Starting phenix.real_space_refine
on Mon Apr 28 15:28:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jh5_36254/04_2025/8jh5_36254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jh5_36254/04_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_36254/04_2025/8jh5_36254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jh5_36254/04_2025/8jh5_36254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jh5_36254/04_2025/8jh5_36254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jh5_36254/04_2025/8jh5_36254.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.079
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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:
    D, B
  Time building chain proxies: 6.07, per 1000 atoms: 0.78
  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: 1.88
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.83
  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: 1.85

  Time building geometry restraints manager: 2.09 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.510
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.610
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.450
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.030   0.002   TRP C  37 
 HIS   0.004   0.001   HIS A   9 
 PHE   0.022   0.002   PHE B 585 
 TYR   0.022   0.002   TYR C  56 
 ARG   0.003   0.001   ARG A 547 

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

*********************** 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  : 0.797 
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: 0.8308 (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: 0.7328 (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: 0.7029 (m100)
REVERT: C   76 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6818 (ttp-110)
REVERT: D   42 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8426 (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: 0.8156 (mt)
REVERT: B  468 MET cc_start: 0.8523 (mmm) cc_final: 0.8295 (mmm)
REVERT: B  499 MET cc_start: 0.8558 (ttp) cc_final: 0.8351 (ttp)
REVERT: B  519 MET cc_start: 0.8552 (mmt) cc_final: 0.8292 (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: 0.2530
  time to fit residues: 74.4844
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  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 49 optimal weight:   40.0000
   chunk 38 optimal weight:   50.0000
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 56 optimal weight:    9.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 HIS
C   7 GLN
B   9 HIS
B  43 ASN
B 127 ASN
** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 570 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.149268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.102515 restraints weight = 12266.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.105602 restraints weight = 6654.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.106519 restraints weight = 4463.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7924  Z= 0.207
  Angle     :  0.675   6.383  10776  Z= 0.349
  Chirality :  0.045   0.145   1246
  Planarity :  0.006   0.046   1320
  Dihedral  :  5.648  34.214   1084
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 10.75 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.59 (0.22), residues: 976
  helix: -3.43 (0.14), residues: 504
  sheet: -0.86 (0.44), residues: 158
  loop : -3.14 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 144 
 HIS   0.003   0.001   HIS B   9 
 PHE   0.027   0.002   PHE A 128 
 TYR   0.027   0.001   TYR C  56 
 ARG   0.007   0.001   ARG A 463 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05488 (  257)
  hydrogen bonds       : angle       5.83152 (  750)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       2.45376 (    4)
  covalent geometry    : bond        0.00492 ( 7922)
  covalent geometry    : angle       0.67326 (10772)

*********************** 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
  211 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 181
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.7318 (tp30) cc_final: 0.6850 (tm-30)
REVERT: A  196 ILE cc_start: 0.8475 (mt) cc_final: 0.7746 (mt)
REVERT: A  468 MET cc_start: 0.8756 (mmm) cc_final: 0.8411 (mmm)
REVERT: A  538 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7327 (tmt170)
REVERT: C   51 TRP cc_start: 0.7249 (m-10) cc_final: 0.6892 (m100)
REVERT: C   76 ARG cc_start: 0.7331 (ttp-170) cc_final: 0.6604 (ttm110)
REVERT: D   42 ARG cc_start: 0.8668 (ptp-110) cc_final: 0.8390 (ptp-110)
REVERT: D   76 ARG cc_start: 0.7311 (ttp-170) cc_final: 0.6436 (ttp-170)
REVERT: D   87 MET cc_start: 0.8433 (mtp) cc_final: 0.8182 (mtt)
REVERT: B  195 GLU cc_start: 0.7239 (tp30) cc_final: 0.7033 (tm-30)
REVERT: B  196 ILE cc_start: 0.8454 (mt) cc_final: 0.7962 (mt)
REVERT: B  468 MET cc_start: 0.8757 (mmm) cc_final: 0.8406 (mmm)
REVERT: B  538 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7245 (tmt170)
  outliers start: 30
  outliers final: 21
  residues processed: 201
  average time/residue: 0.1891
  time to fit residues: 51.3282
Evaluate side-chains
  169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
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 18 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.1788

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.149657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.102351 restraints weight = 12358.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.105416 restraints weight = 6472.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.107479 restraints weight = 4315.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3260

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= 0.151
  Angle     :  0.610   7.363  10776  Z= 0.307
  Chirality :  0.043   0.135   1246
  Planarity :  0.005   0.041   1320
  Dihedral  :  5.246  32.721   1084
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 12.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.24), residues: 976
  helix: -2.39 (0.18), residues: 490
  sheet: -0.48 (0.44), residues: 146
  loop : -2.71 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  37 
 HIS   0.002   0.001   HIS A 203 
 PHE   0.021   0.001   PHE A 128 
 TYR   0.023   0.001   TYR C  56 
 ARG   0.006   0.001   ARG D  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04406 (  257)
  hydrogen bonds       : angle       5.20961 (  750)
  SS BOND              : bond        0.00091 (    2)
  SS BOND              : angle       1.44367 (    4)
  covalent geometry    : bond        0.00358 ( 7922)
  covalent geometry    : angle       0.60908 (10772)

*********************** 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
  184 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8768 (p)
REVERT: A  196 ILE cc_start: 0.8530 (mt) cc_final: 0.8162 (mt)
REVERT: A  468 MET cc_start: 0.8804 (mmm) cc_final: 0.8194 (mmm)
REVERT: A  517 MET cc_start: 0.7945 (mmm) cc_final: 0.7514 (ttm)
REVERT: A  519 MET cc_start: 0.8606 (mmm) cc_final: 0.8378 (mmt)
REVERT: A  538 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7257 (tmt170)
REVERT: A  616 TYR cc_start: 0.8455 (m-80) cc_final: 0.8120 (m-80)
REVERT: C   51 TRP cc_start: 0.7360 (m-10) cc_final: 0.6839 (m-90)
REVERT: C   76 ARG cc_start: 0.6920 (ttp-170) cc_final: 0.6559 (ttm170)
REVERT: C  107 TRP cc_start: 0.7482 (m100) cc_final: 0.7273 (m100)
REVERT: D   41 TYR cc_start: 0.7836 (p90) cc_final: 0.6863 (p90)
REVERT: D   42 ARG cc_start: 0.8654 (ptp-110) cc_final: 0.8249 (ptp-110)
REVERT: D   76 ARG cc_start: 0.7407 (ttp-170) cc_final: 0.5956 (ttp-110)
REVERT: B    8 TYR cc_start: 0.9253 (t80) cc_final: 0.9053 (t80)
REVERT: B  168 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8771 (p)
REVERT: B  196 ILE cc_start: 0.8509 (mt) cc_final: 0.8007 (mt)
REVERT: B  468 MET cc_start: 0.8810 (mmm) cc_final: 0.8200 (mmm)
REVERT: B  517 MET cc_start: 0.7908 (mmm) cc_final: 0.7569 (ttm)
REVERT: B  538 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7196 (tmt170)
REVERT: B  610 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8573 (mp)
REVERT: B  616 TYR cc_start: 0.8257 (m-80) cc_final: 0.7778 (m-80)
  outliers start: 30
  outliers final: 20
  residues processed: 177
  average time/residue: 0.2147
  time to fit residues: 50.4174
Evaluate side-chains
  168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
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  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   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  610 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0030
   chunk 71 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.7392

-------------------------------------------------------------------------------
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 = 0.3770 r_free = 0.3770 target = 0.149558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.101893 restraints weight = 12283.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.104991 restraints weight = 6354.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.106967 restraints weight = 4216.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7924  Z= 0.111
  Angle     :  0.561   8.063  10776  Z= 0.280
  Chirality :  0.042   0.136   1246
  Planarity :  0.004   0.040   1320
  Dihedral  :  4.852  30.675   1084
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 13.16 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.25), residues: 976
  helix: -1.56 (0.21), residues: 494
  sheet:  0.93 (0.53), residues: 100
  loop : -2.38 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  37 
 HIS   0.001   0.001   HIS B 203 
 PHE   0.018   0.001   PHE A 128 
 TYR   0.024   0.001   TYR D  56 
 ARG   0.006   0.000   ARG D  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  257)
  hydrogen bonds       : angle       4.81342 (  750)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       1.27603 (    4)
  covalent geometry    : bond        0.00260 ( 7922)
  covalent geometry    : angle       0.56038 (10772)

*********************** 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
  178 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8698 (p)
REVERT: A  468 MET cc_start: 0.8844 (mmm) cc_final: 0.8611 (mmm)
REVERT: A  517 MET cc_start: 0.7846 (mmm) cc_final: 0.7391 (ttm)
REVERT: A  538 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7323 (tmt170)
REVERT: C   51 TRP cc_start: 0.7168 (m-10) cc_final: 0.6780 (m-90)
REVERT: D   38 MET cc_start: 0.2283 (mtm) cc_final: 0.2049 (mtm)
REVERT: D   41 TYR cc_start: 0.7702 (p90) cc_final: 0.6697 (p90)
REVERT: D   42 ARG cc_start: 0.8559 (ptp-110) cc_final: 0.8243 (ptm160)
REVERT: D   71 ARG cc_start: 0.5082 (ttp-110) cc_final: 0.4717 (ttp-170)
REVERT: B  168 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8699 (p)
REVERT: B  195 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6465 (tm-30)
REVERT: B  196 ILE cc_start: 0.8233 (mt) cc_final: 0.7992 (mt)
REVERT: B  468 MET cc_start: 0.8854 (mmm) cc_final: 0.8608 (mmm)
REVERT: B  517 MET cc_start: 0.7847 (mmm) cc_final: 0.7353 (ttm)
REVERT: B  538 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7253 (tmt170)
REVERT: B  616 TYR cc_start: 0.8408 (m-80) cc_final: 0.8172 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 173
  average time/residue: 0.2110
  time to fit residues: 48.5723
Evaluate side-chains
  164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
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   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 44 optimal weight:   30.0000
   chunk 86 optimal weight:    3.9990
   chunk 82 optimal weight:    0.4980
   chunk 50 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.150501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.101454 restraints weight = 12505.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.104600 restraints weight = 6605.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.106534 restraints weight = 4457.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7924  Z= 0.108
  Angle     :  0.564   7.745  10776  Z= 0.277
  Chirality :  0.042   0.159   1246
  Planarity :  0.004   0.032   1320
  Dihedral  :  4.617  28.728   1084
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.29 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.26), residues: 976
  helix: -1.01 (0.22), residues: 492
  sheet: -0.19 (0.45), residues: 140
  loop : -2.06 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.015   0.001   PHE A 128 
 TYR   0.024   0.001   TYR C  56 
 ARG   0.004   0.000   ARG D  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03363 (  257)
  hydrogen bonds       : angle       4.69214 (  750)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       0.91081 (    4)
  covalent geometry    : bond        0.00256 ( 7922)
  covalent geometry    : angle       0.56408 (10772)

*********************** 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
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8646 (p)
REVERT: A  468 MET cc_start: 0.8879 (mmm) cc_final: 0.8669 (mmm)
REVERT: A  517 MET cc_start: 0.7817 (mmm) cc_final: 0.7420 (ttm)
REVERT: A  538 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7322 (tmt170)
REVERT: A  555 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7229 (tpp)
REVERT: C   51 TRP cc_start: 0.7028 (m-10) cc_final: 0.6710 (m-90)
REVERT: D   41 TYR cc_start: 0.7580 (p90) cc_final: 0.6597 (p90)
REVERT: D   42 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.8070 (ptm160)
REVERT: B  168 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8659 (p)
REVERT: B  195 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6413 (tm-30)
REVERT: B  468 MET cc_start: 0.8882 (mmm) cc_final: 0.8666 (mmm)
REVERT: B  517 MET cc_start: 0.7847 (mmm) cc_final: 0.7326 (ttm)
REVERT: B  538 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7227 (tmt170)
REVERT: B  615 LEU cc_start: 0.8634 (tt) cc_final: 0.8411 (tt)
  outliers start: 27
  outliers final: 21
  residues processed: 166
  average time/residue: 0.1877
  time to fit residues: 42.0218
Evaluate side-chains
  165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
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  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  555 MET
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  555 MET
Chi-restraints excluded: chain B residue  557 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 72 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0970
   chunk 91 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0970
   overall best weight:    0.5376

-------------------------------------------------------------------------------
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 = 0.151422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.103682 restraints weight = 12337.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.106817 restraints weight = 6408.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.108953 restraints weight = 4302.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.4097

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= 0.095
  Angle     :  0.553   7.724  10776  Z= 0.270
  Chirality :  0.041   0.150   1246
  Planarity :  0.004   0.030   1320
  Dihedral  :  4.413  28.116   1084
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 14.73 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.27), residues: 976
  helix: -0.52 (0.23), residues: 490
  sheet: -0.13 (0.45), residues: 140
  loop : -1.79 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  37 
 HIS   0.001   0.000   HIS A 176 
 PHE   0.013   0.001   PHE A 128 
 TYR   0.025   0.001   TYR C  56 
 ARG   0.003   0.000   ARG D  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02981 (  257)
  hydrogen bonds       : angle       4.49735 (  750)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.69800 (    4)
  covalent geometry    : bond        0.00224 ( 7922)
  covalent geometry    : angle       0.55334 (10772)

*********************** 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: 24
    poor density    : 147
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8583 (p)
REVERT: A  468 MET cc_start: 0.8862 (mmm) cc_final: 0.8660 (mmm)
REVERT: A  517 MET cc_start: 0.7793 (mmm) cc_final: 0.7425 (ttm)
REVERT: A  538 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7290 (tmt170)
REVERT: A  555 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7171 (tpp)
REVERT: C   51 TRP cc_start: 0.7022 (m-10) cc_final: 0.6710 (m-90)
REVERT: D   41 TYR cc_start: 0.7439 (p90) cc_final: 0.6046 (p90)
REVERT: D   42 ARG cc_start: 0.8432 (ptp-110) cc_final: 0.7988 (ptm160)
REVERT: D   49 ARG cc_start: 0.8258 (ptp-170) cc_final: 0.7975 (ptm160)
REVERT: B  168 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8574 (p)
REVERT: B  468 MET cc_start: 0.8884 (mmm) cc_final: 0.8682 (mmm)
REVERT: B  538 ARG cc_start: 0.7650 (mtt180) cc_final: 0.7238 (tmt170)
  outliers start: 24
  outliers final: 16
  residues processed: 163
  average time/residue: 0.1923
  time to fit residues: 42.3054
Evaluate side-chains
  160 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
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   33 VAL
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   33 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  467 ILE
Chi-restraints excluded: chain B residue  550 VAL
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 37 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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**
** B 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 = 0.3762 r_free = 0.3762 target = 0.149058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.100295 restraints weight = 12425.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.103447 restraints weight = 6359.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.105514 restraints weight = 4225.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7924  Z= 0.132
  Angle     :  0.584   9.305  10776  Z= 0.283
  Chirality :  0.043   0.146   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.521  28.236   1084
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 14.37 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.27), residues: 976
  helix: -0.35 (0.24), residues: 492
  sheet: -0.02 (0.46), residues: 140
  loop : -1.92 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  37 
 HIS   0.002   0.001   HIS A 570 
 PHE   0.013   0.001   PHE A 128 
 TYR   0.020   0.001   TYR C  56 
 ARG   0.002   0.000   ARG D  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  257)
  hydrogen bonds       : angle       4.59251 (  750)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.59612 (    4)
  covalent geometry    : bond        0.00321 ( 7922)
  covalent geometry    : angle       0.58447 (10772)

*********************** 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
  179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.9132 (t80) cc_final: 0.8920 (t80)
REVERT: A  168 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8653 (p)
REVERT: A  196 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8812 (mp)
REVERT: A  468 MET cc_start: 0.8888 (mmm) cc_final: 0.8646 (mmm)
REVERT: A  517 MET cc_start: 0.7901 (mmm) cc_final: 0.7228 (ttm)
REVERT: A  538 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7261 (tmt170)
REVERT: A  555 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7163 (tpp)
REVERT: C   51 TRP cc_start: 0.6939 (m-10) cc_final: 0.6698 (m-90)
REVERT: C  103 LYS cc_start: 0.7174 (tttt) cc_final: 0.6800 (ptmm)
REVERT: B   25 TYR cc_start: 0.9127 (t80) cc_final: 0.8911 (t80)
REVERT: B  168 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8652 (p)
REVERT: B  195 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6177 (tm-30)
REVERT: B  468 MET cc_start: 0.8888 (mmm) cc_final: 0.8645 (mmm)
REVERT: B  538 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7275 (tmt170)
  outliers start: 36
  outliers final: 27
  residues processed: 166
  average time/residue: 0.1893
  time to fit residues: 42.5283
Evaluate side-chains
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   62 ASN
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  182 MET
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   84 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   62 ASN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  196 ILE
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  619 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 45 optimal weight:    0.2980
   chunk 55 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0070
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.3782 r_free = 0.3782 target = 0.150686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.101935 restraints weight = 12572.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.105141 restraints weight = 6392.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.107297 restraints weight = 4229.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7924  Z= 0.098
  Angle     :  0.571   8.795  10776  Z= 0.275
  Chirality :  0.042   0.153   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.378  28.619   1084
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.22 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.28), residues: 976
  helix: -0.02 (0.24), residues: 490
  sheet:  0.03 (0.46), residues: 140
  loop : -1.64 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.012   0.001   PHE A 128 
 TYR   0.019   0.001   TYR C  56 
 ARG   0.003   0.000   ARG C  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02921 (  257)
  hydrogen bonds       : angle       4.39319 (  750)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       0.56967 (    4)
  covalent geometry    : bond        0.00230 ( 7922)
  covalent geometry    : angle       0.57147 (10772)

*********************** 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
  180 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.9105 (t80) cc_final: 0.8901 (t80)
REVERT: A  168 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8558 (p)
REVERT: A  196 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8814 (mp)
REVERT: A  538 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7306 (tmt170)
REVERT: A  555 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7092 (tpp)
REVERT: C   41 TYR cc_start: 0.8014 (p90) cc_final: 0.7711 (p90)
REVERT: C   51 TRP cc_start: 0.6877 (m-10) cc_final: 0.6670 (m-90)
REVERT: C  103 LYS cc_start: 0.7095 (tttt) cc_final: 0.6841 (ptmm)
REVERT: B  168 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8549 (p)
REVERT: B  195 GLU cc_start: 0.6496 (tm-30) cc_final: 0.6241 (tm-30)
REVERT: B  538 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7239 (tmt170)
  outliers start: 31
  outliers final: 24
  residues processed: 167
  average time/residue: 0.1994
  time to fit residues: 45.1125
Evaluate side-chains
  172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 MET
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  196 ILE
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  555 MET
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   84 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  467 ILE
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 68 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 9 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
B 575 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.150677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.101746 restraints weight = 12661.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.104980 restraints weight = 6476.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.107118 restraints weight = 4292.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.4438

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= 0.099
  Angle     :  0.573   7.666  10776  Z= 0.275
  Chirality :  0.042   0.146   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.318  28.444   1084
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.43 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.28), residues: 976
  helix:  0.18 (0.25), residues: 490
  sheet:  0.12 (0.46), residues: 140
  loop : -1.56 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.012   0.001   PHE A 128 
 TYR   0.018   0.001   TYR C  56 
 ARG   0.002   0.000   ARG D  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02895 (  257)
  hydrogen bonds       : angle       4.31045 (  750)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       0.55742 (    4)
  covalent geometry    : bond        0.00233 ( 7922)
  covalent geometry    : angle       0.57335 (10772)

*********************** 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
  175 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.9065 (t80) cc_final: 0.8864 (t80)
REVERT: A  168 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8562 (p)
REVERT: A  196 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8780 (mp)
REVERT: A  538 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7304 (tmt170)
REVERT: C   41 TYR cc_start: 0.7934 (p90) cc_final: 0.7644 (p90)
REVERT: C   51 TRP cc_start: 0.6666 (m-10) cc_final: 0.6437 (m-90)
REVERT: D   41 TYR cc_start: 0.7424 (p90) cc_final: 0.5950 (p90)
REVERT: D   49 ARG cc_start: 0.8496 (ptm160) cc_final: 0.8106 (ptm160)
REVERT: B   25 TYR cc_start: 0.9059 (t80) cc_final: 0.8850 (t80)
REVERT: B  168 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8553 (p)
REVERT: B  195 GLU cc_start: 0.6420 (tm-30) cc_final: 0.6173 (tm-30)
REVERT: B  538 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7238 (tmt170)
  outliers start: 28
  outliers final: 23
  residues processed: 162
  average time/residue: 0.1886
  time to fit residues: 41.5963
Evaluate side-chains
  170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
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  129 SER
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  196 ILE
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  619 LEU
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   84 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  467 ILE
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 14 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 94 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0570
   chunk 7 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6098

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.150521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.101641 restraints weight = 12540.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.104839 restraints weight = 6425.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.106819 restraints weight = 4268.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.4517

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= 0.099
  Angle     :  0.575   8.090  10776  Z= 0.275
  Chirality :  0.042   0.139   1246
  Planarity :  0.004   0.031   1320
  Dihedral  :  4.280  27.253   1084
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.30 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.28), residues: 976
  helix:  0.32 (0.25), residues: 490
  sheet:  0.12 (0.46), residues: 140
  loop : -1.48 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  37 
 HIS   0.001   0.000   HIS B 203 
 PHE   0.012   0.001   PHE A 128 
 TYR   0.022   0.001   TYR C  56 
 ARG   0.002   0.000   ARG D  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02828 (  257)
  hydrogen bonds       : angle       4.28452 (  750)
  SS BOND              : bond        0.00239 (    2)
  SS BOND              : angle       0.58328 (    4)
  covalent geometry    : bond        0.00235 ( 7922)
  covalent geometry    : angle       0.57490 (10772)

********************** 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
  178 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.9062 (t80) cc_final: 0.8851 (t80)
REVERT: A  168 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8457 (p)
REVERT: A  196 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (mp)
REVERT: A  538 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7283 (tmt170)
REVERT: A  555 MET cc_start: 0.8087 (tpp) cc_final: 0.7028 (tpp)
REVERT: C   41 TYR cc_start: 0.7952 (p90) cc_final: 0.7559 (p90)
REVERT: D   41 TYR cc_start: 0.7334 (p90) cc_final: 0.6240 (p90)
REVERT: B   25 TYR cc_start: 0.9061 (t80) cc_final: 0.8839 (t80)
REVERT: B  168 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8435 (p)
REVERT: B  195 GLU cc_start: 0.6412 (tm-30) cc_final: 0.6166 (tm-30)
REVERT: B  538 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7255 (tmt170)
  outliers start: 28
  outliers final: 24
  residues processed: 166
  average time/residue: 0.1887
  time to fit residues: 42.4901
Evaluate side-chains
  166 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
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  142 ILE
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  196 ILE
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  619 LEU
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue   99 TYR
Chi-restraints excluded: chain D residue   84 TYR
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 TYR
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  182 MET
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  467 ILE
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:    9.9990
   chunk 90 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 71 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.147874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.098602 restraints weight = 12612.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.101712 restraints weight = 6559.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.103796 restraints weight = 4374.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.4536

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= 0.157
  Angle     :  0.623  10.288  10776  Z= 0.300
  Chirality :  0.044   0.124   1246
  Planarity :  0.004   0.032   1320
  Dihedral  :  4.509  28.001   1084
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 16.30 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.28), residues: 976
  helix:  0.20 (0.24), residues: 492
  sheet:  0.17 (0.46), residues: 140
  loop : -1.69 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  37 
 HIS   0.002   0.001   HIS B 176 
 PHE   0.016   0.001   PHE C  72 
 TYR   0.020   0.001   TYR C  56 
 ARG   0.003   0.000   ARG A 471 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03543 (  257)
  hydrogen bonds       : angle       4.44685 (  750)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.62585 (    4)
  covalent geometry    : bond        0.00378 ( 7922)
  covalent geometry    : angle       0.62290 (10772)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2919.38 seconds
wall clock time: 51 minutes 38.28 seconds (3098.28 seconds total)