Starting phenix.real_space_refine
on Sat Dec  9 10:07:08 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/12_2023/7v6a_31740_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/12_2023/7v6a_31740.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/12_2023/7v6a_31740.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/12_2023/7v6a_31740.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/12_2023/7v6a_31740_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/12_2023/7v6a_31740_updated.pdb"
  }
  resolution = 3.6
  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=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2132 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C    5497      2.51       5
     N    1460      2.21       5
     O    1562      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R GLU  395": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8584
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1646
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 131
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 72
    Chain: "B"
      Number of atoms: 2562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2562
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 38
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2195
          Unusual residues: {'5XI': 1}
          Classifications: {'peptide': 277, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 10, 'TRANS': 266, None: 1}
            Not linked:
              pdbres="GLN R 471 "
              pdbres="5XI R 601 "
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 4.95, per 1000 atoms: 0.58
  Number of scatterers: 8584
  At special positions: 0
  Unit cell: (94.2936, 123.414, 123.414, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      65     16.00
     O    1562      8.00
     N    1460      7.00
     C    5497      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 426 " - pdb=" SG  CYS R 429 " distance=2.03

  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: 3.35
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      24 helices and 14 sheets defined
      32.4% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 31
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 271 through 280
    Processing helix  chain 'A' and resid 296 through 307
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'C' and resid 11 through 23
    Processing helix  chain 'C' and resid 30 through 33
      No H-bonds generated for 'chain 'C' and resid 30 through 33'
    Processing helix  chain 'C' and resid 35 through 41
      removed outlier: 3.558A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 59
      removed outlier: 4.192A  pdb=" N   SER R  56 " --> pdb=" O   LEU R  52 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   ILE R  57 " --> pdb=" O   VAL R  53 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   LYS R  58 " --> pdb=" O   MET R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 93
      removed outlier: 4.837A  pdb=" N   PHE R  70 " --> pdb=" O   ASN R  67 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   SER R  85 " --> pdb=" O   GLY R  82 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   MET R  86 " --> pdb=" O   ALA R  83 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ASN R  87 " --> pdb=" O   PHE R  84 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL R  91 " --> pdb=" O   LEU R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 135
      removed outlier: 4.149A  pdb=" N   TYR R 113 " --> pdb=" O   LEU R 109 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   VAL R 114 " --> pdb=" O   ALA R 110 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASN R 117 " --> pdb=" O   TYR R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 143
    Processing helix  chain 'R' and resid 146 through 164
    Processing helix  chain 'R' and resid 166 through 175
    Processing helix  chain 'R' and resid 193 through 223
      removed outlier: 4.017A  pdb=" N   ALA R 202 " --> pdb=" O   GLY R 198 " (cutoff:3.500A)
      removed outlier: 5.254A  pdb=" N   LEU R 206 " --> pdb=" O   ALA R 202 " (cutoff:3.500A)
      Proline residue:  R 207  - end of helix
      removed outlier: 4.386A  pdb=" N   ARG R 223 " --> pdb=" O   SER R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 392 through 412
      removed outlier: 3.654A  pdb=" N   LEU R 406 " --> pdb=" O   ILE R 402 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 419
      No H-bonds generated for 'chain 'R' and resid 416 through 419'
    Processing helix  chain 'R' and resid 432 through 454
      removed outlier: 4.299A  pdb=" N   CYS R 442 " --> pdb=" O   GLY R 438 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   TYR R 443 " --> pdb=" O   TYR R 439 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   VAL R 444 " --> pdb=" O   TRP R 440 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ASN R 445 " --> pdb=" O   LEU R 441 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   SER R 446 " --> pdb=" O   CYS R 442 " (cutoff:3.500A)
      Proline residue:  R 450  - end of helix
    Processing helix  chain 'R' and resid 458 through 469
      removed outlier: 3.742A  pdb=" N   PHE R 464 " --> pdb=" O   PHE R 460 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   ARG R 465 " --> pdb=" O   LYS R 461 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   HIS R 466 " --> pdb=" O   LYS R 462 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   LEU R 468 " --> pdb=" O   PHE R 464 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 263 through 265
      removed outlier: 3.843A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.578A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 178 through 180
      removed outlier: 3.513A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 220 through 222
      removed outlier: 4.186A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.648A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 294 through 298
      removed outlier: 3.580A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 327 through 330
      removed outlier: 6.183A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.435A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 79 through 82
      removed outlier: 3.567A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'B' and resid 250 through 253
      removed outlier: 3.740A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'S' and resid 17 through 21
      removed outlier: 3.513A  pdb=" N   ARG S  18 " --> pdb=" O   MET S  83 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU S  81 " --> pdb=" O   LEU S  20 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'S' and resid 93 through 99
      removed outlier: 3.865A  pdb=" N   TRP S  36 " --> pdb=" O   ALA S  49 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'S' and resid 143 through 146
      removed outlier: 3.599A  pdb=" N   VAL S 143 " --> pdb=" O   ILE S 204 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'S' and resid 214 through 219
      removed outlier: 3.579A  pdb=" N   TRP S 164 " --> pdb=" O   ILE S 177 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    330 hydrogen bonds defined for protein.
    894 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: 2.31

  Time building geometry restraints manager: 3.66 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2252
        1.33 -     1.45: 1739
        1.45 -     1.57: 4685
        1.57 -     1.70: 0
        1.70 -     1.82: 94
  Bond restraints: 8770
  Sorted by residual:
  bond pdb=" C19 5XI R 601 "
       pdb=" N4  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.351  1.479 -0.128 2.00e-02 2.50e+03 4.10e+01
  bond pdb=" C19 5XI R 601 "
       pdb=" O3  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.428 -0.091 2.00e-02 2.50e+03 2.08e+01
  bond pdb=" C8  5XI R 601 "
       pdb=" N1  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.439  1.480 -0.041 2.00e-02 2.50e+03 4.22e+00
  bond pdb=" C9  5XI R 601 "
       pdb=" N2  5XI R 601 "
    ideal  model  delta    sigma   weight residual
    1.452  1.493 -0.041 2.00e-02 2.50e+03 4.12e+00
  bond pdb=" CA  THR B 181 "
       pdb=" CB  THR B 181 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.35e-02 5.49e+03 3.35e+00
  ... (remaining 8765 not shown)

  Histogram of bond angle deviations from ideal:
       98.53 -   105.66: 138
      105.66 -   112.80: 4702
      112.80 -   119.93: 2975
      119.93 -   127.06: 4002
      127.06 -   134.19: 106
  Bond angle restraints: 11923
  Sorted by residual:
  angle pdb=" N   VAL R 418 "
        pdb=" CA  VAL R 418 "
        pdb=" C   VAL R 418 "
      ideal   model   delta    sigma   weight residual
     112.96  108.07    4.89 1.00e+00 1.00e+00 2.39e+01
  angle pdb=" CA  TRP R 435 "
        pdb=" CB  TRP R 435 "
        pdb=" CG  TRP R 435 "
      ideal   model   delta    sigma   weight residual
     113.60  119.04   -5.44 1.90e+00 2.77e-01 8.20e+00
  angle pdb=" N   TRP R 435 "
        pdb=" CA  TRP R 435 "
        pdb=" C   TRP R 435 "
      ideal   model   delta    sigma   weight residual
     111.33  107.91    3.42 1.21e+00 6.83e-01 8.00e+00
  angle pdb=" N   ASP B 246 "
        pdb=" CA  ASP B 246 "
        pdb=" C   ASP B 246 "
      ideal   model   delta    sigma   weight residual
     113.38  110.13    3.25 1.23e+00 6.61e-01 6.96e+00
  angle pdb=" C   ARG S 179 "
        pdb=" N   MET S 180 "
        pdb=" CA  MET S 180 "
      ideal   model   delta    sigma   weight residual
     122.19  118.54    3.65 1.41e+00 5.03e-01 6.71e+00
  ... (remaining 11918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4695
       17.90 -    35.80: 373
       35.80 -    53.70: 78
       53.70 -    71.60: 11
       71.60 -    89.49: 10
  Dihedral angle restraints: 5167
    sinusoidal: 1908
      harmonic: 3259
  Sorted by residual:
  dihedral pdb=" CB  CYS R 426 "
           pdb=" SG  CYS R 426 "
           pdb=" SG  CYS R 429 "
           pdb=" CB  CYS R 429 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.93  -43.93     1      1.00e+01 1.00e-02 2.69e+01
  dihedral pdb=" CA  VAL R 434 "
           pdb=" C   VAL R 434 "
           pdb=" N   TRP R 435 "
           pdb=" CA  TRP R 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  MET S  93 "
           pdb=" C   MET S  93 "
           pdb=" N   TYR S  94 "
           pdb=" CA  TYR S  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.11  -19.89     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 5164 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1222
       0.069 -    0.137: 156
       0.137 -    0.206: 7
       0.206 -    0.274: 0
       0.274 -    0.343: 2
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" C9  5XI R 601 "
            pdb=" C10 5XI R 601 "
            pdb=" C13 5XI R 601 "
            pdb=" N2  5XI R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.30   -2.65    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" C14 5XI R 601 "
            pdb=" C15 5XI R 601 "
            pdb=" C18 5XI R 601 "
            pdb=" N3  5XI R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.62    0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CB  ILE R  93 "
            pdb=" CA  ILE R  93 "
            pdb=" CG1 ILE R  93 "
            pdb=" CG2 ILE R  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.34e-01
  ... (remaining 1384 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 414 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.10e+00
        pdb=" N   PRO R 415 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO R 415 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 415 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA S  40 "    0.037 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO S  41 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO S  41 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO S  41 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 201 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.31e+00
        pdb=" C   ILE R 201 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ILE R 201 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA R 202 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 183
        2.67 -     3.23: 8667
        3.23 -     3.79: 13540
        3.79 -     4.34: 17969
        4.34 -     4.90: 29295
  Nonbonded interactions: 69654
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.113 2.440
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.163 2.440
  nonbonded pdb=" OH  TYR R 439 "
            pdb=" OH  TYR R 443 "
     model   vdw
     2.179 2.440
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   SER B 160 "
     model   vdw
     2.200 2.440
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.210 2.440
  ... (remaining 69649 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          1.880
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     26.180
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.128   8770  Z= 0.267
  Angle     :  0.706   7.697  11923  Z= 0.397
  Chirality :  0.045   0.343   1387
  Planarity :  0.004   0.056   1488
  Dihedral  : 14.081  89.494   3057
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 (0.25), residues: 1104
  helix:  0.44 (0.27), residues: 398
  sheet: -2.68 (0.30), residues: 230
  loop : -1.90 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.029   0.002   TRP B  82 
   HIS   0.005   0.001   HIS S  35 
   PHE   0.029   0.002   PHE B 235 
   TYR   0.020   0.002   TYR S 103 
   ARG   0.008   0.001   ARG S 190 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.907 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.2373
  time to fit residues: 83.5335
Evaluate side-chains
  238 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.944 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3140
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0470
   chunk 45 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 85 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B 110 ASN
S 113 GLN
S 174 GLN
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 417 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8770  Z= 0.222
  Angle     :  0.599  10.884  11923  Z= 0.312
  Chirality :  0.043   0.200   1387
  Planarity :  0.004   0.054   1488
  Dihedral  :  6.156  60.071   1242
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.70 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.80 (0.25), residues: 1104
  helix:  0.37 (0.27), residues: 403
  sheet: -2.28 (0.31), residues: 227
  loop : -1.96 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.002   TRP B 339 
   HIS   0.006   0.001   HIS S  35 
   PHE   0.012   0.002   PHE B 234 
   TYR   0.017   0.001   TYR S 163 
   ARG   0.006   0.001   ARG B 256 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 240
  time to evaluate  : 0.931 
Fit side-chains
  outliers start: 17
  outliers final: 13
  residues processed: 246
  average time/residue: 0.2417
  time to fit residues: 78.3177
Evaluate side-chains
  241 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 228
  time to evaluate  : 0.891 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1222
  time to fit residues: 3.7691
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0010
   chunk 67 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0870
   chunk 33 optimal weight:    0.0570
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.1620

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
S 174 GLN
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8770  Z= 0.145
  Angle     :  0.555  11.511  11923  Z= 0.284
  Chirality :  0.041   0.164   1387
  Planarity :  0.003   0.050   1488
  Dihedral  :  5.858  61.420   1242
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.82 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.56 (0.25), residues: 1104
  helix:  0.54 (0.27), residues: 401
  sheet: -2.13 (0.30), residues: 266
  loop : -1.69 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP R 435 
   HIS   0.007   0.001   HIS S  35 
   PHE   0.014   0.001   PHE S 110 
   TYR   0.012   0.001   TYR B 105 
   ARG   0.003   0.000   ARG B 256 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 244
  time to evaluate  : 0.952 
Fit side-chains
  outliers start: 16
  outliers final: 6
  residues processed: 248
  average time/residue: 0.2387
  time to fit residues: 78.4240
Evaluate side-chains
  233 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 227
  time to evaluate  : 0.939 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0881
  time to fit residues: 2.2234
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0970
   chunk 51 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 87 optimal weight:    0.2980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8770  Z= 0.175
  Angle     :  0.587  11.211  11923  Z= 0.293
  Chirality :  0.041   0.170   1387
  Planarity :  0.003   0.049   1488
  Dihedral  :  5.722  56.558   1242
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.49 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.36 (0.25), residues: 1104
  helix:  0.61 (0.27), residues: 401
  sheet: -1.93 (0.30), residues: 267
  loop : -1.55 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP R 435 
   HIS   0.006   0.001   HIS B  91 
   PHE   0.013   0.001   PHE S  29 
   TYR   0.018   0.001   TYR B 105 
   ARG   0.004   0.000   ARG S 168 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 238
  time to evaluate  : 0.936 
Fit side-chains
  outliers start: 26
  outliers final: 16
  residues processed: 247
  average time/residue: 0.2384
  time to fit residues: 77.8178
Evaluate side-chains
  247 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 231
  time to evaluate  : 0.957 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1021
  time to fit residues: 4.0785
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0980
   chunk 0 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  68 ASN
R 423 ASN
** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6886
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8770  Z= 0.262
  Angle     :  0.632  11.409  11923  Z= 0.322
  Chirality :  0.044   0.163   1387
  Planarity :  0.004   0.052   1488
  Dihedral  :  5.968  52.973   1242
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.05 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.26), residues: 1104
  helix:  0.49 (0.27), residues: 400
  sheet: -1.94 (0.30), residues: 272
  loop : -1.51 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.026   0.002   TRP B 339 
   HIS   0.004   0.001   HIS S  35 
   PHE   0.020   0.002   PHE S  29 
   TYR   0.019   0.002   TYR R 215 
   ARG   0.004   0.000   ARG S 168 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 242
  time to evaluate  : 0.869 
Fit side-chains
  outliers start: 24
  outliers final: 17
  residues processed: 250
  average time/residue: 0.2316
  time to fit residues: 76.6583
Evaluate side-chains
  253 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 236
  time to evaluate  : 0.985 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0869
  time to fit residues: 4.0660
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0000
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 230 ASN
S 130 GLN
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8770  Z= 0.223
  Angle     :  0.626  11.581  11923  Z= 0.316
  Chirality :  0.042   0.166   1387
  Planarity :  0.004   0.052   1488
  Dihedral  :  5.965  52.987   1242
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 24.16 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.37 (0.26), residues: 1104
  helix:  0.52 (0.27), residues: 399
  sheet: -1.84 (0.30), residues: 272
  loop : -1.51 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.002   TRP R 435 
   HIS   0.004   0.001   HIS S  35 
   PHE   0.015   0.001   PHE R 186 
   TYR   0.014   0.001   TYR R 215 
   ARG   0.008   0.000   ARG S 190 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 237
  time to evaluate  : 0.939 
Fit side-chains
  outliers start: 21
  outliers final: 13
  residues processed: 242
  average time/residue: 0.2448
  time to fit residues: 77.9065
Evaluate side-chains
  247 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 234
  time to evaluate  : 0.920 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0858
  time to fit residues: 3.3506
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0870
   chunk 105 optimal weight:    0.0020
   chunk 65 optimal weight:    0.4980
   chunk 64 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.4566

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 423 ASN
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8770  Z= 0.181
  Angle     :  0.610  11.838  11923  Z= 0.303
  Chirality :  0.042   0.239   1387
  Planarity :  0.003   0.051   1488
  Dihedral  :  5.819  51.826   1242
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 25.06 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.15 (0.26), residues: 1104
  helix:  0.66 (0.27), residues: 394
  sheet: -1.59 (0.32), residues: 259
  loop : -1.43 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.024   0.002   TRP R 435 
   HIS   0.006   0.001   HIS S  35 
   PHE   0.019   0.001   PHE R 403 
   TYR   0.013   0.001   TYR R 215 
   ARG   0.009   0.000   ARG S 190 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 243
  time to evaluate  : 0.963 
Fit side-chains
  outliers start: 20
  outliers final: 8
  residues processed: 249
  average time/residue: 0.2498
  time to fit residues: 81.3008
Evaluate side-chains
  245 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 237
  time to evaluate  : 0.907 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0884
  time to fit residues: 2.5799
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 95 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
B 230 ASN
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8770  Z= 0.228
  Angle     :  0.656  11.754  11923  Z= 0.329
  Chirality :  0.043   0.191   1387
  Planarity :  0.004   0.052   1488
  Dihedral  :  5.883  47.688   1242
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 26.73 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.20 (0.26), residues: 1104
  helix:  0.61 (0.27), residues: 394
  sheet: -1.60 (0.32), residues: 264
  loop : -1.45 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.035   0.002   TRP B 169 
   HIS   0.004   0.001   HIS S  35 
   PHE   0.025   0.001   PHE R 403 
   TYR   0.013   0.001   TYR R 215 
   ARG   0.008   0.000   ARG S 168 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 241
  time to evaluate  : 0.990 
Fit side-chains
  outliers start: 14
  outliers final: 7
  residues processed: 246
  average time/residue: 0.2399
  time to fit residues: 77.6998
Evaluate side-chains
  245 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 238
  time to evaluate  : 0.879 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0846
  time to fit residues: 2.3835
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 100 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0010
   chunk 42 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 103 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
C  11 GLN
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8770  Z= 0.201
  Angle     :  0.659  11.859  11923  Z= 0.327
  Chirality :  0.044   0.196   1387
  Planarity :  0.004   0.058   1488
  Dihedral  :  5.868  48.831   1242
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 26.73 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.15 (0.26), residues: 1104
  helix:  0.63 (0.27), residues: 393
  sheet: -1.60 (0.32), residues: 261
  loop : -1.40 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.039   0.002   TRP B 169 
   HIS   0.005   0.001   HIS S  35 
   PHE   0.026   0.001   PHE R 403 
   TYR   0.013   0.001   TYR S 103 
   ARG   0.012   0.001   ARG S 168 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 239
  time to evaluate  : 0.939 
Fit side-chains
  outliers start: 10
  outliers final: 9
  residues processed: 243
  average time/residue: 0.2456
  time to fit residues: 78.3742
Evaluate side-chains
  248 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 239
  time to evaluate  : 0.888 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0922
  time to fit residues: 2.7282
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0270
   chunk 108 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 86 optimal weight:    0.4980
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 266 HIS
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8770  Z= 0.200
  Angle     :  0.665  11.750  11923  Z= 0.332
  Chirality :  0.044   0.177   1387
  Planarity :  0.004   0.065   1488
  Dihedral  :  5.864  49.854   1242
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 27.28 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.11 (0.26), residues: 1104
  helix:  0.65 (0.27), residues: 393
  sheet: -1.55 (0.31), residues: 267
  loop : -1.37 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.039   0.003   TRP B 169 
   HIS   0.005   0.001   HIS S  35 
   PHE   0.027   0.001   PHE R 403 
   TYR   0.033   0.002   TYR S 103 
   ARG   0.015   0.001   ARG S 168 

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 252
  time to evaluate  : 0.800 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 253
  average time/residue: 0.2424
  time to fit residues: 80.5102
Evaluate side-chains
  248 residues out of total 960 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 245
  time to evaluate  : 0.953 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0820
  time to fit residues: 1.7793
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 86 optimal weight:    0.2980
   chunk 36 optimal weight:    0.7980
   chunk 88 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.151310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.134162 restraints weight = 13602.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.137726 restraints weight = 6180.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.139935 restraints weight = 3424.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8770  Z= 0.212
  Angle     :  0.672  11.625  11923  Z= 0.335
  Chirality :  0.044   0.175   1387
  Planarity :  0.004   0.069   1488
  Dihedral  :  5.894  49.490   1242
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 27.84 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -1.13 (0.26), residues: 1104
  helix:  0.65 (0.27), residues: 393
  sheet: -1.65 (0.31), residues: 275
  loop : -1.32 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.039   0.003   TRP B 169 
   HIS   0.004   0.001   HIS S  35 
   PHE   0.027   0.002   PHE R 403 
   TYR   0.033   0.002   TYR S  95 
   ARG   0.013   0.001   ARG S 168 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2305.21 seconds
wall clock time: 42 minutes 40.98 seconds (2560.98 seconds total)