 restraints weight = 3300.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.110316 restraints weight = 3318.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7924  Z= 0.130
  Angle     :  0.577   8.214  10776  Z= 0.287
  Chirality :  0.042   0.134   1246
  Planarity :  0.004   0.034   1320
  Dihedral  :  4.898  31.030   1084
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.41 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.54 (0.25), residues: 976
  helix: -1.58 (0.21), residues: 494
  sheet:  0.88 (0.53), residues: 100
  loop : -2.43 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  71 
 TYR   0.024   0.001   TYR C  56 
 PHE   0.018   0.001   PHE A 128 
 TRP   0.008   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7922)
  covalent geometry    : angle       0.57687 (10772)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       1.14786 (    4)
  hydrogen bonds       : bond        0.03733 (  257)
  hydrogen bonds       : angle       4.84618 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8712 (p)
REVERT: A  195 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6895 (tm-30)
REVERT: A  468 MET cc_start: 0.8818 (mmm) cc_final: 0.8581 (mmm)
REVERT: A  538 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7297 (tmt170)
REVERT: C   51 TRP cc_start: 0.7142 (m-10) cc_final: 0.6721 (m-90)
REVERT: D   22 LEU cc_start: 0.8370 (tt) cc_final: 0.7872 (mt)
REVERT: B  168 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8716 (p)
REVERT: B  195 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6462 (tm-30)
REVERT: B  196 ILE cc_start: 0.8266 (mt) cc_final: 0.8021 (mt)
REVERT: B  468 MET cc_start: 0.8828 (mmm) cc_final: 0.8582 (mmm)
REVERT: B  517 MET cc_start: 0.7914 (mmm) cc_final: 0.7521 (ttm)
REVERT: B  616 TYR cc_start: 0.8363 (m-80) cc_final: 0.8078 (m-80)
  outliers start: 25
  outliers final: 18
  residues processed: 172
  average time/residue: 0.0695
  time to fit residues: 16.3774
Evaluate side-chains
  166 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 49 optimal weight:   30.0000
   chunk 54 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.150137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.106949 restraints weight = 12279.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.107237 restraints weight = 7681.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.107377 restraints weight = 5667.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.108342 restraints weight = 4937.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.108722 restraints weight = 4169.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7924  Z= 0.154
  Angle     :  0.590   7.335  10776  Z= 0.293
  Chirality :  0.043   0.148   1246
  Planarity :  0.004   0.032   1320
  Dihedral  :  4.839  30.194   1084
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 13.41 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -2.09 (0.25), residues: 976
  helix: -1.19 (0.22), residues: 490
  sheet:  1.11 (0.54), residues: 100
  loop : -2.25 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  71 
 TYR   0.026   0.001   TYR C  56 
 PHE   0.021   0.001   PHE C  72 
 TRP   0.007   0.001   TRP D  40 
 HIS   0.002   0.001   HIS B 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7922)
  covalent geometry    : angle       0.58950 (10772)
  SS BOND              : bond        0.00174 (    2)
  SS BOND              : angle       0.97626 (    4)
  hydrogen bonds       : bond        0.03803 (  257)
  hydrogen bonds       : angle       4.82445 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8687 (p)
REVERT: A  195 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6976 (tm-30)
REVERT: A  468 MET cc_start: 0.8876 (mmm) cc_final: 0.8657 (mmm)
REVERT: A  538 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7298 (tmt170)
REVERT: C   51 TRP cc_start: 0.7212 (m-10) cc_final: 0.6790 (m-90)
REVERT: D   22 LEU cc_start: 0.8267 (tt) cc_final: 0.7786 (mt)
REVERT: D   76 ARG cc_start: 0.7286 (ttp-170) cc_final: 0.6838 (ttm170)
REVERT: B  168 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8688 (p)
REVERT: B  195 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6453 (tm-30)
REVERT: B  196 ILE cc_start: 0.8279 (mt) cc_final: 0.8000 (mt)
REVERT: B  468 MET cc_start: 0.8844 (mmm) cc_final: 0.8632 (mmm)
REVERT: B  517 MET cc_start: 0.7929 (mmm) cc_final: 0.7463 (ttm)
  outliers start: 33
  outliers final: 24
  residues processed: 173
  average time/residue: 0.0622
  time to fit residues: 14.6861
Evaluate side-chains
  169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 68 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 188 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.153455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.109865 restraints weight = 12316.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.110041 restraints weight = 7018.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.111381 restraints weight = 5151.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.111995 restraints weight = 4392.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.112328 restraints weight = 3786.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7924  Z= 0.094
  Angle     :  0.545   7.437  10776  Z= 0.268
  Chirality :  0.041   0.162   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.484  29.462   1084
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.34 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.27), residues: 976
  helix: -0.68 (0.23), residues: 496
  sheet: -0.03 (0.46), residues: 140
  loop : -2.00 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  71 
 TYR   0.026   0.001   TYR C  56 
 PHE   0.018   0.001   PHE C  72 
 TRP   0.006   0.001   TRP B 144 
 HIS   0.001   0.000   HIS B 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 7922)
  covalent geometry    : angle       0.54516 (10772)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       0.82131 (    4)
  hydrogen bonds       : bond        0.02898 (  257)
  hydrogen bonds       : angle       4.45620 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8518 (p)
REVERT: A  195 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: A  538 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7273 (tmt170)
REVERT: A  555 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7176 (tpp)
REVERT: C   41 TYR cc_start: 0.8133 (p90) cc_final: 0.7859 (p90)
REVERT: C   51 TRP cc_start: 0.6951 (m-10) cc_final: 0.6616 (m-90)
REVERT: B   25 TYR cc_start: 0.9107 (t80) cc_final: 0.8900 (t80)
REVERT: B  168 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8517 (p)
REVERT: B  195 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6414 (tm-30)
REVERT: B  538 ARG cc_start: 0.7192 (tmt170) cc_final: 0.5757 (tmt170)
REVERT: B  555 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7173 (tpp)
  outliers start: 20
  outliers final: 15
  residues processed: 162
  average time/residue: 0.0708
  time to fit residues: 15.6546
Evaluate side-chains
  158 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  555 MET
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0470
   chunk 43 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0470
   chunk 68 optimal weight:    0.0000
   chunk 91 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.3180

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.152791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.107584 restraints weight = 12349.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.109776 restraints weight = 6870.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.111357 restraints weight = 4193.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.111814 restraints weight = 3479.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.111603 restraints weight = 3268.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.4285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7924  Z= 0.084
  Angle     :  0.541   7.874  10776  Z= 0.263
  Chirality :  0.041   0.154   1246
  Planarity :  0.004   0.030   1320
  Dihedral  :  4.302  28.850   1084
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.82 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.27), residues: 976
  helix: -0.13 (0.24), residues: 488
  sheet:  0.14 (0.46), residues: 140
  loop : -1.70 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  71 
 TYR   0.024   0.001   TYR C  56 
 PHE   0.017   0.001   PHE C  72 
 TRP   0.009   0.001   TRP C  37 
 HIS   0.001   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 7922)
  covalent geometry    : angle       0.54116 (10772)
  SS BOND              : bond        0.00236 (    2)
  SS BOND              : angle       0.69718 (    4)
  hydrogen bonds       : bond        0.02610 (  257)
  hydrogen bonds       : angle       4.28326 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8463 (p)
REVERT: A  195 GLU cc_start: 0.7245 (tm-30) cc_final: 0.7000 (tm-30)
REVERT: A  538 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7290 (tmt170)
REVERT: A  555 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7056 (tpp)
REVERT: C   41 TYR cc_start: 0.7988 (p90) cc_final: 0.7773 (p90)
REVERT: C   51 TRP cc_start: 0.6860 (m-10) cc_final: 0.6602 (m-90)
REVERT: C   85 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8311 (tp)
REVERT: B  168 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8432 (p)
REVERT: B  538 ARG cc_start: 0.7182 (tmt170) cc_final: 0.5749 (tmt170)
REVERT: B  555 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7072 (tpp)
REVERT: B  615 LEU cc_start: 0.8587 (tt) cc_final: 0.7357 (mp)
  outliers start: 25
  outliers final: 16
  residues processed: 162
  average time/residue: 0.0692
  time to fit residues: 15.0265
Evaluate side-chains
  159 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   84 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  555 MET
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 17 optimal weight:    2.9990
   chunk 91 optimal weight:    0.4980
   chunk 42 optimal weight:   10.0000
   chunk 35 optimal weight:    0.7980
   chunk 90 optimal weight:    0.4980
   chunk 64 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.152613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.106323 restraints weight = 12310.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.109365 restraints weight = 6561.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.110877 restraints weight = 4074.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.110730 restraints weight = 3365.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.110906 restraints weight = 3406.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7924  Z= 0.094
  Angle     :  0.564   8.607  10776  Z= 0.270
  Chirality :  0.042   0.178   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.287  28.573   1084
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.30 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.28), residues: 976
  helix:  0.14 (0.24), residues: 488
  sheet:  0.29 (0.47), residues: 140
  loop : -1.62 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.025   0.001   TYR C  56 
 PHE   0.015   0.001   PHE C  72 
 TRP   0.008   0.001   TRP D  37 
 HIS   0.001   0.000   HIS B 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7922)
  covalent geometry    : angle       0.56397 (10772)
  SS BOND              : bond        0.00271 (    2)
  SS BOND              : angle       0.74905 (    4)
  hydrogen bonds       : bond        0.02805 (  257)
  hydrogen bonds       : angle       4.24352 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8467 (p)
REVERT: A  195 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6973 (tm-30)
REVERT: A  196 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8640 (mp)
REVERT: A  538 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7252 (tmt170)
REVERT: A  555 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7039 (tpp)
REVERT: C   41 TYR cc_start: 0.7958 (p90) cc_final: 0.7706 (p90)
REVERT: C   51 TRP cc_start: 0.6754 (m-10) cc_final: 0.6445 (m-90)
REVERT: C   85 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8547 (tp)
REVERT: D   41 TYR cc_start: 0.7306 (p90) cc_final: 0.6135 (p90)
REVERT: D   71 ARG cc_start: 0.5298 (ttp-110) cc_final: 0.4995 (ttp-170)
REVERT: B  168 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8388 (p)
REVERT: B  538 ARG cc_start: 0.7202 (tmt170) cc_final: 0.5739 (tmt170)
REVERT: B  555 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7091 (tpp)
REVERT: B  615 LEU cc_start: 0.8582 (tt) cc_final: 0.7375 (mp)
  outliers start: 24
  outliers final: 14
  residues processed: 154
  average time/residue: 0.0631
  time to fit residues: 13.4633
Evaluate side-chains
  159 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  555 MET
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0970
   chunk 83 optimal weight:    3.9990
   chunk 63 optimal weight:    0.2980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.152560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.106444 restraints weight = 12204.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.109040 restraints weight = 7238.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.110288 restraints weight = 4362.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110653 restraints weight = 3636.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110655 restraints weight = 3259.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7924  Z= 0.095
  Angle     :  0.572   9.413  10776  Z= 0.272
  Chirality :  0.042   0.172   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.297  29.773   1084
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.79 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.28), residues: 976
  helix:  0.35 (0.25), residues: 486
  sheet:  0.38 (0.48), residues: 140
  loop : -1.53 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.024   0.001   TYR C  56 
 PHE   0.017   0.001   PHE C  72 
 TRP   0.010   0.001   TRP C  37 
 HIS   0.001   0.000   HIS A 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 7922)
  covalent geometry    : angle       0.57208 (10772)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.69093 (    4)
  hydrogen bonds       : bond        0.02782 (  257)
  hydrogen bonds       : angle       4.20571 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8398 (p)
REVERT: A  196 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8660 (mp)
REVERT: A  538 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7263 (tmt170)
REVERT: C   41 TYR cc_start: 0.7930 (p90) cc_final: 0.7710 (p90)
REVERT: C   51 TRP cc_start: 0.6665 (m-10) cc_final: 0.6444 (m-90)
REVERT: C   87 MET cc_start: 0.8667 (mmp) cc_final: 0.8032 (mmp)
REVERT: D   41 TYR cc_start: 0.7299 (p90) cc_final: 0.6335 (p90)
REVERT: D   71 ARG cc_start: 0.5273 (ttp-110) cc_final: 0.5063 (ttp-170)
REVERT: B  168 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8394 (p)
REVERT: B  538 ARG cc_start: 0.7298 (tmt170) cc_final: 0.5759 (tmt170)
REVERT: B  555 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7001 (tpp)
REVERT: B  615 LEU cc_start: 0.8570 (tt) cc_final: 0.7359 (mp)
  outliers start: 23
  outliers final: 17
  residues processed: 158
  average time/residue: 0.0647
  time to fit residues: 14.0595
Evaluate side-chains
  160 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  555 MET
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 59 optimal weight:    0.0670
   chunk 95 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.1122

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.149703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.103815 restraints weight = 12322.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.107072 restraints weight = 6455.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108314 restraints weight = 4038.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108249 restraints weight = 3312.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.108489 restraints weight = 3375.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.4515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7924  Z= 0.137
  Angle     :  0.607   9.801  10776  Z= 0.291
  Chirality :  0.044   0.146   1246
  Planarity :  0.004   0.032   1320
  Dihedral  :  4.442  29.586   1084
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.27 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.28), residues: 976
  helix:  0.27 (0.24), residues: 492
  sheet:  0.46 (0.48), residues: 140
  loop : -1.66 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  71 
 TYR   0.026   0.001   TYR C  56 
 PHE   0.017   0.001   PHE C  72 
 TRP   0.010   0.001   TRP A 144 
 HIS   0.001   0.000   HIS A 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7922)
  covalent geometry    : angle       0.60663 (10772)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       0.63738 (    4)
  hydrogen bonds       : bond        0.03386 (  257)
  hydrogen bonds       : angle       4.33366 (  750)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8522 (p)
REVERT: A  196 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8729 (mp)
REVERT: A  538 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7255 (tmt170)
REVERT: A  555 MET cc_start: 0.8165 (tpp) cc_final: 0.7112 (tpp)
REVERT: D   41 TYR cc_start: 0.7357 (p90) cc_final: 0.6399 (p90)
REVERT: B  168 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8515 (p)
REVERT: B  195 GLU cc_start: 0.6470 (tm-30) cc_final: 0.6165 (tm-30)
REVERT: B  538 ARG cc_start: 0.7373 (tmt170) cc_final: 0.5851 (tmt170)
REVERT: B  555 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7154 (tpp)
REVERT: B  615 LEU cc_start: 0.8576 (tt) cc_final: 0.7350 (mp)
  outliers start: 23
  outliers final: 16
  residues processed: 159
  average time/residue: 0.0649
  time to fit residues: 14.0336
Evaluate side-chains
  152 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   49 ARG
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  555 MET
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0670
   chunk 92 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.7518

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.152069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.106510 restraints weight = 12125.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.109450 restraints weight = 6610.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.110865 restraints weight = 4044.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.110971 restraints weight = 3211.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.111256 restraints weight = 3192.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.4646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7924  Z= 0.110
  Angle     :  0.603   9.038  10776  Z= 0.288
  Chirality :  0.043   0.167   1246
  Planarity :  0.004   0.032   1320
  Dihedral  :  4.343  30.164   1084
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.03 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.34 (0.28), residues: 976
  helix:  0.44 (0.25), residues: 488
  sheet:  0.54 (0.48), residues: 140
  loop : -1.43 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.025   0.001   TYR C  56 
 PHE   0.017   0.001   PHE C  72 
 TRP   0.010   0.001   TRP D  37 
 HIS   0.001   0.000   HIS B 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7922)
  covalent geometry    : angle       0.60342 (10772)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       0.68183 (    4)
  hydrogen bonds       : bond        0.03197 (  257)
  hydrogen bonds       : angle       4.22543 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1075.53 seconds
wall clock time: 19 minutes 9.62 seconds (1149.62 seconds total)