Starting phenix.real_space_refine
on Fri Aug 22 20:31:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jh5_36254/08_2025/8jh5_36254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jh5_36254/08_2025/8jh5_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jh5_36254/08_2025/8jh5_36254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jh5_36254/08_2025/8jh5_36254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jh5_36254/08_2025/8jh5_36254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jh5_36254/08_2025/8jh5_36254.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 1.86, per 1000 atoms: 0.24
  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: 0.76
  Conformation dependent library (CDL) restraints added in 586.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.27
  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: 0.96

  Time building geometry restraints manager: 1.07 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:             1.570
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.560
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.630
-------------------------------------------------------------------------------
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 aren 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  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8810 (t0) cc_final: 0.8567 (t0)
REVERT: A  196 ILE cc_start: 0.8605 (mt) cc_final: 0.8127 (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  599 SER cc_start: 0.9165 (p) cc_final: 0.8964 (p)
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: 0.7233 (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: 0.8523 (mmm) cc_final: 0.8291 (mmm)
REVERT: B  499 MET cc_start: 0.8558 (ttp) cc_final: 0.8352 (ttp)
REVERT: B  519 MET cc_start: 0.8552 (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: 0.1010
  time to fit residues: 29.6828
Evaluate side-chains
  157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.149283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.102269 restraints weight = 12475.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.105432 restraints weight = 6567.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.107451 restraints weight = 4376.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.108805 restraints weight = 3422.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.109496 restraints weight = 2956.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7924  Z= 0.183
  Angle     :  0.655   6.439  10776  Z= 0.339
  Chirality :  0.044   0.118   1246
  Planarity :  0.006   0.044   1320
  Dihedral  :  5.577  34.131   1084
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 10.39 %
    Favored  : 85.99 %
  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 aren not related in a simple way.
  whole: -4.50 (0.22), residues: 976
  helix: -3.42 (0.15), residues: 490
  sheet: -0.85 (0.44), residues: 158
  loop : -3.03 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 463 
 TYR   0.027   0.001   TYR C  56 
 PHE   0.026   0.002   PHE A 128 
 TRP   0.015   0.001   TRP B 144 
 HIS   0.004   0.001   HIS A   9 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 7922)
  covalent geometry    : angle       0.65390 (10772)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       2.29034 (    4)
  hydrogen bonds       : bond        0.05618 (  257)
  hydrogen bonds       : angle       5.85957 (  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
  213 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 183
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8751 (t0) cc_final: 0.8549 (t0)
REVERT: A  196 ILE cc_start: 0.8474 (mt) cc_final: 0.8193 (mt)
REVERT: A  468 MET cc_start: 0.8748 (mmm) cc_final: 0.8403 (mmm)
REVERT: A  538 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7339 (tmt170)
REVERT: C   51 TRP cc_start: 0.7412 (m-10) cc_final: 0.7038 (m100)
REVERT: C   76 ARG cc_start: 0.7206 (ttp-170) cc_final: 0.6518 (ttm110)
REVERT: D   42 ARG cc_start: 0.8665 (ptp-110) cc_final: 0.8350 (ptp-110)
REVERT: D   87 MET cc_start: 0.8394 (mtp) cc_final: 0.8126 (mtt)
REVERT: B   62 ASN cc_start: 0.8754 (t0) cc_final: 0.8550 (t0)
REVERT: B  195 GLU cc_start: 0.7307 (tp30) cc_final: 0.7085 (tm-30)
REVERT: B  196 ILE cc_start: 0.8523 (mt) cc_final: 0.8035 (mt)
REVERT: B  468 MET cc_start: 0.8775 (mmm) cc_final: 0.8395 (mmm)
REVERT: B  538 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7249 (tmt170)
  outliers start: 30
  outliers final: 21
  residues processed: 203
  average time/residue: 0.0811
  time to fit residues: 22.5217
Evaluate side-chains
  171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 50 optimal weight:   20.0000
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.149831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.103642 restraints weight = 12343.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.106202 restraints weight = 6263.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.106807 restraints weight = 4518.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.107451 restraints weight = 3730.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.107748 restraints weight = 3759.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7924  Z= 0.150
  Angle     :  0.616   7.309  10776  Z= 0.309
  Chirality :  0.043   0.143   1246
  Planarity :  0.005   0.038   1320
  Dihedral  :  5.244  32.723   1084
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 11.71 %
    Favored  : 84.18 %
  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 aren not related in a simple way.
  whole: -3.52 (0.23), residues: 976
  helix: -2.37 (0.18), residues: 500
  sheet: -0.53 (0.44), residues: 146
  loop : -2.85 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  71 
 TYR   0.023   0.001   TYR C  56 
 PHE   0.021   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        0.00355 ( 7922)
  covalent geometry    : angle       0.61499 (10772)
  SS BOND              : bond        0.00165 (    2)
  SS BOND              : angle       1.47256 (    4)
  hydrogen bonds       : bond        0.04405 (  257)
  hydrogen bonds       : angle       5.20153 (  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
  187 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8755 (p)
REVERT: A  195 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6471 (tm-30)
REVERT: A  196 ILE cc_start: 0.8243 (mt) cc_final: 0.7703 (mt)
REVERT: A  468 MET cc_start: 0.8823 (mmm) cc_final: 0.8223 (mmm)
REVERT: A  517 MET cc_start: 0.7880 (mmm) cc_final: 0.7457 (ttm)
REVERT: A  538 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7297 (tmt170)
REVERT: A  610 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8601 (mp)
REVERT: A  616 TYR cc_start: 0.8308 (m-80) cc_final: 0.7885 (m-80)
REVERT: C   51 TRP cc_start: 0.7196 (m-10) cc_final: 0.6726 (m-90)
REVERT: C   76 ARG cc_start: 0.7123 (ttp-170) cc_final: 0.6717 (ttm170)
REVERT: D   41 TYR cc_start: 0.7735 (p90) cc_final: 0.6694 (p90)
REVERT: D   42 ARG cc_start: 0.8600 (ptp-110) cc_final: 0.8180 (ptp-110)
REVERT: B  168 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8759 (p)
REVERT: B  196 ILE cc_start: 0.8508 (mt) cc_final: 0.8008 (mt)
REVERT: B  468 MET cc_start: 0.8822 (mmm) cc_final: 0.8271 (mmm)
REVERT: B  517 MET cc_start: 0.7904 (mmm) cc_final: 0.7497 (ttm)
REVERT: B  538 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7241 (tmt170)
REVERT: B  610 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8590 (mp)
REVERT: B  616 TYR cc_start: 0.8278 (m-80) cc_final: 0.7830 (m-80)
  outliers start: 34
  outliers final: 20
  residues processed: 175
  average time/residue: 0.0949
  time to fit residues: 22.1165
Evaluate side-chains
  169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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 A residue  562 VAL
Chi-restraints excluded: chain A residue  610 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   74 ILE
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
Chi-restraints excluded: chain B residue  562 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:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 67 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0040
   chunk 21 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   overall best weight:    0.5792

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.151697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.108245 restraints weight = 12364.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.110815 restraints weight = 7486.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.111113 restraints weight = 4587.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.111375 restraints weight = 4225.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.111489 restraints weight = 3660.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7924  Z= 0.101
  Angle     :  0.559   8.398  10776  Z= 0.276
  Chirality :  0.041   0.148   1246
  Planarity :  0.004   0.034   1320
  Dihedral  :  4.822  30.938   1084
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.77 %
    Favored  : 83.70 %
  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 aren not related in a simple way.
  whole: -2.48 (0.25), residues: 976
  helix: -1.54 (0.21), residues: 494
  sheet:  0.91 (0.54), residues: 100
  loop : -2.39 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  71 
 TYR   0.025   0.001   TYR C  56 
 PHE   0.017   0.001   PHE A 128 
 TRP   0.009   0.001   TRP C  37 
 HIS   0.001   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 7922)
  covalent geometry    : angle       0.55891 (10772)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       1.26680 (    4)
  hydrogen bonds       : bond        0.03347 (  257)
  hydrogen bonds       : angle       4.72373 (  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
  183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8609 (p)
REVERT: A  468 MET cc_start: 0.8853 (mmm) cc_final: 0.8617 (mmm)
REVERT: A  517 MET cc_start: 0.7788 (mmm) cc_final: 0.7418 (ttm)
REVERT: A  538 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7299 (tmt170)
REVERT: A  616 TYR cc_start: 0.8398 (m-80) cc_final: 0.8143 (m-80)
REVERT: C   51 TRP cc_start: 0.7270 (m-10) cc_final: 0.6882 (m-90)
REVERT: C   76 ARG cc_start: 0.6733 (ttp-170) cc_final: 0.6505 (ttm170)
REVERT: D   22 LEU cc_start: 0.8078 (tt) cc_final: 0.7591 (mt)
REVERT: D   41 TYR cc_start: 0.7739 (p90) cc_final: 0.6817 (p90)
REVERT: D   42 ARG cc_start: 0.8520 (ptp-110) cc_final: 0.8238 (ptm160)
REVERT: B  145 TYR cc_start: 0.9112 (m-10) cc_final: 0.8878 (m-10)
REVERT: B  168 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8616 (p)
REVERT: B  195 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6506 (tm-30)
REVERT: B  196 ILE cc_start: 0.8279 (mt) cc_final: 0.8029 (mt)
REVERT: B  468 MET cc_start: 0.8829 (mmm) cc_final: 0.8587 (mmm)
REVERT: B  517 MET cc_start: 0.7870 (mmm) cc_final: 0.7286 (ttm)
REVERT: B  538 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7239 (tmt170)
REVERT: B  616 TYR cc_start: 0.8366 (m-80) cc_final: 0.8131 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 177
  average time/residue: 0.0931
  time to fit residues: 21.9996
Evaluate side-chains
  169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
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  619 LEU
Chi-restraints excluded: chain C residue   72 PHE
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  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  557 VAL
Chi-restraints excluded: chain B residue  619 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 49 optimal weight:   50.0000
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.095187 restraints weight = 12734.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.098228 restraints weight = 6772.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.100236 restraints weight = 4578.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.101361 restraints weight = 3625.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.102207 restraints weight = 3177.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   7924  Z= 0.238
  Angle     :  0.658   7.565  10776  Z= 0.327
  Chirality :  0.046   0.141   1246
  Planarity :  0.005   0.035   1320
  Dihedral  :  5.163  30.831   1084
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 13.29 %
    Favored  : 82.85 %
  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 aren not related in a simple way.
  whole: -2.42 (0.25), residues: 976
  helix: -1.45 (0.21), residues: 496
  sheet:  1.02 (0.54), residues: 100
  loop : -2.46 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  71 
 TYR   0.025   0.001   TYR C  56 
 PHE   0.018   0.002   PHE A 128 
 TRP   0.009   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 7922)
  covalent geometry    : angle       0.65788 (10772)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       1.02978 (    4)
  hydrogen bonds       : bond        0.04591 (  257)
  hydrogen bonds       : angle       5.12815 (  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
  178 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8758 (p)
REVERT: A  468 MET cc_start: 0.8919 (mmm) cc_final: 0.8650 (mmm)
REVERT: A  517 MET cc_start: 0.7875 (mmm) cc_final: 0.7606 (ttm)
REVERT: A  538 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7243 (tmt170)
REVERT: C   51 TRP cc_start: 0.7266 (m-10) cc_final: 0.6892 (m-90)
REVERT: C   87 MET cc_start: 0.8010 (mmm) cc_final: 0.7803 (mmm)
REVERT: C  107 TRP cc_start: 0.7514 (m100) cc_final: 0.7013 (m100)
REVERT: B  168 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8781 (p)
REVERT: B  195 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6507 (tm-30)
REVERT: B  196 ILE cc_start: 0.8278 (mt) cc_final: 0.8009 (mt)
REVERT: B  468 MET cc_start: 0.8920 (mmm) cc_final: 0.8651 (mmm)
REVERT: B  517 MET cc_start: 0.8069 (mmm) cc_final: 0.7696 (ttm)
REVERT: B  538 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7270 (tmt170)
REVERT: B  575 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8521 (tm-30)
  outliers start: 32
  outliers final: 26
  residues processed: 171
  average time/residue: 0.0876
  time to fit residues: 20.2271
Evaluate side-chains
  173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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   72 PHE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   78 ASN
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:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 8 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0370
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.151054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.106690 restraints weight = 12502.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.108009 restraints weight = 7327.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108461 restraints weight = 5100.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.109966 restraints weight = 4573.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.109905 restraints weight = 3938.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7924  Z= 0.096
  Angle     :  0.557   7.402  10776  Z= 0.273
  Chirality :  0.041   0.120   1246
  Planarity :  0.004   0.034   1320
  Dihedral  :  4.581  29.257   1084
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.46 %
    Favored  : 82.00 %
  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 aren not related in a simple way.
  whole: -1.77 (0.26), residues: 976
  helix: -0.76 (0.23), residues: 490
  sheet: -0.10 (0.46), residues: 140
  loop : -2.09 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  71 
 TYR   0.025   0.001   TYR C  56 
 PHE   0.014   0.001   PHE C  72 
 TRP   0.010   0.001   TRP C  37 
 HIS   0.001   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 7922)
  covalent geometry    : angle       0.55705 (10772)
  SS BOND              : bond        0.00162 (    2)
  SS BOND              : angle       0.80047 (    4)
  hydrogen bonds       : bond        0.03035 (  257)
  hydrogen bonds       : angle       4.53273 (  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
  171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8545 (p)
REVERT: A  517 MET cc_start: 0.7764 (mmm) cc_final: 0.7541 (ttm)
REVERT: A  538 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7205 (tmt170)
REVERT: A  555 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7165 (tpp)
REVERT: C   51 TRP cc_start: 0.7062 (m-10) cc_final: 0.6657 (m-90)
REVERT: D   41 TYR cc_start: 0.7685 (p90) cc_final: 0.6732 (p90)
REVERT: D   76 ARG cc_start: 0.6707 (mtp180) cc_final: 0.6067 (mtm-85)
REVERT: B  168 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8588 (p)
REVERT: B  195 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6452 (tm-30)
REVERT: B  538 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7196 (tmt170)
REVERT: B  555 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7185 (tpp)
  outliers start: 21
  outliers final: 14
  residues processed: 165
  average time/residue: 0.0928
  time to fit residues: 20.8556
Evaluate side-chains
  159 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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  467 ILE
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   74 ILE
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  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:    0.4980
   chunk 14 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0020
   chunk 68 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0570
   chunk 92 optimal weight:    0.0970
   overall best weight:    0.2304

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.153031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.107561 restraints weight = 12434.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.110087 restraints weight = 6833.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.111356 restraints weight = 4469.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.111661 restraints weight = 3483.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.111919 restraints weight = 3393.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.4321

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= 0.084
  Angle     :  0.554   8.276  10776  Z= 0.266
  Chirality :  0.040   0.125   1246
  Planarity :  0.004   0.034   1320
  Dihedral  :  4.288  28.078   1084
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.67 %
    Favored  : 80.56 %
  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 aren not related in a simple way.
  whole: -1.09 (0.27), residues: 976
  helix: -0.10 (0.24), residues: 482
  sheet:  0.01 (0.46), residues: 140
  loop : -1.80 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  71 
 TYR   0.020   0.001   TYR C  56 
 PHE   0.012   0.001   PHE A 128 
 TRP   0.008   0.001   TRP C  37 
 HIS   0.001   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 7922)
  covalent geometry    : angle       0.55421 (10772)
  SS BOND              : bond        0.00319 (    2)
  SS BOND              : angle       0.82970 (    4)
  hydrogen bonds       : bond        0.02590 (  257)
  hydrogen bonds       : angle       4.28363 (  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
  177 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8840 (mp)
REVERT: A  538 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7197 (tmt170)
REVERT: A  555 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7019 (tpp)
REVERT: A  615 LEU cc_start: 0.8512 (tt) cc_final: 0.7334 (mp)
REVERT: C   51 TRP cc_start: 0.6816 (m-10) cc_final: 0.6585 (m-90)
REVERT: C   87 MET cc_start: 0.7973 (mmm) cc_final: 0.7750 (mmm)
REVERT: C  103 LYS cc_start: 0.7221 (tttt) cc_final: 0.6859 (ptmm)
REVERT: D   41 TYR cc_start: 0.7687 (p90) cc_final: 0.6705 (p90)
REVERT: B  538 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7182 (tmt170)
REVERT: B  555 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7058 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 167
  average time/residue: 0.0978
  time to fit residues: 21.6751
Evaluate side-chains
  157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  182 MET
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   97 VAL
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   14 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
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:   10.0000
   chunk 72 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0070
   chunk 17 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0570
   chunk 44 optimal weight:   10.0000
   overall best weight:    0.4916

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.151336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.101981 restraints weight = 12539.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.105140 restraints weight = 6658.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.107164 restraints weight = 4510.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.108538 restraints weight = 3585.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.109235 restraints weight = 3120.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4457

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= 0.092
  Angle     :  0.561   7.649  10776  Z= 0.268
  Chirality :  0.041   0.148   1246
  Planarity :  0.004   0.033   1320
  Dihedral  :  4.219  27.731   1084
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.67 %
    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 aren not related in a simple way.
  whole: -0.74 (0.28), residues: 976
  helix:  0.20 (0.24), residues: 486
  sheet:  0.18 (0.47), residues: 140
  loop : -1.67 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  71 
 TYR   0.018   0.001   TYR C  56 
 PHE   0.012   0.001   PHE A 128 
 TRP   0.012   0.001   TRP C  37 
 HIS   0.001   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 7922)
  covalent geometry    : angle       0.56051 (10772)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.69191 (    4)
  hydrogen bonds       : bond        0.02770 (  257)
  hydrogen bonds       : angle       4.27842 (  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
  171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8368 (p)
REVERT: A  538 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7266 (tmt170)
REVERT: A  555 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6987 (tpp)
REVERT: A  615 LEU cc_start: 0.8512 (tt) cc_final: 0.7332 (mp)
REVERT: C  103 LYS cc_start: 0.7138 (tttt) cc_final: 0.6926 (ptmm)
REVERT: D   71 ARG cc_start: 0.5482 (ttp-110) cc_final: 0.5278 (ttp-170)
REVERT: B   25 TYR cc_start: 0.9056 (t80) cc_final: 0.8856 (t80)
REVERT: B  168 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8445 (p)
REVERT: B  517 MET cc_start: 0.7929 (mmm) cc_final: 0.7459 (ttm)
REVERT: B  538 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7259 (tmt170)
REVERT: B  555 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7032 (tpp)
REVERT: B  606 MET cc_start: 0.8350 (tpt) cc_final: 0.8089 (tpt)
  outliers start: 21
  outliers final: 13
  residues processed: 160
  average time/residue: 0.0993
  time to fit residues: 21.1884
Evaluate side-chains
  163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
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   74 ILE
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  129 SER
Chi-restraints excluded: chain B residue  168 THR
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:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 70 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 81 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0770
   chunk 83 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.151113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.102046 restraints weight = 12377.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.105294 restraints weight = 6465.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.107442 restraints weight = 4334.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.108777 restraints weight = 3398.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.109505 restraints weight = 2949.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4579

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     :  0.595   9.742  10776  Z= 0.278
  Chirality :  0.042   0.252   1246
  Planarity :  0.004   0.033   1320
  Dihedral  :  4.213  27.871   1084
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.51 %
    Favored  : 80.07 %
  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 aren not related in a simple way.
  whole: -0.55 (0.28), residues: 976
  helix:  0.35 (0.25), residues: 488
  sheet:  0.18 (0.47), residues: 140
  loop : -1.55 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  71 
 TYR   0.018   0.001   TYR C  56 
 PHE   0.012   0.001   PHE A 128 
 TRP   0.011   0.001   TRP D  37 
 HIS   0.001   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7922)
  covalent geometry    : angle       0.59499 (10772)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       0.59107 (    4)
  hydrogen bonds       : bond        0.02742 (  257)
  hydrogen bonds       : angle       4.26534 (  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
  164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8358 (p)
REVERT: A  538 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7289 (tmt170)
REVERT: A  615 LEU cc_start: 0.8472 (tt) cc_final: 0.7275 (mp)
REVERT: C  103 LYS cc_start: 0.7120 (tttt) cc_final: 0.6914 (ptmm)
REVERT: D   41 TYR cc_start: 0.7587 (p90) cc_final: 0.6557 (p90)
REVERT: B   25 TYR cc_start: 0.9050 (t80) cc_final: 0.8849 (t80)
REVERT: B  168 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8360 (p)
REVERT: B  538 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7264 (tmt170)
REVERT: B  606 MET cc_start: 0.8394 (tpt) cc_final: 0.8178 (tpt)
  outliers start: 20
  outliers final: 15
  residues processed: 155
  average time/residue: 0.0895
  time to fit residues: 18.4484
Evaluate side-chains
  161 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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   92 LEU
Chi-restraints excluded: chain A residue  168 THR
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   74 ILE
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  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  614 LEU
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:    0.7980
   chunk 95 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0770
   chunk 66 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 55 optimal weight:   10.0000
   chunk 91 optimal weight:    0.1980
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.4338

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.152585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.103811 restraints weight = 12353.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.106943 restraints weight = 6529.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.109133 restraints weight = 4405.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.110425 restraints weight = 3451.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.111270 restraints weight = 2995.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4707

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= 0.091
  Angle     :  0.585   9.059  10776  Z= 0.274
  Chirality :  0.042   0.180   1246
  Planarity :  0.004   0.032   1320
  Dihedral  :  4.128  26.408   1084
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.36 %
    Favored  : 79.35 %
  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 aren not related in a simple way.
  whole: -0.34 (0.28), residues: 976
  helix:  0.53 (0.25), residues: 488
  sheet:  0.27 (0.48), residues: 140
  loop : -1.45 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  23 
 TYR   0.017   0.001   TYR C  56 
 PHE   0.012   0.001   PHE A 128 
 TRP   0.012   0.001   TRP D  37 
 HIS   0.001   0.000   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 7922)
  covalent geometry    : angle       0.58541 (10772)
  SS BOND              : bond        0.00265 (    2)
  SS BOND              : angle       0.65696 (    4)
  hydrogen bonds       : bond        0.02638 (  257)
  hydrogen bonds       : angle       4.19800 (  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
  170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  168 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8366 (p)
REVERT: A  538 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7271 (tmt170)
REVERT: A  555 MET cc_start: 0.8203 (tpp) cc_final: 0.7084 (tpp)
REVERT: A  615 LEU cc_start: 0.8486 (tt) cc_final: 0.7286 (mp)
REVERT: C   76 ARG cc_start: 0.7163 (ttp-170) cc_final: 0.6847 (ttm170)
REVERT: B  168 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8371 (p)
REVERT: B  195 GLU cc_start: 0.6550 (tm-30) cc_final: 0.6224 (tm-30)
REVERT: B  538 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7280 (tmt170)
REVERT: B  555 MET cc_start: 0.8225 (tpp) cc_final: 0.7138 (tpp)
  outliers start: 19
  outliers final: 16
  residues processed: 163
  average time/residue: 0.0810
  time to fit residues: 17.3868
Evaluate side-chains
  153 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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   92 LEU
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  184 LEU
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   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  168 THR
Chi-restraints excluded: chain B residue  614 LEU
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:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 34 optimal weight:    0.1980
   chunk 44 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   chunk 92 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
C  88 ASN
D   7 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.149476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.099474 restraints weight = 12387.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.102598 restraints weight = 6691.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.104680 restraints weight = 4564.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.105908 restraints weight = 3619.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.106573 restraints weight = 3175.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.4659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7924  Z= 0.146
  Angle     :  0.635  11.938  10776  Z= 0.301
  Chirality :  0.044   0.172   1246
  Planarity :  0.004   0.043   1320
  Dihedral  :  4.373  28.179   1084
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.12 %
    Favored  : 79.23 %
  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 aren not related in a simple way.
  whole: -0.49 (0.28), residues: 976
  helix:  0.44 (0.24), residues: 488
  sheet: -0.03 (0.45), residues: 162
  loop : -1.56 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  71 
 TYR   0.023   0.001   TYR C  56 
 PHE   0.014   0.001   PHE A 128 
 TRP   0.013   0.001   TRP D  37 
 HIS   0.002   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7922)
  covalent geometry    : angle       0.63529 (10772)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       0.61446 (    4)
  hydrogen bonds       : bond        0.03492 (  257)
  hydrogen bonds       : angle       4.36575 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1404.33 seconds
wall clock time: 24 minutes 54.85 seconds (1494.85 seconds total)