Starting phenix.real_space_refine
on Thu May 29 13:26:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xh9_38345/05_2025/8xh9_38345_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xh9_38345/05_2025/8xh9_38345.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xh9_38345/05_2025/8xh9_38345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xh9_38345/05_2025/8xh9_38345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xh9_38345/05_2025/8xh9_38345_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xh9_38345/05_2025/8xh9_38345_trim.cif"
  }
  resolution = 2.58
  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=   0.059
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: 5
    Type Number    sf(0)   Gaussians
     S     156      5.16       5
     C   11040      2.51       5
     N    2508      2.21       5
     O    2688      1.98       5
     H   15864      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 32256
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 2636
          Classifications: {'peptide': 163}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 52
          Unusual residues: {'MC3': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 178
          Unresolved non-hydrogen angles: 223
          Unresolved non-hydrogen dihedrals: 158
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'MC3:plan-2': 5, 'MC3:plan-1': 5}
          Unresolved non-hydrogen planarities: 35
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 9.21, per 1000 atoms: 0.29
  Number of scatterers: 32256
  At special positions: 0
  Unit cell: (97.8, 100.2, 149.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     156     16.00
     O    2688      8.00
     N    2508      7.00
     C   11040      6.00
     H   15864      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=36, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  55 " - pdb=" SG  CYS E 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  55 " - pdb=" SG  CYS D 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  55 " - pdb=" SG  CYS G 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  55 " - pdb=" SG  CYS F 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I  55 " - pdb=" SG  CYS I 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  55 " - pdb=" SG  CYS H 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K  55 " - pdb=" SG  CYS K 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  55 " - pdb=" SG  CYS J 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  55 " - pdb=" SG  CYS L 242 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  62 " - pdb=" SG  CYS C 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  62 " - pdb=" SG  CYS E 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  62 " - pdb=" SG  CYS D 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  62 " - pdb=" SG  CYS G 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  62 " - pdb=" SG  CYS F 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I  62 " - pdb=" SG  CYS I 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  62 " - pdb=" SG  CYS H 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K  62 " - pdb=" SG  CYS K 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  62 " - pdb=" SG  CYS J 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  62 " - pdb=" SG  CYS L 236 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  66 " - pdb=" SG  CYS E 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  66 " - pdb=" SG  CYS D 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  66 " - pdb=" SG  CYS G 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  66 " - pdb=" SG  CYS F 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I  66 " - pdb=" SG  CYS I 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  66 " - pdb=" SG  CYS H 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K  66 " - pdb=" SG  CYS K 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS J  66 " - pdb=" SG  CYS J 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  66 " - pdb=" SG  CYS L 231 " distance=2.04

  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: 8.23
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3696

  Finding SS restraints...
    Secondary structure from input PDB file:
      84 helices and 12 sheets defined
      75.5% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 41
      removed outlier: 4.315A  pdb=" N   ARG A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ILE A  25 " --> pdb=" O   MET A  21 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A  41 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 41 through 46'
    Processing helix  chain 'A' and resid 61 through 71
    Processing helix  chain 'A' and resid 74 through 86
    Processing helix  chain 'A' and resid 87 through 100
    Processing helix  chain 'A' and resid 196 through 222
    Processing helix  chain 'A' and resid 246 through 276
    Processing helix  chain 'B' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE B  25 " --> pdb=" O   MET B  21 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B  41 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL B  45 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   TYR B  46 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 41 through 46'
    Processing helix  chain 'B' and resid 61 through 71
    Processing helix  chain 'B' and resid 74 through 86
    Processing helix  chain 'B' and resid 87 through 100
      removed outlier: 3.500A  pdb=" N   LEU B  91 " --> pdb=" O   CYS B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 222
    Processing helix  chain 'B' and resid 246 through 276
    Processing helix  chain 'C' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE C  25 " --> pdb=" O   MET C  21 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL C  41 " --> pdb=" O   ILE C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 46
      removed outlier: 3.839A  pdb=" N   VAL C  45 " --> pdb=" O   VAL C  41 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   TYR C  46 " --> pdb=" O   GLY C  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 41 through 46'
    Processing helix  chain 'C' and resid 61 through 71
    Processing helix  chain 'C' and resid 74 through 86
    Processing helix  chain 'C' and resid 87 through 100
    Processing helix  chain 'C' and resid 196 through 222
    Processing helix  chain 'C' and resid 246 through 276
    Processing helix  chain 'D' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE D  25 " --> pdb=" O   MET D  21 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL D  41 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL D  45 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR D  46 " --> pdb=" O   GLY D  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 41 through 46'
    Processing helix  chain 'D' and resid 61 through 71
    Processing helix  chain 'D' and resid 74 through 86
    Processing helix  chain 'D' and resid 87 through 100
    Processing helix  chain 'D' and resid 196 through 222
    Processing helix  chain 'D' and resid 246 through 276
    Processing helix  chain 'E' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE E  25 " --> pdb=" O   MET E  21 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL E  41 " --> pdb=" O   ILE E  37 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL E  45 " --> pdb=" O   VAL E  41 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR E  46 " --> pdb=" O   GLY E  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 41 through 46'
    Processing helix  chain 'E' and resid 61 through 71
    Processing helix  chain 'E' and resid 74 through 86
    Processing helix  chain 'E' and resid 87 through 100
    Processing helix  chain 'E' and resid 196 through 222
    Processing helix  chain 'E' and resid 246 through 276
    Processing helix  chain 'F' and resid 21 through 41
      removed outlier: 3.951A  pdb=" N   ILE F  25 " --> pdb=" O   MET F  21 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL F  41 " --> pdb=" O   ILE F  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL F  45 " --> pdb=" O   VAL F  41 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR F  46 " --> pdb=" O   GLY F  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 41 through 46'
    Processing helix  chain 'F' and resid 61 through 71
    Processing helix  chain 'F' and resid 74 through 86
    Processing helix  chain 'F' and resid 87 through 100
    Processing helix  chain 'F' and resid 196 through 222
    Processing helix  chain 'F' and resid 246 through 276
    Processing helix  chain 'G' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL G  41 " --> pdb=" O   ILE G  37 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL G  45 " --> pdb=" O   VAL G  41 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR G  46 " --> pdb=" O   GLY G  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 41 through 46'
    Processing helix  chain 'G' and resid 61 through 71
    Processing helix  chain 'G' and resid 74 through 86
    Processing helix  chain 'G' and resid 87 through 100
    Processing helix  chain 'G' and resid 196 through 222
    Processing helix  chain 'G' and resid 246 through 276
    Processing helix  chain 'H' and resid 21 through 41
      removed outlier: 3.951A  pdb=" N   ILE H  25 " --> pdb=" O   MET H  21 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL H  41 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL H  45 " --> pdb=" O   VAL H  41 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR H  46 " --> pdb=" O   GLY H  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 41 through 46'
    Processing helix  chain 'H' and resid 61 through 71
    Processing helix  chain 'H' and resid 74 through 86
    Processing helix  chain 'H' and resid 87 through 100
    Processing helix  chain 'H' and resid 196 through 222
    Processing helix  chain 'H' and resid 246 through 276
    Processing helix  chain 'I' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE I  25 " --> pdb=" O   MET I  21 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL I  41 " --> pdb=" O   ILE I  37 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 41 through 46
      removed outlier: 3.839A  pdb=" N   VAL I  45 " --> pdb=" O   VAL I  41 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR I  46 " --> pdb=" O   GLY I  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 41 through 46'
    Processing helix  chain 'I' and resid 61 through 71
    Processing helix  chain 'I' and resid 74 through 86
    Processing helix  chain 'I' and resid 87 through 100
    Processing helix  chain 'I' and resid 196 through 222
    Processing helix  chain 'I' and resid 246 through 276
    Processing helix  chain 'J' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE J  25 " --> pdb=" O   MET J  21 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL J  41 " --> pdb=" O   ILE J  37 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL J  45 " --> pdb=" O   VAL J  41 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   TYR J  46 " --> pdb=" O   GLY J  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 41 through 46'
    Processing helix  chain 'J' and resid 61 through 71
    Processing helix  chain 'J' and resid 74 through 86
    Processing helix  chain 'J' and resid 87 through 100
    Processing helix  chain 'J' and resid 196 through 222
    Processing helix  chain 'J' and resid 246 through 276
    Processing helix  chain 'K' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE K  25 " --> pdb=" O   MET K  21 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL K  41 " --> pdb=" O   ILE K  37 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 41 through 46
      removed outlier: 3.839A  pdb=" N   VAL K  45 " --> pdb=" O   VAL K  41 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR K  46 " --> pdb=" O   GLY K  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 41 through 46'
    Processing helix  chain 'K' and resid 61 through 71
    Processing helix  chain 'K' and resid 74 through 86
    Processing helix  chain 'K' and resid 87 through 100
    Processing helix  chain 'K' and resid 196 through 222
    Processing helix  chain 'K' and resid 246 through 276
    Processing helix  chain 'L' and resid 21 through 41
      removed outlier: 3.950A  pdb=" N   ILE L  25 " --> pdb=" O   MET L  21 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL L  41 " --> pdb=" O   ILE L  37 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 41 through 46
      removed outlier: 3.840A  pdb=" N   VAL L  45 " --> pdb=" O   VAL L  41 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   TYR L  46 " --> pdb=" O   GLY L  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 41 through 46'
    Processing helix  chain 'L' and resid 61 through 71
    Processing helix  chain 'L' and resid 74 through 86
    Processing helix  chain 'L' and resid 87 through 100
    Processing helix  chain 'L' and resid 196 through 222
    Processing helix  chain 'L' and resid 246 through 276
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55
      removed outlier: 3.635A  pdb=" N   VAL A  54 " --> pdb=" O   TYR A 243 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55
      removed outlier: 3.635A  pdb=" N   VAL B  54 " --> pdb=" O   TYR B 243 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55
      removed outlier: 3.635A  pdb=" N   VAL C  54 " --> pdb=" O   TYR C 243 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55
      removed outlier: 3.634A  pdb=" N   VAL D  54 " --> pdb=" O   TYR D 243 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55
      removed outlier: 3.635A  pdb=" N   VAL E  54 " --> pdb=" O   TYR E 243 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55
      removed outlier: 3.635A  pdb=" N   VAL F  54 " --> pdb=" O   TYR F 243 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55
      removed outlier: 3.635A  pdb=" N   VAL G  54 " --> pdb=" O   TYR G 243 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55
      removed outlier: 3.634A  pdb=" N   VAL H  54 " --> pdb=" O   TYR H 243 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55
      removed outlier: 3.635A  pdb=" N   VAL I  54 " --> pdb=" O   TYR I 243 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55
      removed outlier: 3.634A  pdb=" N   VAL J  54 " --> pdb=" O   TYR J 243 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55
      removed outlier: 3.634A  pdb=" N   VAL K  54 " --> pdb=" O   TYR K 243 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.635A  pdb=" N   VAL L  54 " --> pdb=" O   TYR L 243 " (cutoff:3.500A)

    1151 hydrogen bonds defined for protein.
    3417 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: 10.37

  Time building geometry restraints manager: 9.91 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 15828
        1.02 -     1.22: 36
        1.22 -     1.42: 6900
        1.42 -     1.62: 9612
        1.62 -     1.83: 204
  Bond restraints: 32580
  Sorted by residual:
  bond pdb=" NE  ARG K  24 "
       pdb=" HE  ARG K  24 "
    ideal  model  delta    sigma   weight residual
    0.860  0.970 -0.110 2.00e-02 2.50e+03 3.02e+01
  bond pdb=" NE  ARG A  24 "
       pdb=" HE  ARG A  24 "
    ideal  model  delta    sigma   weight residual
    0.860  0.970 -0.110 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" NE  ARG C  24 "
       pdb=" HE  ARG C  24 "
    ideal  model  delta    sigma   weight residual
    0.860  0.969 -0.109 2.00e-02 2.50e+03 2.99e+01
  bond pdb=" NE  ARG B  24 "
       pdb=" HE  ARG B  24 "
    ideal  model  delta    sigma   weight residual
    0.860  0.969 -0.109 2.00e-02 2.50e+03 2.99e+01
  bond pdb=" NE  ARG J  24 "
       pdb=" HE  ARG J  24 "
    ideal  model  delta    sigma   weight residual
    0.860  0.969 -0.109 2.00e-02 2.50e+03 2.99e+01
  ... (remaining 32575 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 51539
        1.13 -     2.26: 5896
        2.26 -     3.39: 552
        3.39 -     4.51: 164
        4.51 -     5.64: 73
  Bond angle restraints: 58224
  Sorted by residual:
  angle pdb=" C   VAL B  98 "
        pdb=" N   HIS B  99 "
        pdb=" CA  HIS B  99 "
      ideal   model   delta    sigma   weight residual
     120.29  116.46    3.83 1.42e+00 4.96e-01 7.26e+00
  angle pdb=" C   VAL H  98 "
        pdb=" N   HIS H  99 "
        pdb=" CA  HIS H  99 "
      ideal   model   delta    sigma   weight residual
     120.29  116.48    3.81 1.42e+00 4.96e-01 7.20e+00
  angle pdb=" C   VAL I  98 "
        pdb=" N   HIS I  99 "
        pdb=" CA  HIS I  99 "
      ideal   model   delta    sigma   weight residual
     120.29  116.50    3.79 1.42e+00 4.96e-01 7.13e+00
  angle pdb=" C   VAL D  98 "
        pdb=" N   HIS D  99 "
        pdb=" CA  HIS D  99 "
      ideal   model   delta    sigma   weight residual
     120.29  116.51    3.78 1.42e+00 4.96e-01 7.09e+00
  angle pdb=" C   VAL J  98 "
        pdb=" N   HIS J  99 "
        pdb=" CA  HIS J  99 "
      ideal   model   delta    sigma   weight residual
     120.29  116.52    3.77 1.42e+00 4.96e-01 7.05e+00
  ... (remaining 58219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 13136
       16.86 -    33.72: 1516
       33.72 -    50.58: 727
       50.58 -    67.44: 281
       67.44 -    84.29: 24
  Dihedral angle restraints: 15684
    sinusoidal: 8496
      harmonic: 7188
  Sorted by residual:
  dihedral pdb=" CB  GLU I 241 "
           pdb=" CG  GLU I 241 "
           pdb=" CD  GLU I 241 "
           pdb=" OE1 GLU I 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.29  -84.29     1      3.00e+01 1.11e-03 9.61e+00
  dihedral pdb=" CB  GLU C 241 "
           pdb=" CG  GLU C 241 "
           pdb=" CD  GLU C 241 "
           pdb=" OE1 GLU C 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.23  -84.23     1      3.00e+01 1.11e-03 9.59e+00
  dihedral pdb=" CB  GLU E 241 "
           pdb=" CG  GLU E 241 "
           pdb=" CD  GLU E 241 "
           pdb=" OE1 GLU E 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.23  -84.23     1      3.00e+01 1.11e-03 9.59e+00
  ... (remaining 15681 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1550
       0.033 -    0.065: 641
       0.065 -    0.098: 305
       0.098 -    0.130: 60
       0.130 -    0.163: 24
  Chirality restraints: 2580
  Sorted by residual:
  chirality pdb=" CA  ARG H 246 "
            pdb=" N   ARG H 246 "
            pdb=" C   ARG H 246 "
            pdb=" CB  ARG H 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.61e-01
  chirality pdb=" CA  ARG G 246 "
            pdb=" N   ARG G 246 "
            pdb=" C   ARG G 246 "
            pdb=" CB  ARG G 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.58e-01
  chirality pdb=" CA  ARG K 246 "
            pdb=" N   ARG K 246 "
            pdb=" C   ARG K 246 "
            pdb=" CB  ARG K 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-01
  ... (remaining 2577 not shown)

  Planarity restraints: 4572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  20 "   -0.018 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" N   MET C  21 "    0.057 2.00e-02 2.50e+03
        pdb=" CA  MET C  21 "   -0.015 2.00e-02 2.50e+03
        pdb=" H   MET C  21 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  20 "   -0.018 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" N   MET D  21 "    0.057 2.00e-02 2.50e+03
        pdb=" CA  MET D  21 "   -0.015 2.00e-02 2.50e+03
        pdb=" H   MET D  21 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  20 "   -0.018 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" N   MET F  21 "    0.057 2.00e-02 2.50e+03
        pdb=" CA  MET F  21 "   -0.015 2.00e-02 2.50e+03
        pdb=" H   MET F  21 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 4569 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 5385
        2.29 -     2.87: 65839
        2.87 -     3.44: 77764
        3.44 -     4.02: 104107
        4.02 -     4.60: 158959
  Nonbonded interactions: 412054
  Sorted by model distance:
  nonbonded pdb=" O   SER K 245 "
            pdb=" HZ2 LYS K 250 "
     model   vdw
     1.712 2.450
  nonbonded pdb=" O   SER B 245 "
            pdb=" HZ2 LYS B 250 "
     model   vdw
     1.712 2.450
  nonbonded pdb=" O   SER H 245 "
            pdb=" HZ2 LYS H 250 "
     model   vdw
     1.713 2.450
  nonbonded pdb=" O   SER I 245 "
            pdb=" HZ2 LYS I 250 "
     model   vdw
     1.713 2.450
  nonbonded pdb=" O   SER E 245 "
            pdb=" HZ2 LYS E 250 "
     model   vdw
     1.713 2.450
  ... (remaining 412049 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: 0.15
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

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:             3.860
  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:             0.570
  Extract box with map and model:          1.170
  Check model and map are aligned:         0.220
  Set scattering table:                    0.270
  Process input model:                     57.000
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:10.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   73.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  16752  Z= 0.222
  Angle     :  0.860   5.643  22548  Z= 0.463
  Chirality :  0.044   0.163   2580
  Planarity :  0.006   0.043   2712
  Dihedral  : 15.039  84.294   6132
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.86 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  1.63 (0.17), residues: 1908
  helix:  1.98 (0.13), residues: 1332
  sheet:  1.10 (0.36), residues: 120
  loop : -1.73 (0.24), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G  79 
 HIS   0.009   0.003   HIS I 274 
 PHE   0.019   0.002   PHE D  53 
 TYR   0.015   0.002   TYR I  67 
 ARG   0.004   0.001   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11271 ( 1151)
  hydrogen bonds       : angle       3.95775 ( 3417)
  SS BOND              : bond        0.00736 (   36)
  SS BOND              : angle       1.18826 (   72)
  covalent geometry    : bond        0.00400 (16716)
  covalent geometry    : angle       0.85910 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 2.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.7461 (t70) cc_final: 0.7246 (t0)
REVERT: A   69 ARG cc_start: 0.7633 (tpt170) cc_final: 0.7384 (tpt90)
REVERT: A  232 ASN cc_start: 0.8025 (p0) cc_final: 0.7815 (p0)
REVERT: A  239 GLU cc_start: 0.7882 (tt0) cc_final: 0.7606 (tt0)
REVERT: B  232 ASN cc_start: 0.7951 (p0) cc_final: 0.7718 (p0)
REVERT: B  239 GLU cc_start: 0.7945 (tt0) cc_final: 0.7659 (tt0)
REVERT: C   47 ASP cc_start: 0.7503 (t70) cc_final: 0.7299 (t0)
REVERT: C  232 ASN cc_start: 0.8090 (p0) cc_final: 0.7862 (p0)
REVERT: C  239 GLU cc_start: 0.7868 (tt0) cc_final: 0.7612 (tt0)
REVERT: D   69 ARG cc_start: 0.7760 (tpt170) cc_final: 0.7464 (tpt90)
REVERT: D  232 ASN cc_start: 0.8027 (p0) cc_final: 0.7737 (p0)
REVERT: D  239 GLU cc_start: 0.7994 (tt0) cc_final: 0.7733 (tt0)
REVERT: E  232 ASN cc_start: 0.8076 (p0) cc_final: 0.7793 (p0)
REVERT: E  239 GLU cc_start: 0.7955 (tt0) cc_final: 0.7675 (tt0)
REVERT: F  232 ASN cc_start: 0.7952 (p0) cc_final: 0.7651 (p0)
REVERT: F  239 GLU cc_start: 0.7965 (tt0) cc_final: 0.7639 (tt0)
REVERT: G   47 ASP cc_start: 0.7477 (t70) cc_final: 0.7255 (t0)
REVERT: G   69 ARG cc_start: 0.7656 (tpt170) cc_final: 0.7377 (tpt90)
REVERT: H   47 ASP cc_start: 0.7528 (t70) cc_final: 0.7321 (t0)
REVERT: H  232 ASN cc_start: 0.8053 (p0) cc_final: 0.7846 (p0)
REVERT: H  239 GLU cc_start: 0.7808 (tt0) cc_final: 0.7572 (tt0)
REVERT: I  232 ASN cc_start: 0.8122 (p0) cc_final: 0.7872 (p0)
REVERT: J   69 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7438 (tpt90)
REVERT: J  232 ASN cc_start: 0.8030 (p0) cc_final: 0.7749 (p0)
REVERT: J  239 GLU cc_start: 0.8031 (tt0) cc_final: 0.7774 (tt0)
REVERT: K   52 MET cc_start: 0.8320 (mmt) cc_final: 0.8067 (mmt)
REVERT: K   69 ARG cc_start: 0.7781 (tpt170) cc_final: 0.7499 (tpt90)
REVERT: K  232 ASN cc_start: 0.7909 (p0) cc_final: 0.7654 (p0)
REVERT: K  239 GLU cc_start: 0.8169 (tt0) cc_final: 0.7912 (tt0)
REVERT: L  232 ASN cc_start: 0.7998 (p0) cc_final: 0.7733 (p0)
REVERT: L  239 GLU cc_start: 0.7944 (tt0) cc_final: 0.7654 (tt0)
  outliers start: 0
  outliers final: 6
  residues processed: 312
  average time/residue: 1.6286
  time to fit residues: 600.8676
Evaluate side-chains
  234 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 228
  time to evaluate  : 2.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain E residue  273 ASN
Chi-restraints excluded: chain F residue  273 ASN
Chi-restraints excluded: chain I residue  273 ASN
Chi-restraints excluded: chain K residue  273 ASN
Chi-restraints excluded: chain L residue  273 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 162 optimal weight:    6.9990
   chunk 145 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9980
   chunk 150 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 112 optimal weight:   10.0000
   chunk 174 optimal weight:    3.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.191527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.136925 restraints weight = 46302.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.76
r_work: 0.3507 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  16752  Z= 0.176
  Angle     :  0.590   4.889  22548  Z= 0.321
  Chirality :  0.042   0.130   2580
  Planarity :  0.004   0.030   2712
  Dihedral  :  5.910  29.789   2604
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.65 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  3.42 (0.18), residues: 1908
  helix:  3.29 (0.12), residues: 1344
  sheet:  2.28 (0.43), residues: 120
  loop : -1.27 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP G  79 
 HIS   0.004   0.001   HIS C 274 
 PHE   0.007   0.001   PHE I  33 
 TYR   0.013   0.002   TYR L  67 
 ARG   0.002   0.000   ARG G 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08214 ( 1151)
  hydrogen bonds       : angle       3.60797 ( 3417)
  SS BOND              : bond        0.00587 (   36)
  SS BOND              : angle       1.13734 (   72)
  covalent geometry    : bond        0.00388 (16716)
  covalent geometry    : angle       0.58776 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 211
  time to evaluate  : 2.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7508 (tpt90)
REVERT: A  232 ASN cc_start: 0.8271 (p0) cc_final: 0.7982 (p0)
REVERT: B   43 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6958 (tp30)
REVERT: B   69 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7490 (tpt90)
REVERT: B  239 GLU cc_start: 0.8113 (tt0) cc_final: 0.7896 (tt0)
REVERT: C   21 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.5401 (mpt)
REVERT: D   69 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7531 (tpt90)
REVERT: D  232 ASN cc_start: 0.8248 (p0) cc_final: 0.7923 (p0)
REVERT: F  239 GLU cc_start: 0.8059 (tt0) cc_final: 0.7815 (tt0)
REVERT: G   69 ARG cc_start: 0.7823 (tpt170) cc_final: 0.7509 (tpt90)
REVERT: G  232 ASN cc_start: 0.8246 (p0) cc_final: 0.8009 (p0)
REVERT: J   69 ARG cc_start: 0.7845 (tpt170) cc_final: 0.7538 (tpt90)
REVERT: J  232 ASN cc_start: 0.8234 (p0) cc_final: 0.7892 (p0)
REVERT: K   69 ARG cc_start: 0.7842 (tpt170) cc_final: 0.7544 (tpt90)
REVERT: K  232 ASN cc_start: 0.8177 (p0) cc_final: 0.7949 (p0)
REVERT: K  239 GLU cc_start: 0.8291 (tt0) cc_final: 0.8051 (tt0)
  outliers start: 36
  outliers final: 19
  residues processed: 223
  average time/residue: 1.8238
  time to fit residues: 472.8826
Evaluate side-chains
  227 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 206
  time to evaluate  : 2.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  273 ASN
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain F residue   95 THR
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   21 MET
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue  224 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 157 optimal weight:    0.7980
   chunk 176 optimal weight:    7.9990
   chunk 128 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 129 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.189908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.134448 restraints weight = 46753.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 1.80
r_work: 0.3479 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  16752  Z= 0.170
  Angle     :  0.576   5.193  22548  Z= 0.310
  Chirality :  0.043   0.138   2580
  Planarity :  0.004   0.033   2712
  Dihedral  :  5.909  31.381   2594
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.50 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  3.93 (0.18), residues: 1908
  helix:  3.83 (0.12), residues: 1344
  sheet:  2.19 (0.42), residues: 120
  loop : -1.58 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP C  79 
 HIS   0.005   0.002   HIS C 274 
 PHE   0.009   0.002   PHE K 253 
 TYR   0.011   0.002   TYR K 243 
 ARG   0.003   0.001   ARG E  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08027 ( 1151)
  hydrogen bonds       : angle       3.42707 ( 3417)
  SS BOND              : bond        0.00563 (   36)
  SS BOND              : angle       1.26208 (   72)
  covalent geometry    : bond        0.00364 (16716)
  covalent geometry    : angle       0.57287 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 216
  time to evaluate  : 2.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ARG cc_start: 0.7808 (tpt170) cc_final: 0.7514 (tpt90)
REVERT: A  232 ASN cc_start: 0.8357 (p0) cc_final: 0.8020 (p0)
REVERT: C   21 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5603 (mpt)
REVERT: D   69 ARG cc_start: 0.7825 (tpt170) cc_final: 0.7503 (tpt90)
REVERT: D  232 ASN cc_start: 0.8382 (p0) cc_final: 0.8032 (p0)
REVERT: G   69 ARG cc_start: 0.7808 (tpt170) cc_final: 0.7495 (tpt90)
REVERT: G  232 ASN cc_start: 0.8317 (p0) cc_final: 0.7975 (p0)
REVERT: J   69 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7485 (tpt90)
REVERT: J  232 ASN cc_start: 0.8384 (p0) cc_final: 0.8032 (p0)
  outliers start: 34
  outliers final: 34
  residues processed: 233
  average time/residue: 1.8022
  time to fit residues: 489.6386
Evaluate side-chains
  252 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 217
  time to evaluate  : 2.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 MET
Chi-restraints excluded: chain A residue   90 SER
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain B residue   21 MET
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  273 ASN
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   90 SER
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  273 ASN
Chi-restraints excluded: chain E residue   21 MET
Chi-restraints excluded: chain E residue   90 SER
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   86 VAL
Chi-restraints excluded: chain G residue   90 SER
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   21 MET
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   90 SER
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain J residue   21 MET
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain J residue  273 ASN
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue  224 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 148 optimal weight:    0.0370
   chunk 91 optimal weight:    0.5980
   chunk 111 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 177 optimal weight:    6.9990
   chunk 155 optimal weight:    5.9990
   chunk 159 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 127 optimal weight:    7.9990
   overall best weight:    2.1264

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.191717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.135700 restraints weight = 46431.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 1.84
r_work: 0.3500 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  16752  Z= 0.139
  Angle     :  0.516   4.432  22548  Z= 0.276
  Chirality :  0.041   0.127   2580
  Planarity :  0.003   0.031   2712
  Dihedral  :  5.437  27.756   2594
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.00 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  4.18 (0.18), residues: 1908
  helix:  4.04 (0.12), residues: 1344
  sheet:  2.37 (0.43), residues: 120
  loop : -1.61 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G  79 
 HIS   0.004   0.001   HIS D 274 
 PHE   0.008   0.001   PHE G  33 
 TYR   0.010   0.002   TYR L  67 
 ARG   0.002   0.000   ARG K  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07047 ( 1151)
  hydrogen bonds       : angle       3.34980 ( 3417)
  SS BOND              : bond        0.00335 (   36)
  SS BOND              : angle       0.99821 (   72)
  covalent geometry    : bond        0.00292 (16716)
  covalent geometry    : angle       0.51390 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 216
  time to evaluate  : 2.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5643 (mpt)
REVERT: A   69 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7507 (tpt90)
REVERT: A  232 ASN cc_start: 0.8369 (p0) cc_final: 0.8027 (p0)
REVERT: C   21 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.5606 (mpt)
REVERT: D   69 ARG cc_start: 0.7810 (tpt170) cc_final: 0.7493 (tpt90)
REVERT: D  232 ASN cc_start: 0.8398 (p0) cc_final: 0.8033 (p0)
REVERT: G   69 ARG cc_start: 0.7820 (tpt170) cc_final: 0.7500 (tpt90)
REVERT: G  232 ASN cc_start: 0.8300 (p0) cc_final: 0.7930 (p0)
REVERT: J   69 ARG cc_start: 0.7812 (tpt170) cc_final: 0.7495 (tpt90)
REVERT: J  232 ASN cc_start: 0.8395 (p0) cc_final: 0.8019 (p0)
  outliers start: 36
  outliers final: 32
  residues processed: 228
  average time/residue: 1.8236
  time to fit residues: 485.9351
Evaluate side-chains
  246 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 212
  time to evaluate  : 2.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 MET
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain B residue   21 MET
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  273 ASN
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   47 ASP
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain H residue  273 ASN
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   47 ASP
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain J residue   21 MET
Chi-restraints excluded: chain J residue   41 VAL
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain J residue  273 ASN
Chi-restraints excluded: chain K residue   41 VAL
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue  224 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 188 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 94 optimal weight:    6.9990
   chunk 145 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 128 optimal weight:   10.0000
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.189882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.133520 restraints weight = 46275.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.82
r_work: 0.3477 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  16752  Z= 0.165
  Angle     :  0.558   5.162  22548  Z= 0.297
  Chirality :  0.042   0.139   2580
  Planarity :  0.004   0.034   2712
  Dihedral  :  5.940  31.012   2592
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.22 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  4.18 (0.19), residues: 1908
  helix:  4.06 (0.12), residues: 1344
  sheet:  2.28 (0.43), residues: 120
  loop : -1.65 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP J  79 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.008   0.001   PHE E  53 
 TYR   0.011   0.002   TYR J  67 
 ARG   0.003   0.000   ARG L  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07580 ( 1151)
  hydrogen bonds       : angle       3.34216 ( 3417)
  SS BOND              : bond        0.00524 (   36)
  SS BOND              : angle       1.29437 (   72)
  covalent geometry    : bond        0.00372 (16716)
  covalent geometry    : angle       0.55418 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 218
  time to evaluate  : 2.426 
Fit side-chains
   revert: symmetry clash
REVERT: C   21 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5741 (mpt)
  outliers start: 52
  outliers final: 37
  residues processed: 242
  average time/residue: 1.7107
  time to fit residues: 484.9406
Evaluate side-chains
  251 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 213
  time to evaluate  : 2.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  273 ASN
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 VAL
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   21 MET
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain I residue   47 ASP
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain J residue   21 MET
Chi-restraints excluded: chain J residue   41 VAL
Chi-restraints excluded: chain J residue   47 ASP
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain J residue  273 ASN
Chi-restraints excluded: chain K residue   21 MET
Chi-restraints excluded: chain K residue   41 VAL
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue  224 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 157 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 121 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 133 optimal weight:    1.9990
   chunk 169 optimal weight:   10.0000
   chunk 75 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 159 optimal weight:    7.9990
   chunk 142 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.188056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131492 restraints weight = 46128.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.82
r_work: 0.3449 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  16752  Z= 0.197
  Angle     :  0.602   5.822  22548  Z= 0.323
  Chirality :  0.044   0.150   2580
  Planarity :  0.004   0.037   2712
  Dihedral  :  6.704  34.927   2592
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.99 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  4.01 (0.19), residues: 1908
  helix:  3.92 (0.12), residues: 1344
  sheet:  2.29 (0.44), residues: 120
  loop : -1.69 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.003   TRP B  79 
 HIS   0.005   0.002   HIS E 274 
 PHE   0.011   0.002   PHE B 253 
 TYR   0.012   0.002   TYR G  67 
 ARG   0.004   0.000   ARG L  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08348 ( 1151)
  hydrogen bonds       : angle       3.39333 ( 3417)
  SS BOND              : bond        0.00700 (   36)
  SS BOND              : angle       1.57728 (   72)
  covalent geometry    : bond        0.00467 (16716)
  covalent geometry    : angle       0.59599 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 218
  time to evaluate  : 2.259 
Fit side-chains
   revert: symmetry clash
REVERT: C   21 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5810 (mpt)
  outliers start: 59
  outliers final: 45
  residues processed: 232
  average time/residue: 1.7300
  time to fit residues: 467.4091
Evaluate side-chains
  261 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 215
  time to evaluate  : 2.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain B residue   21 MET
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  273 ASN
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain E residue   21 MET
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain F residue  275 LEU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 VAL
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   21 MET
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain I residue   47 ASP
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain I residue  273 ASN
Chi-restraints excluded: chain J residue   21 MET
Chi-restraints excluded: chain J residue   41 VAL
Chi-restraints excluded: chain J residue   47 ASP
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain J residue  273 ASN
Chi-restraints excluded: chain K residue   21 MET
Chi-restraints excluded: chain K residue   41 VAL
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue  224 SER
Chi-restraints excluded: chain L residue  273 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 186 optimal weight:    4.9990
   chunk 165 optimal weight:    3.9990
   chunk 155 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 128 optimal weight:   10.0000
   chunk 144 optimal weight:   10.0000
   chunk 154 optimal weight:    0.0970
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.191292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.134999 restraints weight = 45487.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.77
r_work: 0.3443 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  16752  Z= 0.136
  Angle     :  0.506   4.426  22548  Z= 0.273
  Chirality :  0.041   0.128   2580
  Planarity :  0.004   0.033   2712
  Dihedral  :  5.609  29.811   2592
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.17 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  4.26 (0.19), residues: 1908
  helix:  4.18 (0.12), residues: 1344
  sheet:  2.34 (0.44), residues: 120
  loop : -1.85 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G  79 
 HIS   0.003   0.001   HIS B 274 
 PHE   0.007   0.001   PHE L  33 
 TYR   0.011   0.002   TYR C  67 
 ARG   0.002   0.000   ARG K  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06934 ( 1151)
  hydrogen bonds       : angle       3.29796 ( 3417)
  SS BOND              : bond        0.00333 (   36)
  SS BOND              : angle       1.02780 (   72)
  covalent geometry    : bond        0.00286 (16716)
  covalent geometry    : angle       0.50343 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 215
  time to evaluate  : 2.657 
Fit side-chains
REVERT: C   21 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5933 (mpt)
  outliers start: 33
  outliers final: 36
  residues processed: 228
  average time/residue: 1.8203
  time to fit residues: 485.7713
Evaluate side-chains
  250 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 213
  time to evaluate  : 2.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  273 ASN
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 VAL
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   21 MET
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain J residue   21 MET
Chi-restraints excluded: chain J residue   41 VAL
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain J residue  273 ASN
Chi-restraints excluded: chain K residue   21 MET
Chi-restraints excluded: chain K residue   41 VAL
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue  224 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.188819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.131918 restraints weight = 45393.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.78
r_work: 0.3408 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  16752  Z= 0.183
  Angle     :  0.581   5.713  22548  Z= 0.311
  Chirality :  0.043   0.150   2580
  Planarity :  0.004   0.036   2712
  Dihedral  :  6.459  32.991   2592
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.95 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  4.20 (0.19), residues: 1908
  helix:  4.08 (0.12), residues: 1344
  sheet:  2.52 (0.46), residues: 120
  loop : -1.76 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  79 
 HIS   0.003   0.001   HIS B 274 
 PHE   0.010   0.002   PHE D 253 
 TYR   0.011   0.002   TYR D 243 
 ARG   0.002   0.000   ARG K  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07895 ( 1151)
  hydrogen bonds       : angle       3.35060 ( 3417)
  SS BOND              : bond        0.00633 (   36)
  SS BOND              : angle       1.53111 (   72)
  covalent geometry    : bond        0.00428 (16716)
  covalent geometry    : angle       0.57561 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 220
  time to evaluate  : 2.462 
Fit side-chains
REVERT: C   21 MET cc_start: 0.6214 (OUTLIER) cc_final: 0.5931 (mpt)
  outliers start: 41
  outliers final: 40
  residues processed: 234
  average time/residue: 1.7615
  time to fit residues: 480.9620
Evaluate side-chains
  258 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 217
  time to evaluate  : 2.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 MET
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain B residue   21 MET
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  273 ASN
Chi-restraints excluded: chain E residue   21 MET
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 VAL
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   21 MET
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain J residue   21 MET
Chi-restraints excluded: chain J residue   41 VAL
Chi-restraints excluded: chain J residue   47 ASP
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain J residue  273 ASN
Chi-restraints excluded: chain K residue   21 MET
Chi-restraints excluded: chain K residue   41 VAL
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue  224 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 170 optimal weight:    4.9990
   chunk 177 optimal weight:    6.9990
   chunk 136 optimal weight:    9.9990
   chunk 138 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 129 optimal weight:    6.9990
   chunk 122 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 112 optimal weight:   10.0000
   chunk 132 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.189025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.132301 restraints weight = 45329.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.77
r_work: 0.3410 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  16752  Z= 0.174
  Angle     :  0.565   5.336  22548  Z= 0.304
  Chirality :  0.043   0.141   2580
  Planarity :  0.004   0.037   2712
  Dihedral  :  6.405  34.071   2592
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.78 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  4.18 (0.19), residues: 1908
  helix:  4.07 (0.12), residues: 1344
  sheet:  2.61 (0.47), residues: 120
  loop : -1.81 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP B  79 
 HIS   0.003   0.001   HIS E 274 
 PHE   0.009   0.002   PHE I  33 
 TYR   0.012   0.002   TYR C  67 
 ARG   0.002   0.000   ARG K  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07785 ( 1151)
  hydrogen bonds       : angle       3.34086 ( 3417)
  SS BOND              : bond        0.00572 (   36)
  SS BOND              : angle       1.40551 (   72)
  covalent geometry    : bond        0.00402 (16716)
  covalent geometry    : angle       0.56077 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 217
  time to evaluate  : 2.560 
Fit side-chains
REVERT: C   21 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5956 (mpt)
  outliers start: 39
  outliers final: 40
  residues processed: 231
  average time/residue: 1.7817
  time to fit residues: 480.2269
Evaluate side-chains
  257 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 216
  time to evaluate  : 2.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 MET
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain B residue   21 MET
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain D residue  273 ASN
Chi-restraints excluded: chain E residue   21 MET
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 VAL
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   21 MET
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain J residue   21 MET
Chi-restraints excluded: chain J residue   41 VAL
Chi-restraints excluded: chain J residue   47 ASP
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain J residue  273 ASN
Chi-restraints excluded: chain K residue   21 MET
Chi-restraints excluded: chain K residue   41 VAL
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue  224 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 152 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 145 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.188733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.132033 restraints weight = 45289.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.77
r_work: 0.3404 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  16752  Z= 0.182
  Angle     :  0.582   5.690  22548  Z= 0.312
  Chirality :  0.043   0.147   2580
  Planarity :  0.004   0.037   2712
  Dihedral  :  6.650  36.173   2592
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.95 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  4.17 (0.19), residues: 1908
  helix:  4.04 (0.12), residues: 1344
  sheet:  2.82 (0.49), residues: 120
  loop : -1.81 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  79 
 HIS   0.003   0.001   HIS B 274 
 PHE   0.010   0.002   PHE I  33 
 TYR   0.012   0.002   TYR L  67 
 ARG   0.002   0.000   ARG K  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07979 ( 1151)
  hydrogen bonds       : angle       3.35442 ( 3417)
  SS BOND              : bond        0.00610 (   36)
  SS BOND              : angle       1.49658 (   72)
  covalent geometry    : bond        0.00425 (16716)
  covalent geometry    : angle       0.57650 (22476)

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

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

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3816 Ramachandran restraints generated.
    1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 217
  time to evaluate  : 2.512 
Fit side-chains
REVERT: C   21 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5924 (mpt)
  outliers start: 37
  outliers final: 38
  residues processed: 230
  average time/residue: 1.7647
  time to fit residues: 472.7560
Evaluate side-chains
  255 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 216
  time to evaluate  : 2.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 MET
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  273 ASN
Chi-restraints excluded: chain B residue   21 MET
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue  224 SER
Chi-restraints excluded: chain E residue   21 MET
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue  224 SER
Chi-restraints excluded: chain F residue   21 MET
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue  224 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   41 VAL
Chi-restraints excluded: chain G residue  224 SER
Chi-restraints excluded: chain G residue  273 ASN
Chi-restraints excluded: chain H residue   21 MET
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  224 SER
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   41 VAL
Chi-restraints excluded: chain I residue  224 SER
Chi-restraints excluded: chain J residue   21 MET
Chi-restraints excluded: chain J residue   41 VAL
Chi-restraints excluded: chain J residue  224 SER
Chi-restraints excluded: chain J residue  273 ASN
Chi-restraints excluded: chain K residue   21 MET
Chi-restraints excluded: chain K residue   41 VAL
Chi-restraints excluded: chain K residue  224 SER
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   41 VAL
Chi-restraints excluded: chain L residue  224 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 173 optimal weight:    1.9990
   chunk 139 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 169 optimal weight:    8.9990
   chunk 179 optimal weight:    3.9990
   chunk 162 optimal weight:    1.9990
   chunk 156 optimal weight:    2.9990
   chunk 141 optimal weight:    0.0370
   chunk 90 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.9260

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
B 207 ASN
C 207 ASN
D 207 ASN
E 207 ASN
F 207 ASN
G 207 ASN
H 207 ASN
I 207 ASN
J 207 ASN
K 207 ASN
L 207 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.192803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.136793 restraints weight = 45217.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 1.77
r_work: 0.3467 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  16752  Z= 0.114
  Angle     :  0.469   4.431  22548  Z= 0.256
  Chirality :  0.040   0.136   2580
  Planarity :  0.003   0.028   2712
  Dihedral  :  5.181  28.168   2592
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 17.74 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  4.41 (0.19), residues: 1908
  helix:  4.31 (0.12), residues: 1344
  sheet:  2.66 (0.46), residues: 120
  loop : -1.98 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G  79 
 HIS   0.003   0.001   HIS E 274 
 PHE   0.006   0.001   PHE C  53 
 TYR   0.008   0.001   TYR C  67 
 ARG   0.002   0.000   ARG D  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06082 ( 1151)
  hydrogen bonds       : angle       3.22883 ( 3417)
  SS BOND              : bond        0.00150 (   36)
  SS BOND              : angle       0.81380 (   72)
  covalent geometry    : bond        0.00213 (16716)
  covalent geometry    : angle       0.46770 (22476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 23534.40 seconds
wall clock time: 401 minutes 48.43 seconds (24108.43 seconds total)