Starting phenix.real_space_refine (version: 1.21rc1)
on Sat Sep 30 18:17:10 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/09_2023/7nch_12266.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/09_2023/7nch_12266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/09_2023/7nch_12266.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/09_2023/7nch_12266.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/09_2023/7nch_12266.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/09_2023/7nch_12266.pdb"
  }
  resolution = 3.84
  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=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     C    3408      2.51       5
     N     972      2.21       5
     O    1116      1.98       5
     H    5796      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib"
  Total number of atoms: 11292
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 941
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
          Chain breaks: 1
  Time building chain proxies: 5.00, per 1000 atoms: 0.44
  Number of scatterers: 11292
  At special positions: 0
  Unit cell: (100.1, 89.1, 53.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     O    1116      8.00
     N     972      7.00
     C    3408      6.00
     H    5796      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 8.60
  Conformation dependent library (CDL) restraints added in 962.1 milliseconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 21
      removed outlier: 3.537A  pdb=" N   ALA B  17 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA A  18 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA B  19 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLU A  20 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LYS B  21 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA C  17 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA C  19 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS C  21 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA D  17 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ALA D  19 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS D  21 " --> pdb=" O   GLU C  20 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA E  19 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ALA F  19 " --> pdb=" O   ALA E  18 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS F  21 " --> pdb=" O   GLU E  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41
      removed outlier: 3.516A  pdb=" N   GLY A  41 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY B  41 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   TYR C  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR D  39 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55
      removed outlier: 8.236A  pdb=" N   GLY A  51 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ALA B  53 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   ALA A  53 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL B  55 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL A  55 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   HIS B  50 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   ALA C  53 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 9.035A  pdb=" N   VAL B  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 10.752A  pdb=" N   VAL C  55 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 8.866A  pdb=" N   THR B  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 8.958A  pdb=" N   HIS C  50 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   ALA D  53 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   VAL C  52 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 10.750A  pdb=" N   VAL D  55 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 8.845A  pdb=" N   THR C  54 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   VAL D  49 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLY E  51 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   GLY D  51 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   ALA E  53 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   ALA D  53 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   VAL E  55 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   VAL D  55 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 9.070A  pdb=" N   HIS E  50 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   ALA F  53 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
      removed outlier: 9.280A  pdb=" N   VAL E  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 10.951A  pdb=" N   VAL F  55 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 9.095A  pdb=" N   THR E  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 66
      removed outlier: 6.929A  pdb=" N   VAL C  63 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   VAL D  63 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL E  63 " --> pdb=" O   THR F  64 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 72
      removed outlier: 5.999A  pdb=" N   ALA A  69 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   THR B  72 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL A  71 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   ALA B  69 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   THR C  72 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL B  71 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 85 through 88
      removed outlier: 6.592A  pdb=" N   GLY A  86 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLY B  86 " --> pdb=" O   ALA C  85 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY C  86 " --> pdb=" O   ALA D  85 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 16 through 21
      removed outlier: 3.518A  pdb=" N   ALA H  17 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA H  19 " --> pdb=" O   ALA G  18 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   GLU G  20 " --> pdb=" O   ALA H  19 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   LYS H  21 " --> pdb=" O   GLU G  20 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA I  17 " --> pdb=" O   VAL H  16 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA I  19 " --> pdb=" O   ALA H  18 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LYS I  21 " --> pdb=" O   GLU H  20 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA J  17 " --> pdb=" O   VAL I  16 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA J  19 " --> pdb=" O   ALA I  18 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS J  21 " --> pdb=" O   GLU I  20 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA K  19 " --> pdb=" O   ALA J  18 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LYS K  21 " --> pdb=" O   GLU J  20 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA L  19 " --> pdb=" O   ALA K  18 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LYS L  21 " --> pdb=" O   GLU K  20 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 39 through 41
      removed outlier: 3.511A  pdb=" N   GLY G  41 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   TYR H  39 " --> pdb=" O   VAL I  40 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY I  41 " --> pdb=" O   VAL J  40 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 49 through 55
      removed outlier: 4.687A  pdb=" N   VAL G  49 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   GLY H  51 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   GLY G  51 " --> pdb=" O   GLY H  51 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   ALA H  53 " --> pdb=" O   GLY G  51 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ALA G  53 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   VAL H  55 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL G  55 " --> pdb=" O   VAL H  55 " (cutoff:3.500A)
      removed outlier: 9.051A  pdb=" N   HIS H  50 " --> pdb=" O   GLY I  51 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   ALA I  53 " --> pdb=" O   HIS H  50 " (cutoff:3.500A)
      removed outlier: 9.005A  pdb=" N   VAL H  52 " --> pdb=" O   ALA I  53 " (cutoff:3.500A)
      removed outlier: 10.793A  pdb=" N   VAL I  55 " --> pdb=" O   VAL H  52 " (cutoff:3.500A)
      removed outlier: 8.896A  pdb=" N   THR H  54 " --> pdb=" O   VAL I  55 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   HIS I  50 " --> pdb=" O   GLY J  51 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   ALA J  53 " --> pdb=" O   HIS I  50 " (cutoff:3.500A)
      removed outlier: 9.158A  pdb=" N   VAL I  52 " --> pdb=" O   ALA J  53 " (cutoff:3.500A)
      removed outlier: 10.796A  pdb=" N   VAL J  55 " --> pdb=" O   VAL I  52 " (cutoff:3.500A)
      removed outlier: 8.866A  pdb=" N   THR I  54 " --> pdb=" O   VAL J  55 " (cutoff:3.500A)
      removed outlier: 9.085A  pdb=" N   HIS J  50 " --> pdb=" O   GLY K  51 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   ALA K  53 " --> pdb=" O   HIS J  50 " (cutoff:3.500A)
      removed outlier: 9.263A  pdb=" N   VAL J  52 " --> pdb=" O   ALA K  53 " (cutoff:3.500A)
      removed outlier: 10.885A  pdb=" N   VAL K  55 " --> pdb=" O   VAL J  52 " (cutoff:3.500A)
      removed outlier: 8.925A  pdb=" N   THR J  54 " --> pdb=" O   VAL K  55 " (cutoff:3.500A)
      removed outlier: 9.056A  pdb=" N   HIS K  50 " --> pdb=" O   GLY L  51 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   ALA L  53 " --> pdb=" O   HIS K  50 " (cutoff:3.500A)
      removed outlier: 9.290A  pdb=" N   VAL K  52 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 10.872A  pdb=" N   VAL L  55 " --> pdb=" O   VAL K  52 " (cutoff:3.500A)
      removed outlier: 8.993A  pdb=" N   THR K  54 " --> pdb=" O   VAL L  55 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 66
      removed outlier: 7.089A  pdb=" N   VAL I  63 " --> pdb=" O   THR J  64 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   VAL J  63 " --> pdb=" O   THR K  64 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   VAL K  63 " --> pdb=" O   THR L  64 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 85 through 88
      removed outlier: 6.536A  pdb=" N   GLY G  86 " --> pdb=" O   SER H  87 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER I  87 " --> pdb=" O   GLY H  86 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ILE H  88 " --> pdb=" O   SER I  87 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY I  86 " --> pdb=" O   ALA J  85 " (cutoff:3.500A)

    50 hydrogen bonds defined for protein.
    141 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: 3.55

  Time building geometry restraints manager: 8.93 seconds

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

  Histogram of bond lengths:
        0.82 -     0.97: 4723
        0.97 -     1.13: 1073
        1.13 -     1.28: 984
        1.28 -     1.44: 1089
        1.44 -     1.59: 3423
  Bond restraints: 11292
  Sorted by residual:
  bond pdb=" C   GLY F  86 "
       pdb=" N   SER F  87 "
    ideal  model  delta    sigma   weight residual
    1.330  1.359 -0.029 1.26e-02 6.30e+03 5.24e+00
  bond pdb=" N   VAL A  40 "
       pdb=" CA  VAL A  40 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.44e-02 4.82e+03 5.21e+00
  bond pdb=" C   ALA L  18 "
       pdb=" N   ALA L  19 "
    ideal  model  delta    sigma   weight residual
    1.330  1.358 -0.028 1.26e-02 6.30e+03 5.05e+00
  bond pdb=" C   GLU L  20 "
       pdb=" N   LYS L  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.362 -0.032 1.45e-02 4.76e+03 4.94e+00
  bond pdb=" C   ALA F  18 "
       pdb=" N   ALA F  19 "
    ideal  model  delta    sigma   weight residual
    1.330  1.358 -0.028 1.26e-02 6.30e+03 4.83e+00
  ... (remaining 11287 not shown)

  Histogram of bond angle deviations from ideal:
       73.97 -    85.28: 6
       85.28 -    96.58: 0
       96.58 -   107.88: 2613
      107.88 -   119.19: 14178
      119.19 -   130.49: 3735
  Bond angle restraints: 20532
  Sorted by residual:
  angle pdb=" N   THR I  44 "
        pdb=" CA  THR I  44 "
        pdb=" HA  THR I  44 "
      ideal   model   delta    sigma   weight residual
     110.00   73.97   36.03 3.00e+00 1.11e-01 1.44e+02
  angle pdb=" N   THR C  44 "
        pdb=" CA  THR C  44 "
        pdb=" HA  THR C  44 "
      ideal   model   delta    sigma   weight residual
     110.00   74.30   35.70 3.00e+00 1.11e-01 1.42e+02
  angle pdb=" C   THR I  44 "
        pdb=" CA  THR I  44 "
        pdb=" HA  THR I  44 "
      ideal   model   delta    sigma   weight residual
     109.00   74.27   34.73 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" C   THR C  44 "
        pdb=" CA  THR C  44 "
        pdb=" HA  THR C  44 "
      ideal   model   delta    sigma   weight residual
     109.00   74.54   34.46 3.00e+00 1.11e-01 1.32e+02
  angle pdb=" CB  THR C  44 "
        pdb=" CA  THR C  44 "
        pdb=" HA  THR C  44 "
      ideal   model   delta    sigma   weight residual
     109.00   79.67   29.33 3.00e+00 1.11e-01 9.56e+01
  ... (remaining 20527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3679
       17.96 -    35.93: 240
       35.93 -    53.89: 47
       53.89 -    71.85: 222
       71.85 -    89.81: 24
  Dihedral angle restraints: 4212
    sinusoidal: 1956
      harmonic: 2256
  Sorted by residual:
  dihedral pdb=" CA  ILE A  88 "
           pdb=" C   ILE A  88 "
           pdb=" N   ALA A  89 "
           pdb=" CA  ALA A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.02   28.98     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  ILE G  88 "
           pdb=" C   ILE G  88 "
           pdb=" N   ALA G  89 "
           pdb=" CA  ALA G  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.53   28.47     0      5.00e+00 4.00e-02 3.24e+01
  dihedral pdb=" CA  VAL A  74 "
           pdb=" C   VAL A  74 "
           pdb=" N   THR A  75 "
           pdb=" CA  THR A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.59   28.41     0      5.00e+00 4.00e-02 3.23e+01
  ... (remaining 4209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 681
       0.092 -    0.185: 244
       0.185 -    0.277: 55
       0.277 -    0.369: 2
       0.369 -    0.461: 2
  Chirality restraints: 984
  Sorted by residual:
  chirality pdb=" CA  THR C  44 "
            pdb=" N   THR C  44 "
            pdb=" C   THR C  44 "
            pdb=" CB  THR C  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.06    0.46 2.00e-01 2.50e+01 5.31e+00
  chirality pdb=" CA  THR I  44 "
            pdb=" N   THR I  44 "
            pdb=" C   THR I  44 "
            pdb=" CB  THR I  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.08    0.45 2.00e-01 2.50e+01 5.03e+00
  chirality pdb=" CA  ILE G  88 "
            pdb=" N   ILE G  88 "
            pdb=" C   ILE G  88 "
            pdb=" CB  ILE G  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.80   -0.37 2.00e-01 2.50e+01 3.34e+00
  ... (remaining 981 not shown)

  Planarity restraints: 1716
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN L  24 "   -0.030 2.00e-02 2.50e+03   3.56e-02 1.90e+01
        pdb=" CD  GLN L  24 "    0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLN L  24 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE2 GLN L  24 "    0.054 2.00e-02 2.50e+03
        pdb="HE21 GLN L  24 "   -0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN L  24 "   -0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  39 "   -0.022 2.00e-02 2.50e+03   2.51e-02 1.88e+01
        pdb=" CG  TYR H  39 "    0.070 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  39 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  39 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  39 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  39 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  39 "   -0.018 2.00e-02 2.50e+03
        pdb=" OH  TYR H  39 "    0.008 2.00e-02 2.50e+03
        pdb=" HD1 TYR H  39 "   -0.023 2.00e-02 2.50e+03
        pdb=" HD2 TYR H  39 "   -0.026 2.00e-02 2.50e+03
        pdb=" HE1 TYR H  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR H  39 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN F  24 "   -0.029 2.00e-02 2.50e+03   3.49e-02 1.82e+01
        pdb=" CD  GLN F  24 "    0.031 2.00e-02 2.50e+03
        pdb=" OE1 GLN F  24 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 GLN F  24 "    0.053 2.00e-02 2.50e+03
        pdb="HE21 GLN F  24 "   -0.000 2.00e-02 2.50e+03
        pdb="HE22 GLN F  24 "   -0.051 2.00e-02 2.50e+03
  ... (remaining 1713 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.23: 603
        2.23 -     2.80: 22255
        2.80 -     3.36: 25990
        3.36 -     3.93: 32857
        3.93 -     4.50: 50921
  Nonbonded interactions: 132626
  Sorted by model distance:
  nonbonded pdb=" HG  SER E  87 "
            pdb=" O   SER F  87 "
     model   vdw
     1.662 1.850
  nonbonded pdb=" H   THR I  44 "
            pdb=" HA  THR I  44 "
     model   vdw
     1.664 1.816
  nonbonded pdb=" HG  SER K  87 "
            pdb=" O   SER L  87 "
     model   vdw
     1.667 1.850
  nonbonded pdb=" H   THR C  44 "
            pdb=" HA  THR C  44 "
     model   vdw
     1.674 1.816
  nonbonded pdb=" HG1 THR C  44 "
            pdb=" O   THR D  44 "
     model   vdw
     1.726 1.850
  ... (remaining 132621 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  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:             0.180
  Extract box with map and model:          4.160
  Check model and map are aligned:         0.170
  Set scattering table:                    0.110
  Process input model:                     36.600
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.060
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4929
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      :  0.013   0.069   5496  Z= 0.900
  Angle     :  1.606   7.507   7416  Z= 0.967
  Chirality :  0.095   0.461    984
  Planarity :  0.005   0.026    924
  Dihedral  : 14.676  89.811   1848
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.78 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.70 (0.15), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.12), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 155
  average time/residue: 0.4356
  time to fit residues: 84.7716
Evaluate side-chains
  85 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.875 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1232
  time to fit residues: 1.2636
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
I  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5131
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5496  Z= 0.252
  Angle     :  0.740   6.866   7416  Z= 0.437
  Chirality :  0.053   0.384    984
  Planarity :  0.003   0.015    924
  Dihedral  :  8.298  26.470    804
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.89 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.90 (0.17), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.13), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 9
  residues processed: 97
  average time/residue: 0.3771
  time to fit residues: 47.8953
Evaluate side-chains
  78 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.872 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1253
  time to fit residues: 2.9795
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.5784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5305
moved from start:          0.4794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5496  Z= 0.262
  Angle     :  0.696   6.347   7416  Z= 0.406
  Chirality :  0.052   0.389    984
  Planarity :  0.003   0.015    924
  Dihedral  :  7.487  25.581    804
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.93 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.31 (0.18), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.14), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 12
  residues processed: 77
  average time/residue: 0.3961
  time to fit residues: 39.2465
Evaluate side-chains
  77 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.783 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.1181
  time to fit residues: 3.5235
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5324
moved from start:          0.5286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5496  Z= 0.214
  Angle     :  0.604   5.602   7416  Z= 0.354
  Chirality :  0.052   0.386    984
  Planarity :  0.002   0.012    924
  Dihedral  :  6.963  23.371    804
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.90 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 16.67 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.33 (0.19), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.14), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 68
  average time/residue: 0.4148
  time to fit residues: 36.9778
Evaluate side-chains
  63 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.821 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1191
  time to fit residues: 1.5197
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 35 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
H  62 GLN
I  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5300
moved from start:          0.5769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5496  Z= 0.165
  Angle     :  0.547   5.317   7416  Z= 0.318
  Chirality :  0.052   0.380    984
  Planarity :  0.002   0.009    924
  Dihedral  :  6.204  20.511    804
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 18.70 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.13 (0.19), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 71
  average time/residue: 0.3453
  time to fit residues: 33.0563
Evaluate side-chains
  67 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.859 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1219
  time to fit residues: 1.4386
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
I  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5353
moved from start:          0.6134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5496  Z= 0.188
  Angle     :  0.553   4.826   7416  Z= 0.323
  Chirality :  0.052   0.391    984
  Planarity :  0.002   0.011    924
  Dihedral  :  6.130  19.610    804
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.07 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 18.70 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.18 (0.19), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 5
  residues processed: 65
  average time/residue: 0.3409
  time to fit residues: 30.3478
Evaluate side-chains
  62 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.941 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1406
  time to fit residues: 2.3315
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    0.2980
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    0.2980
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5389
moved from start:          0.6572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5496  Z= 0.194
  Angle     :  0.552   5.803   7416  Z= 0.319
  Chirality :  0.052   0.388    984
  Planarity :  0.002   0.011    924
  Dihedral  :  5.944  18.369    804
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.24 %
    Favored  : 87.76 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 19.81 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.20), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 62
  average time/residue: 0.2781
  time to fit residues: 25.1280
Evaluate side-chains
  58 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.861 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1345
  time to fit residues: 1.5250
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5504
moved from start:          0.7064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5496  Z= 0.278
  Angle     :  0.630   4.985   7416  Z= 0.365
  Chirality :  0.053   0.399    984
  Planarity :  0.003   0.016    924
  Dihedral  :  6.683  21.622    804
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.32 %
    Favored  : 85.68 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 21.11 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.58 (0.19), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 61
  average time/residue: 0.2384
  time to fit residues: 22.0453
Evaluate side-chains
  65 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.847 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1236
  time to fit residues: 2.8364
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 58 optimal weight:    0.2980
   chunk 61 optimal weight:    0.0970
   chunk 64 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5445
moved from start:          0.7148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5496  Z= 0.180
  Angle     :  0.556   4.633   7416  Z= 0.319
  Chirality :  0.053   0.385    984
  Planarity :  0.002   0.020    924
  Dihedral  :  5.949  17.840    804
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.72 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 20.37 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.41 (0.20), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.15), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 61
  average time/residue: 0.2732
  time to fit residues: 24.3179
Evaluate side-chains
  62 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.914 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1451
  time to fit residues: 2.2402
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0010
   chunk 45 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0270
   overall best weight:    0.4044

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5386
moved from start:          0.7335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5496  Z= 0.155
  Angle     :  0.522   5.155   7416  Z= 0.298
  Chirality :  0.053   0.380    984
  Planarity :  0.002   0.015    924
  Dihedral  :  5.334  17.692    804
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.48 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.21), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.16), residues: 768

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2451
  time to fit residues: 21.1658
Evaluate side-chains
  56 residues out of total 540 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.819 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9640
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.196230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.165111 restraints weight = 24762.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.176644 restraints weight = 10849.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.183319 restraints weight = 5553.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.4761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5561
moved from start:          0.7510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5496  Z= 0.178
  Angle     :  0.529   4.640   7416  Z= 0.303
  Chirality :  0.053   0.389    984
  Planarity :  0.002   0.014    924
  Dihedral  :  5.400  17.806    804
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.41 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.14 (0.21), residues: 768
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.16), residues: 768
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3307.87 seconds
wall clock time: 58 minutes 54.82 seconds (3534.82 seconds total)