Starting phenix.real_space_refine
on Wed Mar 12 09:29:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y9t_33691/03_2025/7y9t_33691.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y9t_33691/03_2025/7y9t_33691.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y9t_33691/03_2025/7y9t_33691.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y9t_33691/03_2025/7y9t_33691.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y9t_33691/03_2025/7y9t_33691.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y9t_33691/03_2025/7y9t_33691.cif"
  }
  resolution = 3.1
  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=   0.005 sd=   0.122
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    5054      2.51       5
     N    1274      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 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7726
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 2962
          Classifications: {'peptide': 380}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 361}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 901
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 5.85, per 1000 atoms: 0.76
  Number of scatterers: 7726
  At special positions: 0
  Unit cell: (125.4, 106.7, 95.7, 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    1274      7.00
     C    5054      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    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: 1.55
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1848

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 8 sheets defined
      51.2% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 30
      removed outlier: 3.575A  pdb=" N   HIS A   9 " --> pdb=" O   ALA A   5 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A  13 " --> pdb=" O   HIS A   9 " (cutoff:3.500A)
      Proline residue:  A  16  - end of helix
      removed outlier: 3.686A  pdb=" N   ALA A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET A  21 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A  23 " --> pdb=" O   VAL A  19 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ALA A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL A  28 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 49
      removed outlier: 3.759A  pdb=" N   SER A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLY A  41 " --> pdb=" O   ASP A  37 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A  42 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ARG A  44 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 60
      removed outlier: 3.543A  pdb=" N   LEU A  53 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 86
      removed outlier: 3.791A  pdb=" N   LEU A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 93
      removed outlier: 3.709A  pdb=" N   LEU A  92 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 104
      removed outlier: 3.563A  pdb=" N   ILE A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 126
    Processing helix  chain 'A' and resid 128 through 143
      removed outlier: 3.631A  pdb=" N   MET A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL A 134 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN A 135 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 157
      removed outlier: 3.543A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   PHE A 152 " --> pdb=" O   MET A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 165
      removed outlier: 3.891A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   GLU A 163 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 460 through 471
      removed outlier: 3.840A  pdb=" N   LEU A 466 " --> pdb=" O   THR A 462 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   MET A 468 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 478
      No H-bonds generated for 'chain 'A' and resid 476 through 478'
    Processing helix  chain 'A' and resid 479 through 496
      removed outlier: 3.612A  pdb=" N   ILE A 491 " --> pdb=" O   THR A 487 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   PHE A 493 " --> pdb=" O   SER A 489 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LYS A 494 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TRP A 495 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 512
      removed outlier: 4.754A  pdb=" N   LEU A 510 " --> pdb=" O   SER A 506 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP A 512 " --> pdb=" O   SER A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 529
      removed outlier: 3.684A  pdb=" N   MET A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 544
      removed outlier: 3.531A  pdb=" N   ALA A 541 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 549
      removed outlier: 3.723A  pdb=" N   PHE A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 563
      removed outlier: 3.715A  pdb=" N   VAL A 557 " --> pdb=" O   ALA A 553 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA A 558 " --> pdb=" O   VAL A 554 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL A 562 " --> pdb=" O   ALA A 558 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A 563 " --> pdb=" O   SER A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 573
      removed outlier: 3.701A  pdb=" N   HIS A 570 " --> pdb=" O   GLY A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 591
      removed outlier: 3.541A  pdb=" N   VAL A 586 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 608
      removed outlier: 3.594A  pdb=" N   LEU A 607 " --> pdb=" O   ILE A 603 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 621
      removed outlier: 3.884A  pdb=" N   LEU A 615 " --> pdb=" O   PRO A 611 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR A 616 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY A 621 " --> pdb=" O   TYR A 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 30
      removed outlier: 3.575A  pdb=" N   HIS B   9 " --> pdb=" O   ALA B   5 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B  13 " --> pdb=" O   HIS B   9 " (cutoff:3.500A)
      Proline residue:  B  16  - end of helix
      removed outlier: 3.686A  pdb=" N   ALA B  20 " --> pdb=" O   PRO B  16 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   MET B  21 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B  23 " --> pdb=" O   VAL B  19 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER B  27 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 49
      removed outlier: 3.759A  pdb=" N   SER B  40 " --> pdb=" O   PRO B  36 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLY B  41 " --> pdb=" O   ASP B  37 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B  42 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ARG B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 60
      removed outlier: 3.543A  pdb=" N   LEU B  53 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 86
      removed outlier: 3.791A  pdb=" N   LEU B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 93
      removed outlier: 3.709A  pdb=" N   LEU B  92 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 104
      removed outlier: 3.563A  pdb=" N   ILE B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 126
    Processing helix  chain 'B' and resid 128 through 143
      removed outlier: 3.630A  pdb=" N   MET B 133 " --> pdb=" O   SER B 129 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL B 134 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN B 135 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 157
      removed outlier: 3.544A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   PHE B 152 " --> pdb=" O   MET B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 165
      removed outlier: 3.891A  pdb=" N   ILE B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   GLU B 163 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 460 through 471
      removed outlier: 3.840A  pdb=" N   LEU B 466 " --> pdb=" O   THR B 462 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   MET B 468 " --> pdb=" O   LEU B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 478
      No H-bonds generated for 'chain 'B' and resid 476 through 478'
    Processing helix  chain 'B' and resid 479 through 496
      removed outlier: 3.612A  pdb=" N   ILE B 491 " --> pdb=" O   THR B 487 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE B 493 " --> pdb=" O   SER B 489 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LYS B 494 " --> pdb=" O   LEU B 490 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TRP B 495 " --> pdb=" O   ILE B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 512
      removed outlier: 4.754A  pdb=" N   LEU B 510 " --> pdb=" O   SER B 506 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP B 512 " --> pdb=" O   SER B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 529
      removed outlier: 3.685A  pdb=" N   MET B 519 " --> pdb=" O   LEU B 515 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET B 526 " --> pdb=" O   LEU B 522 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B 528 " --> pdb=" O   LEU B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 544
      removed outlier: 3.531A  pdb=" N   ALA B 541 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 549
      removed outlier: 3.723A  pdb=" N   PHE B 548 " --> pdb=" O   ALA B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 563
      removed outlier: 3.715A  pdb=" N   VAL B 557 " --> pdb=" O   ALA B 553 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA B 558 " --> pdb=" O   VAL B 554 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 562 " --> pdb=" O   ALA B 558 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY B 563 " --> pdb=" O   SER B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 573
      removed outlier: 3.701A  pdb=" N   HIS B 570 " --> pdb=" O   GLY B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 591
      removed outlier: 3.541A  pdb=" N   VAL B 586 " --> pdb=" O   ILE B 582 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 608
      removed outlier: 3.594A  pdb=" N   LEU B 607 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE B 608 " --> pdb=" O   PHE B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 621
      removed outlier: 3.884A  pdb=" N   LEU B 615 " --> pdb=" O   PRO B 611 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR B 616 " --> pdb=" O   ILE B 612 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY B 621 " --> pdb=" O   TYR B 617 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177
      removed outlier: 4.860A  pdb=" N   ILE A 172 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   VAL A 204 " --> pdb=" O   ILE A 172 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   SER A 174 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   VAL A 206 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   HIS A 176 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR C 107 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 7 through 11
      removed outlier: 3.522A  pdb=" N   GLN D   7 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   VAL D   9 " --> pdb=" O   ALA D  27 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   SER D  11 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL D  83 " --> pdb=" O   CYS D  26 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 16
      removed outlier: 5.430A  pdb=" N   GLY D  14 " --> pdb=" O   THR D 116 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54
      removed outlier: 6.672A  pdb=" N   TRP D  40 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR D  41 " --> pdb=" O   TYR D  99 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR D  99 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 107 through 109
      removed outlier: 6.663A  pdb=" N   TYR D 107 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   ILE B 196 " --> pdb=" O   TYR D 107 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ARG D 109 " --> pdb=" O   ILE B 196 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   ILE B 172 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   VAL B 204 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   SER B 174 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   VAL B 206 " --> pdb=" O   SER B 174 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   HIS B 176 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 7 through 11
      removed outlier: 3.522A  pdb=" N   GLN C   7 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   VAL C   9 " --> pdb=" O   ALA C  27 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   SER C  11 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL C  83 " --> pdb=" O   CYS C  26 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 16
      removed outlier: 5.428A  pdb=" N   GLY C  14 " --> pdb=" O   THR C 116 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 54
      removed outlier: 6.672A  pdb=" N   TRP C  40 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR C  41 " --> pdb=" O   TYR C  99 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR C  99 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)

    253 hydrogen bonds defined for protein.
    747 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: 1.80

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.05 -     1.20: 78
        1.20 -     1.36: 2361
        1.36 -     1.51: 2924
        1.51 -     1.66: 2447
        1.66 -     1.81: 100
  Bond restraints: 7910
  Sorted by residual:
  bond pdb=" C   ILE B 582 "
       pdb=" O   ILE B 582 "
    ideal  model  delta    sigma   weight residual
    1.236  1.054  0.182 1.19e-02 7.06e+03 2.35e+02
  bond pdb=" C   ILE A 582 "
       pdb=" O   ILE A 582 "
    ideal  model  delta    sigma   weight residual
    1.236  1.054  0.182 1.19e-02 7.06e+03 2.35e+02
  bond pdb=" C   THR A 146 "
       pdb=" O   THR A 146 "
    ideal  model  delta    sigma   weight residual
    1.236  1.088  0.148 1.31e-02 5.83e+03 1.27e+02
  bond pdb=" C   THR B 146 "
       pdb=" O   THR B 146 "
    ideal  model  delta    sigma   weight residual
    1.236  1.088  0.148 1.31e-02 5.83e+03 1.27e+02
  bond pdb=" C   ILE A 573 "
       pdb=" O   ILE A 573 "
    ideal  model  delta    sigma   weight residual
    1.239  1.112  0.127 1.13e-02 7.83e+03 1.26e+02
  ... (remaining 7905 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.63: 10368
        3.63 -     7.26: 302
        7.26 -    10.89: 62
       10.89 -    14.53: 18
       14.53 -    18.16: 4
  Bond angle restraints: 10754
  Sorted by residual:
  angle pdb=" N   LEU B 149 "
        pdb=" CA  LEU B 149 "
        pdb=" C   LEU B 149 "
      ideal   model   delta    sigma   weight residual
     113.88   95.72   18.16 1.23e+00 6.61e-01 2.18e+02
  angle pdb=" N   LEU A 149 "
        pdb=" CA  LEU A 149 "
        pdb=" C   LEU A 149 "
      ideal   model   delta    sigma   weight residual
     113.88   95.72   18.16 1.23e+00 6.61e-01 2.18e+02
  angle pdb=" N   ILE B 574 "
        pdb=" CA  ILE B 574 "
        pdb=" C   ILE B 574 "
      ideal   model   delta    sigma   weight residual
     113.53  104.01    9.52 9.80e-01 1.04e+00 9.43e+01
  angle pdb=" N   ILE A 574 "
        pdb=" CA  ILE A 574 "
        pdb=" C   ILE A 574 "
      ideal   model   delta    sigma   weight residual
     113.53  104.02    9.51 9.80e-01 1.04e+00 9.42e+01
  angle pdb=" N   TRP A  89 "
        pdb=" CA  TRP A  89 "
        pdb=" C   TRP A  89 "
      ideal   model   delta    sigma   weight residual
     112.68  101.81   10.87 1.33e+00 5.65e-01 6.67e+01
  ... (remaining 10749 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.19: 4339
       15.19 -    30.38: 227
       30.38 -    45.57: 81
       45.57 -    60.77: 12
       60.77 -    75.96: 4
  Dihedral angle restraints: 4663
    sinusoidal: 1789
      harmonic: 2874
  Sorted by residual:
  dihedral pdb=" N   SER A 106 "
           pdb=" C   SER A 106 "
           pdb=" CA  SER A 106 "
           pdb=" CB  SER A 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  103.69   19.11     0      2.50e+00 1.60e-01 5.84e+01
  dihedral pdb=" N   SER B 106 "
           pdb=" C   SER B 106 "
           pdb=" CA  SER B 106 "
           pdb=" CB  SER B 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  103.74   19.06     0      2.50e+00 1.60e-01 5.81e+01
  dihedral pdb=" CA  GLN C  56 "
           pdb=" C   GLN C  56 "
           pdb=" N   SER C  57 "
           pdb=" CA  SER C  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -143.98  -36.02     0      5.00e+00 4.00e-02 5.19e+01
  ... (remaining 4660 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.152: 1184
       0.152 -    0.304: 52
       0.304 -    0.455: 6
       0.455 -    0.607: 6
       0.607 -    0.759: 2
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CA  SER A  27 "
            pdb=" N   SER A  27 "
            pdb=" C   SER A  27 "
            pdb=" CB  SER A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.75    0.76 2.00e-01 2.50e+01 1.44e+01
  chirality pdb=" CA  SER B  27 "
            pdb=" N   SER B  27 "
            pdb=" C   SER B  27 "
            pdb=" CB  SER B  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.75    0.76 2.00e-01 2.50e+01 1.44e+01
  chirality pdb=" CA  HIS A 594 "
            pdb=" N   HIS A 594 "
            pdb=" C   HIS A 594 "
            pdb=" CB  HIS A 594 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.73e+00
  ... (remaining 1247 not shown)

  Planarity restraints: 1322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 104 "    0.023 2.00e-02 2.50e+03   4.41e-02 1.95e+01
        pdb=" C   LEU A 104 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   LEU A 104 "    0.027 2.00e-02 2.50e+03
        pdb=" N   PHE A 105 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 104 "   -0.023 2.00e-02 2.50e+03   4.40e-02 1.93e+01
        pdb=" C   LEU B 104 "    0.076 2.00e-02 2.50e+03
        pdb=" O   LEU B 104 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   PHE B 105 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 582 "    0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   ILE A 582 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   ILE A 582 "    0.023 2.00e-02 2.50e+03
        pdb=" N   VAL A 583 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1319 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 101
        2.61 -     3.18: 5935
        3.18 -     3.75: 10939
        3.75 -     4.33: 15320
        4.33 -     4.90: 25900
  Nonbonded interactions: 58195
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C  26 "
            pdb=" SG  CYS C 100 "
     model   vdw
     2.034 3.760
  nonbonded pdb=" NH2 ARG D 101 "
            pdb=" OE2 GLU B 191 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" OE2 GLU A 191 "
            pdb=" NH2 ARG C 101 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" ND2 ASN A  43 "
            pdb=" OG  SER A 521 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" ND2 ASN B  43 "
            pdb=" OG  SER B 521 "
     model   vdw
     2.335 3.120
  ... (remaining 58190 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 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  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:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.560
  Find NCS groups from input model:        0.120
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
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      :  0.018   0.182   7910  Z= 1.201
  Angle     :  1.561  18.157  10754  Z= 0.912
  Chirality :  0.088   0.759   1250
  Planarity :  0.010   0.077   1322
  Dihedral  : 11.121  75.956   2812
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  4.57 %
    Favored  : 94.47 %
  Cbeta Deviations :  1.95 %
  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: -6.23 (0.18), residues: 980
  helix: -4.72 (0.08), residues: 522
  sheet: -1.93 (0.49), residues: 126
  loop : -3.58 (0.25), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.004   TRP A  31 
 HIS   0.006   0.003   HIS A 594 
 PHE   0.024   0.004   PHE B 585 
 TYR   0.039   0.004   TYR B 617 
 ARG   0.005   0.001   ARG A 539 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 154
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8572 (ttt)
REVERT: A  201 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8095 (mtpt)
REVERT: A  208 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7187 (ttm-80)
REVERT: A  468 MET cc_start: 0.8810 (mmm) cc_final: 0.8172 (mmm)
REVERT: B   21 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8558 (ttt)
REVERT: B  201 LYS cc_start: 0.8468 (mmtp) cc_final: 0.8102 (mtpt)
REVERT: B  208 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7191 (ttm-80)
REVERT: B  468 MET cc_start: 0.8819 (mmm) cc_final: 0.8207 (mmm)
  outliers start: 8
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2463
  time to fit residues: 49.5045
Evaluate side-chains
  97 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 MET
Chi-restraints excluded: chain B residue   21 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0060
   chunk 39 optimal weight:    0.0060
   chunk 76 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0670
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.3950

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
A 164 GLN
B  95 ASN
B 164 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.182279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.124182 restraints weight = 9056.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.98
r_work: 0.3230 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7910  Z= 0.157
  Angle     :  0.596   6.498  10754  Z= 0.315
  Chirality :  0.042   0.142   1250
  Planarity :  0.007   0.048   1322
  Dihedral  :  5.100  31.218   1078
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  8.17 %
    Favored  : 90.26 %
  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: -4.85 (0.20), residues: 980
  helix: -3.36 (0.15), residues: 528
  sheet: -2.36 (0.46), residues: 116
  loop : -2.88 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  37 
 HIS   0.004   0.001   HIS A   9 
 PHE   0.014   0.001   PHE A 585 
 TYR   0.010   0.001   TYR D  41 
 ARG   0.003   0.000   ARG B 531 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.8768 (mttp) cc_final: 0.8445 (mttm)
REVERT: A  180 ASP cc_start: 0.8096 (t0) cc_final: 0.7849 (t0)
REVERT: A  201 LYS cc_start: 0.8455 (mmtp) cc_final: 0.7887 (mtpt)
REVERT: A  508 SER cc_start: 0.9264 (t) cc_final: 0.9014 (m)
REVERT: A  539 ARG cc_start: 0.8595 (mtt-85) cc_final: 0.8083 (mtt90)
REVERT: A  606 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8859 (tpt)
REVERT: D   38 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7886 (mtp)
REVERT: D   39 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8210 (mt-10)
REVERT: D   75 SER cc_start: 0.8465 (t) cc_final: 0.8230 (p)
REVERT: C   51 TRP cc_start: 0.7358 (m-10) cc_final: 0.6978 (m-90)
REVERT: B   32 LYS cc_start: 0.8845 (mttp) cc_final: 0.8499 (mttm)
REVERT: B  180 ASP cc_start: 0.8078 (t0) cc_final: 0.7826 (t0)
REVERT: B  201 LYS cc_start: 0.8424 (mmtp) cc_final: 0.7875 (mtpt)
REVERT: B  539 ARG cc_start: 0.8562 (mtt-85) cc_final: 0.8082 (mtt90)
  outliers start: 13
  outliers final: 5
  residues processed: 124
  average time/residue: 0.2329
  time to fit residues: 37.7935
Evaluate side-chains
  107 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0870
   chunk 70 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
B  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.161692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.112102 restraints weight = 9264.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.85
r_work: 0.2873 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7910  Z= 0.169
  Angle     :  0.543   7.123  10754  Z= 0.281
  Chirality :  0.042   0.136   1250
  Planarity :  0.005   0.048   1322
  Dihedral  :  4.618  29.023   1072
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 10.22 %
    Favored  : 87.86 %
  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: -3.78 (0.22), residues: 980
  helix: -2.36 (0.19), residues: 530
  sheet: -1.78 (0.49), residues: 110
  loop : -2.68 (0.27), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  37 
 HIS   0.002   0.001   HIS A   9 
 PHE   0.011   0.002   PHE C  72 
 TYR   0.013   0.001   TYR D  41 
 ARG   0.002   0.000   ARG C 109 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  180 ASP cc_start: 0.8033 (t0) cc_final: 0.7712 (t0)
REVERT: A  467 ILE cc_start: 0.8677 (mm) cc_final: 0.8439 (mm)
REVERT: A  539 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.8169 (mtt90)
REVERT: D   39 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7981 (mt-10)
REVERT: D   75 SER cc_start: 0.8461 (t) cc_final: 0.8203 (p)
REVERT: B  124 MET cc_start: 0.8493 (mtp) cc_final: 0.8073 (mtp)
REVERT: B  180 ASP cc_start: 0.8041 (t0) cc_final: 0.7734 (t0)
REVERT: B  201 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7656 (mtpt)
REVERT: B  539 ARG cc_start: 0.8525 (mtt-85) cc_final: 0.8172 (mtt90)
  outliers start: 16
  outliers final: 9
  residues processed: 108
  average time/residue: 0.1597
  time to fit residues: 25.1298
Evaluate side-chains
  96 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  205 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 85 optimal weight:    0.0070
   chunk 73 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
B 203 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.180318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.122905 restraints weight = 9053.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.27
r_work: 0.3179 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7910  Z= 0.167
  Angle     :  0.523   7.205  10754  Z= 0.270
  Chirality :  0.042   0.135   1250
  Planarity :  0.005   0.050   1322
  Dihedral  :  4.446  27.680   1072
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 10.70 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.24), residues: 980
  helix: -1.75 (0.21), residues: 520
  sheet: -1.55 (0.48), residues: 110
  loop : -2.38 (0.27), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  37 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.009   0.001   PHE B 585 
 TYR   0.014   0.001   TYR D  41 
 ARG   0.001   0.000   ARG C 109 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A   23 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (tp)
REVERT: A  539 ARG cc_start: 0.8520 (mtt-85) cc_final: 0.8151 (mtt90)
REVERT: D   39 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: B   23 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8471 (tp)
REVERT: B   32 LYS cc_start: 0.8935 (mttp) cc_final: 0.8621 (mttm)
REVERT: B  124 MET cc_start: 0.8654 (mtp) cc_final: 0.8248 (mtp)
REVERT: B  180 ASP cc_start: 0.8032 (t0) cc_final: 0.7711 (t0)
REVERT: B  201 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7541 (mtpt)
REVERT: B  539 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.8126 (mtt90)
  outliers start: 15
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1843
  time to fit residues: 28.5070
Evaluate side-chains
  93 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   95 ASN
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  205 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 89 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0070
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.165929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.115183 restraints weight = 8874.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.76
r_work: 0.2835 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7910  Z= 0.162
  Angle     :  0.513   7.365  10754  Z= 0.263
  Chirality :  0.041   0.131   1250
  Planarity :  0.005   0.050   1322
  Dihedral  :  4.338  26.237   1072
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.22 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.25), residues: 980
  helix: -1.36 (0.22), residues: 520
  sheet: -1.45 (0.48), residues: 110
  loop : -2.17 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  37 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.017   0.001   PHE A  87 
 TYR   0.014   0.001   TYR D  41 
 ARG   0.001   0.000   ARG C 109 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A   23 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8424 (tp)
REVERT: A  539 ARG cc_start: 0.8520 (mtt-85) cc_final: 0.8172 (mtt90)
REVERT: B   23 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8418 (tp)
REVERT: B  124 MET cc_start: 0.8710 (mtp) cc_final: 0.8268 (mtp)
REVERT: B  201 LYS cc_start: 0.8320 (mmtp) cc_final: 0.7642 (mtpt)
REVERT: B  539 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.8142 (mtt90)
  outliers start: 18
  outliers final: 13
  residues processed: 101
  average time/residue: 0.2581
  time to fit residues: 37.9977
Evaluate side-chains
  102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   95 ASN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  205 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 93 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.165361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.114607 restraints weight = 8816.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.80
r_work: 0.2827 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7910  Z= 0.182
  Angle     :  0.525   7.610  10754  Z= 0.268
  Chirality :  0.042   0.127   1250
  Planarity :  0.005   0.050   1322
  Dihedral  :  4.315  26.179   1072
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 10.70 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.25), residues: 980
  helix: -1.11 (0.22), residues: 520
  sheet: -1.38 (0.49), residues: 110
  loop : -2.07 (0.29), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  40 
 HIS   0.003   0.001   HIS A   9 
 PHE   0.015   0.001   PHE A  87 
 TYR   0.016   0.001   TYR D  41 
 ARG   0.001   0.000   ARG C 109 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A   23 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8455 (tp)
REVERT: A  539 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.8191 (mtt90)
REVERT: B   23 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8458 (tp)
REVERT: B  124 MET cc_start: 0.8730 (mtp) cc_final: 0.8331 (mtp)
REVERT: B  201 LYS cc_start: 0.8303 (mmtp) cc_final: 0.7570 (mtpt)
REVERT: B  539 ARG cc_start: 0.8515 (mtt-85) cc_final: 0.8165 (mtt90)
  outliers start: 19
  outliers final: 14
  residues processed: 104
  average time/residue: 0.1838
  time to fit residues: 27.8047
Evaluate side-chains
  106 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   95 ASN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   95 ASN
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  205 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.165276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.113103 restraints weight = 8815.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.77
r_work: 0.2824 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7910  Z= 0.177
  Angle     :  0.521   7.730  10754  Z= 0.266
  Chirality :  0.042   0.124   1250
  Planarity :  0.005   0.050   1322
  Dihedral  :  4.254  25.528   1072
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.06 %
    Favored  : 86.66 %
  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: -1.97 (0.25), residues: 980
  helix: -0.82 (0.22), residues: 520
  sheet: -0.93 (0.54), residues: 86
  loop : -1.95 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  40 
 HIS   0.002   0.001   HIS B   9 
 PHE   0.014   0.001   PHE A  87 
 TYR   0.014   0.001   TYR D  41 
 ARG   0.001   0.000   ARG C 109 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 1.309 
Fit side-chains
REVERT: A   23 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8461 (tp)
REVERT: A  539 ARG cc_start: 0.8534 (mtt-85) cc_final: 0.8191 (mtt90)
REVERT: C   51 TRP cc_start: 0.7057 (m-90) cc_final: 0.6751 (m-90)
REVERT: B   23 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8462 (tp)
REVERT: B  124 MET cc_start: 0.8792 (mtp) cc_final: 0.8318 (mtp)
REVERT: B  201 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7507 (mtpt)
REVERT: B  539 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8168 (mtt90)
  outliers start: 19
  outliers final: 13
  residues processed: 103
  average time/residue: 0.2127
  time to fit residues: 31.1341
Evaluate side-chains
  101 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  205 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   chunk 89 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0000
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5384

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.168517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.118753 restraints weight = 8902.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 1.78
r_work: 0.2836 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7910  Z= 0.143
  Angle     :  0.502   7.720  10754  Z= 0.255
  Chirality :  0.041   0.130   1250
  Planarity :  0.005   0.050   1322
  Dihedral  :  4.128  24.678   1072
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 11.54 %
    Favored  : 86.54 %
  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: -1.65 (0.25), residues: 980
  helix: -0.48 (0.23), residues: 518
  sheet: -0.92 (0.52), residues: 86
  loop : -1.89 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  40 
 HIS   0.002   0.000   HIS A   9 
 PHE   0.013   0.001   PHE A  87 
 TYR   0.014   0.001   TYR D  41 
 ARG   0.001   0.000   ARG C 109 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A   92 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7395 (mp)
REVERT: A  539 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.8186 (mtt90)
REVERT: C   51 TRP cc_start: 0.6957 (m-90) cc_final: 0.6672 (m-90)
REVERT: B   92 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7422 (mp)
REVERT: B  124 MET cc_start: 0.8750 (mtp) cc_final: 0.8345 (mtp)
REVERT: B  201 LYS cc_start: 0.8255 (mmtp) cc_final: 0.7482 (mtpt)
REVERT: B  539 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.8163 (mtt90)
  outliers start: 16
  outliers final: 12
  residues processed: 109
  average time/residue: 0.2222
  time to fit residues: 34.0002
Evaluate side-chains
  106 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0010
   chunk 41 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 97 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.6188

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.165763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.114818 restraints weight = 8982.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.79
r_work: 0.2840 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7910  Z= 0.154
  Angle     :  0.509   7.757  10754  Z= 0.258
  Chirality :  0.041   0.124   1250
  Planarity :  0.005   0.050   1322
  Dihedral  :  4.114  23.683   1072
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.54 %
    Favored  : 86.42 %
  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: -1.43 (0.26), residues: 980
  helix: -0.28 (0.23), residues: 518
  sheet: -0.83 (0.52), residues: 86
  loop : -1.82 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  40 
 HIS   0.002   0.001   HIS A   9 
 PHE   0.012   0.001   PHE A  87 
 TYR   0.013   0.001   TYR D  41 
 ARG   0.001   0.000   ARG C 109 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A   92 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7478 (mp)
REVERT: A  539 ARG cc_start: 0.8504 (mtt-85) cc_final: 0.8166 (mtt90)
REVERT: B  124 MET cc_start: 0.8766 (mtp) cc_final: 0.8345 (mtp)
REVERT: B  201 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7416 (mtpt)
REVERT: B  539 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.8148 (mtt90)
  outliers start: 17
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1616
  time to fit residues: 23.6311
Evaluate side-chains
  99 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 56 optimal weight:    0.2980
   chunk 12 optimal weight:    0.0000
   chunk 6 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.166111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.115406 restraints weight = 8911.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.79
r_work: 0.2834 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7910  Z= 0.146
  Angle     :  0.506   7.377  10754  Z= 0.255
  Chirality :  0.041   0.125   1250
  Planarity :  0.005   0.050   1322
  Dihedral  :  4.053  23.278   1072
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.02 %
    Favored  : 86.42 %
  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: -1.22 (0.26), residues: 980
  helix: -0.06 (0.23), residues: 518
  sheet: -0.73 (0.52), residues: 86
  loop : -1.80 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  40 
 HIS   0.002   0.000   HIS A   9 
 PHE   0.020   0.001   PHE B  87 
 TYR   0.013   0.001   TYR D  41 
 ARG   0.001   0.000   ARG C 109 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   92 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7622 (mp)
REVERT: A  539 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.8190 (mtt90)
REVERT: B   32 LYS cc_start: 0.8941 (mttp) cc_final: 0.8597 (mttm)
REVERT: B  124 MET cc_start: 0.8760 (mtp) cc_final: 0.8347 (mtp)
REVERT: B  201 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7457 (mtpt)
REVERT: B  539 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8173 (mtt90)
  outliers start: 13
  outliers final: 12
  residues processed: 107
  average time/residue: 0.1912
  time to fit residues: 28.5070
Evaluate side-chains
  102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  606 MET
Chi-restraints excluded: chain D residue    6 VAL
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain C residue    6 VAL
Chi-restraints excluded: chain C residue  115 VAL
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  502 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 82 optimal weight:    0.3980
   chunk 54 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.163392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.117237 restraints weight = 8959.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.80
r_work: 0.2823 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7910  Z= 0.186
  Angle     :  0.535   7.907  10754  Z= 0.267
  Chirality :  0.042   0.182   1250
  Planarity :  0.005   0.050   1322
  Dihedral  :  4.123  22.370   1072
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.90 %
    Favored  : 86.30 %
  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: -1.21 (0.26), residues: 980
  helix: -0.07 (0.23), residues: 518
  sheet: -0.73 (0.53), residues: 86
  loop : -1.78 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  37 
 HIS   0.002   0.001   HIS A   9 
 PHE   0.020   0.002   PHE B  87 
 TYR   0.014   0.001   TYR C  41 
 ARG   0.001   0.000   ARG A 208 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4800.53 seconds
wall clock time: 85 minutes 40.78 seconds (5140.78 seconds total)