Starting phenix.real_space_refine
on Mon Sep 23 21:23:29 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/09_2024/7qv5_14167_trim.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/09_2024/7qv5_14167.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/09_2024/7qv5_14167.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/09_2024/7qv5_14167.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/09_2024/7qv5_14167_trim.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv5_14167/09_2024/7qv5_14167_trim.cif"
  }
  resolution = 3.0
  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=   0.005
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    1638      2.51       5
     N     495      2.21       5
     O     432      1.98       5
     H    2997      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 5562
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 271
          Classifications: {'peptide': 17}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 16}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 239
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 106
          Classifications: {'peptide': 7}
          Modifications used: {'NH3': 1}
          Link IDs: {'TRANS': 6}
  Restraints were copied for chains:
    D, G, J, M, P, S, V, Y, E, H, K, N, Q, T, W, Z, F, I, L, O, R, U,
    X, a
  Time building chain proxies: 1.64, per 1000 atoms: 0.29
  Number of scatterers: 5562
  At special positions: 0
  Unit cell: (114.75, 123.25, 29.75, 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     432      8.00
     N     495      7.00
     C    1638      6.00
     H    2997      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  - 3.00
        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=18, symmetry=0
  Number of additional bonds: simple=18, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 326.7 milliseconds
  

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  612

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 65.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 16
      removed outlier: 6.552A  pdb=" N   LEU A   5 " --> pdb=" O   ILE J   6 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   LYS J   8 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG A   7 " --> pdb=" O   LYS J   8 " (cutoff:3.500A)
      removed outlier: 8.400A  pdb=" N   VAL J  10 " --> pdb=" O   ARG A   7 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA A   9 " --> pdb=" O   VAL J  10 " (cutoff:3.500A)
      removed outlier: 8.466A  pdb=" N   VAL J  12 " --> pdb=" O   ALA A   9 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   SER A  11 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   LYS J  14 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE A  13 " --> pdb=" O   LYS J  14 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ILE J  16 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ASN A  15 " --> pdb=" O   ILE J  16 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU J   5 " --> pdb=" O   ILE S   6 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   LYS S   8 " --> pdb=" O   LEU J   5 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG J   7 " --> pdb=" O   LYS S   8 " (cutoff:3.500A)
      removed outlier: 8.400A  pdb=" N   VAL S  10 " --> pdb=" O   ARG J   7 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA J   9 " --> pdb=" O   VAL S  10 " (cutoff:3.500A)
      removed outlier: 8.466A  pdb=" N   VAL S  12 " --> pdb=" O   ALA J   9 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   SER J  11 " --> pdb=" O   VAL S  12 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   LYS S  14 " --> pdb=" O   SER J  11 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE J  13 " --> pdb=" O   LYS S  14 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   ILE S  16 " --> pdb=" O   ILE J  13 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ASN J  15 " --> pdb=" O   ILE S  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 16
      removed outlier: 6.337A  pdb=" N   ARG B   7 " --> pdb=" O   LYS K   8 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   VAL K  10 " --> pdb=" O   ARG B   7 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ALA B   9 " --> pdb=" O   VAL K  10 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   VAL K  12 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER B  11 " --> pdb=" O   VAL K  12 " (cutoff:3.500A)
      removed outlier: 8.282A  pdb=" N   LYS K  14 " --> pdb=" O   SER B  11 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE B  13 " --> pdb=" O   LYS K  14 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE K  16 " --> pdb=" O   ILE B  13 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASN B  15 " --> pdb=" O   ILE K  16 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ARG K   7 " --> pdb=" O   LYS T   8 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   VAL T  10 " --> pdb=" O   ARG K   7 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA K   9 " --> pdb=" O   VAL T  10 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   VAL T  12 " --> pdb=" O   ALA K   9 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER K  11 " --> pdb=" O   VAL T  12 " (cutoff:3.500A)
      removed outlier: 8.282A  pdb=" N   LYS T  14 " --> pdb=" O   SER K  11 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE K  13 " --> pdb=" O   LYS T  14 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE T  16 " --> pdb=" O   ILE K  13 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ASN K  15 " --> pdb=" O   ILE T  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6
    Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 16
      removed outlier: 6.553A  pdb=" N   LEU D   5 " --> pdb=" O   ILE M   6 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   LYS M   8 " --> pdb=" O   LEU D   5 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ARG D   7 " --> pdb=" O   LYS M   8 " (cutoff:3.500A)
      removed outlier: 8.400A  pdb=" N   VAL M  10 " --> pdb=" O   ARG D   7 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA D   9 " --> pdb=" O   VAL M  10 " (cutoff:3.500A)
      removed outlier: 8.466A  pdb=" N   VAL M  12 " --> pdb=" O   ALA D   9 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   SER D  11 " --> pdb=" O   VAL M  12 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   LYS M  14 " --> pdb=" O   SER D  11 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE D  13 " --> pdb=" O   LYS M  14 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ILE M  16 " --> pdb=" O   ILE D  13 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ASN D  15 " --> pdb=" O   ILE M  16 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LEU M   5 " --> pdb=" O   ILE V   6 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   LYS V   8 " --> pdb=" O   LEU M   5 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ARG M   7 " --> pdb=" O   LYS V   8 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   VAL V  10 " --> pdb=" O   ARG M   7 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA M   9 " --> pdb=" O   VAL V  10 " (cutoff:3.500A)
      removed outlier: 8.466A  pdb=" N   VAL V  12 " --> pdb=" O   ALA M   9 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   SER M  11 " --> pdb=" O   VAL V  12 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   LYS V  14 " --> pdb=" O   SER M  11 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE M  13 " --> pdb=" O   LYS V  14 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   ILE V  16 " --> pdb=" O   ILE M  13 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ASN M  15 " --> pdb=" O   ILE V  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 16
      removed outlier: 6.338A  pdb=" N   ARG E   7 " --> pdb=" O   LYS N   8 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   VAL N  10 " --> pdb=" O   ARG E   7 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ALA E   9 " --> pdb=" O   VAL N  10 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   VAL N  12 " --> pdb=" O   ALA E   9 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER E  11 " --> pdb=" O   VAL N  12 " (cutoff:3.500A)
      removed outlier: 8.282A  pdb=" N   LYS N  14 " --> pdb=" O   SER E  11 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE E  13 " --> pdb=" O   LYS N  14 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE N  16 " --> pdb=" O   ILE E  13 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ASN E  15 " --> pdb=" O   ILE N  16 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ARG N   7 " --> pdb=" O   LYS W   8 " (cutoff:3.500A)
      removed outlier: 8.454A  pdb=" N   VAL W  10 " --> pdb=" O   ARG N   7 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ALA N   9 " --> pdb=" O   VAL W  10 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   VAL W  12 " --> pdb=" O   ALA N   9 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER N  11 " --> pdb=" O   VAL W  12 " (cutoff:3.500A)
      removed outlier: 8.282A  pdb=" N   LYS W  14 " --> pdb=" O   SER N  11 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ILE N  13 " --> pdb=" O   LYS W  14 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE W  16 " --> pdb=" O   ILE N  13 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ASN N  15 " --> pdb=" O   ILE W  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 16
      removed outlier: 6.551A  pdb=" N   LEU G   5 " --> pdb=" O   ILE P   6 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   LYS P   8 " --> pdb=" O   LEU G   5 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ARG G   7 " --> pdb=" O   LYS P   8 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   VAL P  10 " --> pdb=" O   ARG G   7 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA G   9 " --> pdb=" O   VAL P  10 " (cutoff:3.500A)
      removed outlier: 8.466A  pdb=" N   VAL P  12 " --> pdb=" O   ALA G   9 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   SER G  11 " --> pdb=" O   VAL P  12 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   LYS P  14 " --> pdb=" O   SER G  11 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE G  13 " --> pdb=" O   LYS P  14 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ILE P  16 " --> pdb=" O   ILE G  13 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ASN G  15 " --> pdb=" O   ILE P  16 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU P   5 " --> pdb=" O   ILE Y   6 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   LYS Y   8 " --> pdb=" O   LEU P   5 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG P   7 " --> pdb=" O   LYS Y   8 " (cutoff:3.500A)
      removed outlier: 8.399A  pdb=" N   VAL Y  10 " --> pdb=" O   ARG P   7 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA P   9 " --> pdb=" O   VAL Y  10 " (cutoff:3.500A)
      removed outlier: 8.466A  pdb=" N   VAL Y  12 " --> pdb=" O   ALA P   9 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   SER P  11 " --> pdb=" O   VAL Y  12 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   LYS Y  14 " --> pdb=" O   SER P  11 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE P  13 " --> pdb=" O   LYS Y  14 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ILE Y  16 " --> pdb=" O   ILE P  13 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ASN P  15 " --> pdb=" O   ILE Y  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 16
      removed outlier: 6.337A  pdb=" N   ARG H   7 " --> pdb=" O   LYS Q   8 " (cutoff:3.500A)
      removed outlier: 8.454A  pdb=" N   VAL Q  10 " --> pdb=" O   ARG H   7 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA H   9 " --> pdb=" O   VAL Q  10 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   VAL Q  12 " --> pdb=" O   ALA H   9 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER H  11 " --> pdb=" O   VAL Q  12 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   LYS Q  14 " --> pdb=" O   SER H  11 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ILE H  13 " --> pdb=" O   LYS Q  14 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ILE Q  16 " --> pdb=" O   ILE H  13 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ASN H  15 " --> pdb=" O   ILE Q  16 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ARG Q   7 " --> pdb=" O   LYS Z   8 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   VAL Z  10 " --> pdb=" O   ARG Q   7 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA Q   9 " --> pdb=" O   VAL Z  10 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   VAL Z  12 " --> pdb=" O   ALA Q   9 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   SER Q  11 " --> pdb=" O   VAL Z  12 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   LYS Z  14 " --> pdb=" O   SER Q  11 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ILE Q  13 " --> pdb=" O   LYS Z  14 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ILE Z  16 " --> pdb=" O   ILE Q  13 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ASN Q  15 " --> pdb=" O   ILE Z  16 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 6

    24 hydrogen bonds defined for protein.
    72 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 1.72 seconds

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

  Histogram of bond lengths:
        0.84 -     0.98: 2997
        0.98 -     1.12: 0
        1.12 -     1.26: 414
        1.26 -     1.40: 414
        1.40 -     1.54: 1692
  Bond restraints: 5517
  Sorted by residual:
  bond pdb=" N   ASP T   4 "
       pdb=" CA  ASP T   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.15e+00
  bond pdb=" N   ASP W   4 "
       pdb=" CA  ASP W   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.13e+00
  bond pdb=" N   ASP Z   4 "
       pdb=" CA  ASP Z   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   ASP N   4 "
       pdb=" CA  ASP N   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   ASP K   4 "
       pdb=" CA  ASP K   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  ... (remaining 5512 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 9545
        0.91 -     1.81: 542
        1.81 -     2.72: 20
        2.72 -     3.62: 9
        3.62 -     4.53: 9
  Bond angle restraints: 10125
  Sorted by residual:
  angle pdb=" N   VAL F   2 "
        pdb=" CA  VAL F   2 "
        pdb=" C   VAL F   2 "
      ideal   model   delta    sigma   weight residual
     109.34  106.05    3.29 2.08e+00 2.31e-01 2.49e+00
  angle pdb=" N   VAL R   2 "
        pdb=" CA  VAL R   2 "
        pdb=" C   VAL R   2 "
      ideal   model   delta    sigma   weight residual
     109.34  106.07    3.27 2.08e+00 2.31e-01 2.47e+00
  angle pdb=" N   VAL a   2 "
        pdb=" CA  VAL a   2 "
        pdb=" C   VAL a   2 "
      ideal   model   delta    sigma   weight residual
     109.34  106.07    3.27 2.08e+00 2.31e-01 2.47e+00
  angle pdb=" N   VAL I   2 "
        pdb=" CA  VAL I   2 "
        pdb=" C   VAL I   2 "
      ideal   model   delta    sigma   weight residual
     109.34  106.08    3.26 2.08e+00 2.31e-01 2.46e+00
  angle pdb=" N   VAL U   2 "
        pdb=" CA  VAL U   2 "
        pdb=" C   VAL U   2 "
      ideal   model   delta    sigma   weight residual
     109.34  106.08    3.26 2.08e+00 2.31e-01 2.45e+00
  ... (remaining 10120 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.80: 2097
       12.80 -    25.59: 126
       25.59 -    38.39: 69
       38.39 -    51.18: 30
       51.18 -    63.98: 45
  Dihedral angle restraints: 2367
    sinusoidal: 1440
      harmonic: 927
  Sorted by residual:
  dihedral pdb=" CA  LEU S   5 "
           pdb=" CB  LEU S   5 "
           pdb=" CG  LEU S   5 "
           pdb=" CD1 LEU S   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  145.53   34.47     3      1.50e+01 4.44e-03 5.84e+00
  dihedral pdb=" CA  LEU G   5 "
           pdb=" CB  LEU G   5 "
           pdb=" CG  LEU G   5 "
           pdb=" CD1 LEU G   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  145.54   34.46     3      1.50e+01 4.44e-03 5.84e+00
  dihedral pdb=" CA  LEU J   5 "
           pdb=" CB  LEU J   5 "
           pdb=" CG  LEU J   5 "
           pdb=" CD1 LEU J   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  145.55   34.45     3      1.50e+01 4.44e-03 5.84e+00
  ... (remaining 2364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 166
       0.024 -    0.049: 121
       0.049 -    0.073: 46
       0.073 -    0.097: 111
       0.097 -    0.121: 24
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  ILE H   6 "
            pdb=" N   ILE H   6 "
            pdb=" C   ILE H   6 "
            pdb=" CB  ILE H   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.68e-01
  chirality pdb=" CA  ILE T   6 "
            pdb=" N   ILE T   6 "
            pdb=" C   ILE T   6 "
            pdb=" CB  ILE T   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.66e-01
  chirality pdb=" CA  ILE B   6 "
            pdb=" N   ILE B   6 "
            pdb=" C   ILE B   6 "
            pdb=" CB  ILE B   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 465 not shown)

  Planarity restraints: 702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R   1 "    0.002 2.00e-02 2.50e+03   3.83e-03 1.47e-01
        pdb=" N   VAL R   2 "   -0.007 2.00e-02 2.50e+03
        pdb=" CA  VAL R   2 "    0.002 2.00e-02 2.50e+03
        pdb=" H   VAL R   2 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY I   1 "    0.002 2.00e-02 2.50e+03   3.75e-03 1.41e-01
        pdb=" N   VAL I   2 "   -0.006 2.00e-02 2.50e+03
        pdb=" CA  VAL I   2 "    0.002 2.00e-02 2.50e+03
        pdb=" H   VAL I   2 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY a   1 "    0.002 2.00e-02 2.50e+03   3.68e-03 1.35e-01
        pdb=" N   VAL a   2 "   -0.006 2.00e-02 2.50e+03
        pdb=" CA  VAL a   2 "    0.002 2.00e-02 2.50e+03
        pdb=" H   VAL a   2 "    0.003 2.00e-02 2.50e+03
  ... (remaining 699 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.41: 2845
        2.41 -     2.90: 12424
        2.90 -     3.40: 10124
        3.40 -     3.90: 14682
        3.90 -     4.40: 19123
  Nonbonded interactions: 59198
  Sorted by model distance:
  nonbonded pdb=" HD2 ARG G   7 "
            pdb="HH11 ARG G   7 "
     model   vdw
     1.908 2.270
  nonbonded pdb=" HD2 ARG P   7 "
            pdb="HH11 ARG P   7 "
     model   vdw
     1.909 2.270
  nonbonded pdb=" HD2 ARG Y   7 "
            pdb="HH11 ARG Y   7 "
     model   vdw
     1.909 2.270
  nonbonded pdb=" HD2 ARG J   7 "
            pdb="HH11 ARG J   7 "
     model   vdw
     1.909 2.270
  nonbonded pdb=" HD2 ARG A   7 "
            pdb="HH11 ARG A   7 "
     model   vdw
     1.909 2.270
  ... (remaining 59193 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'V'
  selection = chain 'Y'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'Z'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'X'
  selection = chain 'a'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             2.010
  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:             0.080
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.750
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
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      :  0.010   0.035   2520  Z= 0.633
  Angle     :  0.442   3.285   3348  Z= 0.231
  Chirality :  0.057   0.121    468
  Planarity :  0.002   0.008    387
  Dihedral  :  9.436  34.465    954
  Min Nonbonded Distance : 2.689

Molprobity Statistics.
  All-atom Clashscore : 1.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.35), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.27), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.441 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 4.7791
  time to fit residues: 97.2212
Evaluate side-chains
  8 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 8
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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: 0.8403
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2520  Z= 0.158
  Angle     :  0.407   3.331   3348  Z= 0.200
  Chirality :  0.060   0.126    468
  Planarity :  0.002   0.007    387
  Dihedral  :  3.117   7.395    342
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 0.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.36), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.28), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.441 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 2.1744
  time to fit residues: 42.9381
Evaluate side-chains
  11 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 14 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
B  15 ASN
D  15 ASN
E  15 ASN
G  15 ASN
H  15 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2520  Z= 0.107
  Angle     :  0.334   2.585   3348  Z= 0.173
  Chirality :  0.062   0.128    468
  Planarity :  0.001   0.007    387
  Dihedral  :  2.609   6.041    342
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 0.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.38), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.52 (0.29), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG T   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  11 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.513 
Fit side-chains
REVERT: N    8 LYS cc_start: 0.7515 (tttt) cc_final: 0.7220 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 11
  average time/residue: 2.9880
  time to fit residues: 34.1059
Evaluate side-chains
  10 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0020
   overall best weight:    2.1794

-------------------------------------------------------------------------------
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: 0.8452
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   2520  Z= 0.217
  Angle     :  0.393   2.298   3348  Z= 0.203
  Chirality :  0.059   0.131    468
  Planarity :  0.002   0.009    387
  Dihedral  :  3.258   7.807    342
  Min Nonbonded Distance : 2.708

Molprobity Statistics.
  All-atom Clashscore : 0.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.37), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.28), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG P   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.396 
Fit side-chains
REVERT: N    8 LYS cc_start: 0.7532 (tttt) cc_final: 0.7205 (ttmt)
REVERT: X    4 ASP cc_start: 0.8495 (m-30) cc_final: 0.8281 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 4.5110
  time to fit residues: 78.1253
Evaluate side-chains
  16 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0570
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7702

-------------------------------------------------------------------------------
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: 0.8428
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2520  Z= 0.103
  Angle     :  0.330   2.314   3348  Z= 0.172
  Chirality :  0.061   0.125    468
  Planarity :  0.001   0.006    387
  Dihedral  :  2.524   5.535    342
  Min Nonbonded Distance : 2.716

Molprobity Statistics.
  All-atom Clashscore : 0.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.07 %
    Favored  : 89.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.38), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.29), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.407 
Fit side-chains
REVERT: U    4 ASP cc_start: 0.8344 (m-30) cc_final: 0.8101 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 4.1480
  time to fit residues: 84.5967
Evaluate side-chains
  16 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    0.0980
   chunk 9 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0670
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0070
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0050
   chunk 3 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.2150

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

Flipped N/Q/H residues before XYZ refinement:
B  15 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.012   2520  Z= 0.090
  Angle     :  0.318   2.176   3348  Z= 0.164
  Chirality :  0.062   0.123    468
  Planarity :  0.001   0.012    387
  Dihedral  :  2.142   5.394    342
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.40), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG a   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.429 
Fit side-chains
REVERT: K    8 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7215 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 2.8000
  time to fit residues: 69.0355
Evaluate side-chains
  17 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 13 optimal weight:    0.4980
   chunk 15 optimal weight:    0.2980
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0370
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
D  15 ASN
G  15 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.011   2520  Z= 0.086
  Angle     :  0.308   2.001   3348  Z= 0.161
  Chirality :  0.061   0.125    468
  Planarity :  0.001   0.006    387
  Dihedral  :  2.215   5.143    342
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 0.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.41), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG U   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.428 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 4.1199
  time to fit residues: 67.3730
Evaluate side-chains
  15 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0570
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
B  15 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.014   2520  Z= 0.095
  Angle     :  0.334   4.448   3348  Z= 0.170
  Chirality :  0.061   0.125    468
  Planarity :  0.001   0.010    387
  Dihedral  :  2.255   5.044    342
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 0.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 12.50 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.41), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.25 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.445 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 17
  average time/residue: 3.6385
  time to fit residues: 63.3946
Evaluate side-chains
  16 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0060
   chunk 0 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.8002

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
G  15 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.011   2520  Z= 0.175
  Angle     :  0.365   3.444   3348  Z= 0.189
  Chirality :  0.060   0.128    468
  Planarity :  0.001   0.007    387
  Dihedral  :  2.739   6.419    342
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 0.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.19 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.40), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG U   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.502 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 4.5723
  time to fit residues: 70.1509
Evaluate side-chains
  15 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 0 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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: 0.8456
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.011   2520  Z= 0.167
  Angle     :  0.353   3.466   3348  Z= 0.183
  Chirality :  0.060   0.125    468
  Planarity :  0.001   0.006    387
  Dihedral  :  2.674   6.378    342
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 0.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.19 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.39), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG M   7 

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.550 
Fit side-chains
REVERT: U    4 ASP cc_start: 0.8365 (m-30) cc_final: 0.8156 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 4.5740
  time to fit residues: 65.5960
Evaluate side-chains
  14 residues out of total 288 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4081 r_free = 0.4081 target = 0.128882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.082317 restraints weight = 8236.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.30
r_work: 0.3291 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2520  Z= 0.105
  Angle     :  0.326   3.341   3348  Z= 0.168
  Chirality :  0.061   0.123    468
  Planarity :  0.001   0.006    387
  Dihedral  :  2.398   5.800    342
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 0.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.89 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.40), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.56 (0.30), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I   7 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2765.81 seconds
wall clock time: 48 minutes 22.89 seconds (2902.89 seconds total)