Starting phenix.real_space_refine
on Fri Feb 16 03:48:16 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvf_32852/02_2024/7wvf_32852_updated.pdb"
  }
  resolution = 3.91
  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=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      90      5.49       5
     S      38      5.16       5
     C    8738      2.51       5
     N    2408      2.21       5
     O    2975      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C PHE  243": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 14249
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 659, 5284
          Classifications: {'peptide': 659}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 5284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 659, 5284
          Classifications: {'peptide': 659}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 917
          Classifications: {'RNA': 46}
          Modifications used: {'5*END': 1, 'rna3p_pyr': 46}
          Link IDs: {'rna3p': 45}
    Chain: "F"
      Number of atoms: 1009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 1009
          Classifications: {'RNA': 46}
          Modifications used: {'5*END': 1, 'rna3p': 46}
          Link IDs: {'rna3p': 45}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 135
          Unresolved non-hydrogen dihedrals: 45
    Chain: "C"
      Number of atoms: 1755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1755
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 213}
          Chain breaks: 1
  Time building chain proxies: 7.47, per 1000 atoms: 0.52
  Number of scatterers: 14249
  At special positions: 0
  Unit cell: (96.6985, 95.612, 203.176, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P      90     15.00
     O    2975      8.00
     N    2408      7.00
     C    8738      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 649 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  95 " - pdb=" SG  CYS B 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 649 " - pdb=" SG  CYS B 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  25 " - pdb=" SG  CYS C 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 167 " - pdb=" SG  CYS C 232 " 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: 5.85
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2952

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      8.7% alpha, 12.6% beta
      0 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 6.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 71
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.503A  pdb=" N   LYS A  97 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 194
      removed outlier: 4.674A  pdb=" N   ILE A 193 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 244
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.960A  pdb=" N   TRP A 273 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 404
      removed outlier: 4.516A  pdb=" N   SER A 403 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 452
      No H-bonds generated for 'chain 'A' and resid 450 through 452'
    Processing helix  chain 'A' and resid 544 through 546
      No H-bonds generated for 'chain 'A' and resid 544 through 546'
    Processing helix  chain 'A' and resid 627 through 630
      No H-bonds generated for 'chain 'A' and resid 627 through 630'
    Processing helix  chain 'A' and resid 632 through 634
      No H-bonds generated for 'chain 'A' and resid 632 through 634'
    Processing helix  chain 'A' and resid 655 through 662
    Processing helix  chain 'A' and resid 671 through 674
      No H-bonds generated for 'chain 'A' and resid 671 through 674'
    Processing helix  chain 'A' and resid 681 through 683
      No H-bonds generated for 'chain 'A' and resid 681 through 683'
    Processing helix  chain 'B' and resid 68 through 71
    Processing helix  chain 'B' and resid 92 through 97
      removed outlier: 3.503A  pdb=" N   LYS B  97 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 194
      removed outlier: 4.674A  pdb=" N   ILE B 193 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 244
    Processing helix  chain 'B' and resid 269 through 273
      removed outlier: 3.959A  pdb=" N   TRP B 273 " --> pdb=" O   GLY B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 404
      removed outlier: 4.516A  pdb=" N   SER B 403 " --> pdb=" O   THR B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 452
      No H-bonds generated for 'chain 'B' and resid 450 through 452'
    Processing helix  chain 'B' and resid 544 through 546
      No H-bonds generated for 'chain 'B' and resid 544 through 546'
    Processing helix  chain 'B' and resid 627 through 630
      No H-bonds generated for 'chain 'B' and resid 627 through 630'
    Processing helix  chain 'B' and resid 632 through 634
      No H-bonds generated for 'chain 'B' and resid 632 through 634'
    Processing helix  chain 'B' and resid 655 through 662
    Processing helix  chain 'B' and resid 671 through 674
      No H-bonds generated for 'chain 'B' and resid 671 through 674'
    Processing helix  chain 'B' and resid 681 through 683
      No H-bonds generated for 'chain 'B' and resid 681 through 683'
    Processing helix  chain 'C' and resid 94 through 96
      No H-bonds generated for 'chain 'C' and resid 94 through 96'
    Processing helix  chain 'C' and resid 224 through 226
      No H-bonds generated for 'chain 'C' and resid 224 through 226'
    Processing sheet with id=  A, first strand: chain 'A' and resid 34 through 36
      removed outlier: 6.409A  pdb=" N   VAL A  55 " --> pdb=" O   ALA A  35 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   SER A  79 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL A 103 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   GLU A 127 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   THR A 151 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   GLU A 175 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   LYS A 201 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  A
    Processing sheet with id=  B, first strand: chain 'A' and resid 225 through 227
      removed outlier: 6.365A  pdb=" N   ASN A 252 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   MET A 278 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TYR A 302 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   TYR A 326 " --> pdb=" O   PHE A 303 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  B
    Processing sheet with id=  C, first strand: chain 'A' and resid 383 through 385
      removed outlier: 6.137A  pdb=" N   ILE A 411 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   VAL A 435 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   GLU A 460 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ARG A 484 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE A 510 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE A 534 " --> pdb=" O   LEU A 511 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ILE A 566 " --> pdb=" O   LEU A 535 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ILE A 590 " --> pdb=" O   LEU A 567 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   SER A 614 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   GLU A 639 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'A' and resid 444 through 446
      removed outlier: 6.405A  pdb=" N   TYR A 468 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  D
    Processing sheet with id=  E, first strand: chain 'B' and resid 34 through 36
      removed outlier: 6.409A  pdb=" N   VAL B  55 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   SER B  79 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL B 103 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   GLU B 127 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   THR B 151 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   GLU B 175 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   LYS B 201 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  E
    Processing sheet with id=  F, first strand: chain 'B' and resid 225 through 227
      removed outlier: 6.364A  pdb=" N   ASN B 252 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   MET B 278 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TYR B 302 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   TYR B 326 " --> pdb=" O   PHE B 303 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  F
    Processing sheet with id=  G, first strand: chain 'B' and resid 383 through 385
      removed outlier: 6.136A  pdb=" N   ILE B 411 " --> pdb=" O   LEU B 384 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   VAL B 435 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   GLU B 460 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ARG B 484 " --> pdb=" O   ILE B 461 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ILE B 510 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE B 534 " --> pdb=" O   LEU B 511 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ILE B 566 " --> pdb=" O   LEU B 535 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ILE B 590 " --> pdb=" O   LEU B 567 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   SER B 614 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   GLU B 639 " --> pdb=" O   LEU B 615 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  G
    Processing sheet with id=  H, first strand: chain 'B' and resid 444 through 446
      removed outlier: 6.405A  pdb=" N   TYR B 468 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  H
    Processing sheet with id=  I, first strand: chain 'C' and resid 6 through 11
    Processing sheet with id=  J, first strand: chain 'C' and resid 119 through 121
      removed outlier: 6.804A  pdb=" N   ALA C  37 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   LYS C  58 " --> pdb=" O   ALA C  37 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ARG C  43 " --> pdb=" O   TRP C  52 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   TRP C  52 " --> pdb=" O   ARG C  43 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'C' and resid 154 through 157
      removed outlier: 6.052A  pdb=" N   LYS C 248 " --> pdb=" O   VAL C 155 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   VAL C 157 " --> pdb=" O   LYS C 248 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   THR C 250 " --> pdb=" O   VAL C 157 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'C' and resid 163 through 168
    Processing sheet with id=  M, first strand: chain 'C' and resid 240 through 243
      removed outlier: 6.138A  pdb=" N   GLN C 181 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   LEU C 190 " --> pdb=" O   GLN C 181 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'C' and resid 103 through 106
      removed outlier: 4.172A  pdb=" N   TYR C 114 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER C 106 " --> pdb=" O   ILE C 112 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   ILE C 112 " --> pdb=" O   SER C 106 " (cutoff:3.500A)

    89 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 4.25

  Time building geometry restraints manager: 6.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4296
        1.34 -     1.46: 3499
        1.46 -     1.58: 6717
        1.58 -     1.70: 180
        1.70 -     1.81: 54
  Bond restraints: 14746
  Sorted by residual:
  bond pdb=" C2    I F  22 "
       pdb=" N3    I F  22 "
    ideal  model  delta    sigma   weight residual
    1.462  1.312  0.150 2.00e-02 2.50e+03 5.59e+01
  bond pdb=" C2    I F  42 "
       pdb=" N3    I F  42 "
    ideal  model  delta    sigma   weight residual
    1.462  1.313  0.149 2.00e-02 2.50e+03 5.55e+01
  bond pdb=" C2    I F  21 "
       pdb=" N3    I F  21 "
    ideal  model  delta    sigma   weight residual
    1.462  1.313  0.149 2.00e-02 2.50e+03 5.53e+01
  bond pdb=" C2    I F   4 "
       pdb=" N3    I F   4 "
    ideal  model  delta    sigma   weight residual
    1.462  1.314  0.148 2.00e-02 2.50e+03 5.50e+01
  bond pdb=" C2    I F  31 "
       pdb=" N3    I F  31 "
    ideal  model  delta    sigma   weight residual
    1.462  1.314  0.148 2.00e-02 2.50e+03 5.50e+01
  ... (remaining 14741 not shown)

  Histogram of bond angle deviations from ideal:
       99.92 -   106.74: 808
      106.74 -   113.55: 8499
      113.55 -   120.36: 5143
      120.36 -   127.18: 5669
      127.18 -   133.99: 333
  Bond angle restraints: 20452
  Sorted by residual:
  angle pdb=" C1'   I F  37 "
        pdb=" N9    I F  37 "
        pdb=" C4    I F  37 "
      ideal   model   delta    sigma   weight residual
     106.08  123.87  -17.79 3.00e+00 1.11e-01 3.51e+01
  angle pdb=" C1'   I F  43 "
        pdb=" N9    I F  43 "
        pdb=" C4    I F  43 "
      ideal   model   delta    sigma   weight residual
     106.08  123.85  -17.77 3.00e+00 1.11e-01 3.51e+01
  angle pdb=" C1'   I F  26 "
        pdb=" N9    I F  26 "
        pdb=" C4    I F  26 "
      ideal   model   delta    sigma   weight residual
     106.08  123.75  -17.67 3.00e+00 1.11e-01 3.47e+01
  angle pdb=" C1'   I F  27 "
        pdb=" N9    I F  27 "
        pdb=" C4    I F  27 "
      ideal   model   delta    sigma   weight residual
     106.08  123.75  -17.67 3.00e+00 1.11e-01 3.47e+01
  angle pdb=" C1'   I F  19 "
        pdb=" N9    I F  19 "
        pdb=" C4    I F  19 "
      ideal   model   delta    sigma   weight residual
     106.08  123.73  -17.65 3.00e+00 1.11e-01 3.46e+01
  ... (remaining 20447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 8004
       17.98 -    35.97: 404
       35.97 -    53.95: 184
       53.95 -    71.93: 125
       71.93 -    89.92: 142
  Dihedral angle restraints: 8859
    sinusoidal: 4326
      harmonic: 4533
  Sorted by residual:
  dihedral pdb=" CB  CYS C  25 "
           pdb=" SG  CYS C  25 "
           pdb=" SG  CYS C 102 "
           pdb=" CB  CYS C 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.18   29.82     1      1.00e+01 1.00e-02 1.27e+01
  dihedral pdb=" CA  TYR C 101 "
           pdb=" C   TYR C 101 "
           pdb=" N   CYS C 102 "
           pdb=" CA  CYS C 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.44   16.56     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  SER C  60 "
           pdb=" C   SER C  60 "
           pdb=" N   LYS C  61 "
           pdb=" CA  LYS C  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.33   15.67     0      5.00e+00 4.00e-02 9.82e+00
  ... (remaining 8856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1343
       0.031 -    0.061: 581
       0.061 -    0.092: 174
       0.092 -    0.123: 86
       0.123 -    0.154: 14
  Chirality restraints: 2198
  Sorted by residual:
  chirality pdb=" CA  ILE A 577 "
            pdb=" N   ILE A 577 "
            pdb=" C   ILE A 577 "
            pdb=" CB  ILE A 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.89e-01
  chirality pdb=" CA  ILE B 577 "
            pdb=" N   ILE B 577 "
            pdb=" C   ILE B 577 "
            pdb=" CB  ILE B 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" CA  ILE A 138 "
            pdb=" N   ILE A 138 "
            pdb=" C   ILE A 138 "
            pdb=" CB  ILE A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.61e-01
  ... (remaining 2195 not shown)

  Planarity restraints: 2335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   I F  19 "   -0.218 2.00e-02 2.50e+03   5.95e-01 7.97e+03
        pdb=" C2'   I F  19 "    0.194 2.00e-02 2.50e+03
        pdb=" C3'   I F  19 "    0.597 2.00e-02 2.50e+03
        pdb=" C4'   I F  19 "   -0.439 2.00e-02 2.50e+03
        pdb=" C5'   I F  19 "   -0.051 2.00e-02 2.50e+03
        pdb=" N9    I F  19 "    0.914 2.00e-02 2.50e+03
        pdb=" O2'   I F  19 "   -0.951 2.00e-02 2.50e+03
        pdb=" O3'   I F  19 "    0.614 2.00e-02 2.50e+03
        pdb=" O4'   I F  19 "   -0.660 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   I F   2 "    0.214 2.00e-02 2.50e+03   5.92e-01 7.89e+03
        pdb=" C2'   I F   2 "   -0.208 2.00e-02 2.50e+03
        pdb=" C3'   I F   2 "   -0.591 2.00e-02 2.50e+03
        pdb=" C4'   I F   2 "    0.445 2.00e-02 2.50e+03
        pdb=" C5'   I F   2 "    0.040 2.00e-02 2.50e+03
        pdb=" N9    I F   2 "   -0.917 2.00e-02 2.50e+03
        pdb=" O2'   I F   2 "    0.924 2.00e-02 2.50e+03
        pdb=" O3'   I F   2 "   -0.594 2.00e-02 2.50e+03
        pdb=" O4'   I F   2 "    0.688 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   I F  15 "   -0.217 2.00e-02 2.50e+03   5.91e-01 7.86e+03
        pdb=" C2'   I F  15 "    0.204 2.00e-02 2.50e+03
        pdb=" C3'   I F  15 "    0.592 2.00e-02 2.50e+03
        pdb=" C4'   I F  15 "   -0.443 2.00e-02 2.50e+03
        pdb=" C5'   I F  15 "   -0.044 2.00e-02 2.50e+03
        pdb=" N9    I F  15 "    0.912 2.00e-02 2.50e+03
        pdb=" O2'   I F  15 "   -0.930 2.00e-02 2.50e+03
        pdb=" O3'   I F  15 "    0.597 2.00e-02 2.50e+03
        pdb=" O4'   I F  15 "   -0.673 2.00e-02 2.50e+03
  ... (remaining 2332 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 3062
        2.78 -     3.31: 12790
        3.31 -     3.84: 24964
        3.84 -     4.37: 30666
        4.37 -     4.90: 48954
  Nonbonded interactions: 120436
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C  57 "
            pdb=" OH  TYR C 107 "
     model   vdw
     2.252 2.440
  nonbonded pdb=" OD2 ASP A 192 "
            pdb=" OH  TYR C  63 "
     model   vdw
     2.309 2.440
  nonbonded pdb=" OG  SER A 115 "
            pdb=" OG1 THR A 118 "
     model   vdw
     2.329 2.440
  nonbonded pdb=" OG  SER B 115 "
            pdb=" OG1 THR B 118 "
     model   vdw
     2.329 2.440
  nonbonded pdb=" OD1 ASN A 507 "
            pdb=" NZ  LYS A 531 "
     model   vdw
     2.346 2.520
  ... (remaining 120431 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             3.560
  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:             0.010
  Extract box with map and model:          10.560
  Check model and map are aligned:         0.220
  Set scattering table:                    0.130
  Process input model:                     42.590
  Find NCS groups from input model:        0.600
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
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      :  0.014   0.150  14746  Z= 0.909
  Angle     :  1.429  17.786  20452  Z= 0.521
  Chirality :  0.041   0.154   2198
  Planarity :  0.081   0.595   2335
  Dihedral  : 19.246  89.919   5889
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.32 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.63 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.99 (0.22), residues: 1538
  helix: -1.04 (0.66), residues: 74
  sheet: -1.43 (0.30), residues: 340
  loop : -0.32 (0.20), residues: 1124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 115 
 HIS   0.003   0.001   HIS A 548 
 PHE   0.016   0.001   PHE C  85 
 TYR   0.015   0.001   TYR C  63 
 ARG   0.006   0.001   ARG A 489 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  482 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 481
  time to evaluate  : 1.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ASN cc_start: 0.8837 (m-40) cc_final: 0.8598 (t0)
REVERT: A  216 CYS cc_start: 0.8853 (p) cc_final: 0.8600 (p)
REVERT: A  244 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7632 (tp30)
REVERT: A  311 GLN cc_start: 0.7578 (mt0) cc_final: 0.7321 (mm110)
REVERT: A  327 LEU cc_start: 0.7743 (tp) cc_final: 0.7523 (tp)
REVERT: A  393 LEU cc_start: 0.8156 (tp) cc_final: 0.7900 (tp)
REVERT: A  438 LEU cc_start: 0.7895 (mt) cc_final: 0.7409 (tp)
REVERT: A  441 ASN cc_start: 0.6917 (m-40) cc_final: 0.6648 (m-40)
REVERT: A  479 VAL cc_start: 0.8124 (m) cc_final: 0.7797 (m)
REVERT: A  513 LEU cc_start: 0.8074 (mt) cc_final: 0.7576 (mt)
REVERT: A  516 ASN cc_start: 0.7801 (m-40) cc_final: 0.7281 (m-40)
REVERT: A  520 ASN cc_start: 0.7990 (t0) cc_final: 0.6992 (p0)
REVERT: A  540 ASN cc_start: 0.8073 (m-40) cc_final: 0.7739 (m110)
REVERT: A  550 ASN cc_start: 0.7664 (t0) cc_final: 0.7444 (t0)
REVERT: A  583 LYS cc_start: 0.8320 (pttt) cc_final: 0.7964 (tptp)
REVERT: B  131 MET cc_start: 0.7225 (ttp) cc_final: 0.6819 (tmm)
REVERT: B  233 LEU cc_start: 0.8038 (mt) cc_final: 0.7317 (tp)
REVERT: B  253 LEU cc_start: 0.8685 (tp) cc_final: 0.8470 (tp)
REVERT: B  323 ASN cc_start: 0.8245 (t0) cc_final: 0.8038 (t0)
REVERT: B  353 TRP cc_start: 0.8106 (m100) cc_final: 0.7699 (m100)
REVERT: B  393 LEU cc_start: 0.8147 (tp) cc_final: 0.7938 (tt)
REVERT: B  399 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8285 (tt0)
REVERT: B  434 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7136 (mp0)
REVERT: B  441 ASN cc_start: 0.8150 (m-40) cc_final: 0.7755 (m110)
REVERT: B  466 ASN cc_start: 0.8147 (m-40) cc_final: 0.7847 (m110)
REVERT: B  486 MET cc_start: 0.8367 (mmm) cc_final: 0.8017 (mtp)
REVERT: B  540 ASN cc_start: 0.6931 (m-40) cc_final: 0.6119 (m-40)
REVERT: B  556 TYR cc_start: 0.8871 (m-80) cc_final: 0.8451 (m-80)
REVERT: B  571 SER cc_start: 0.6959 (t) cc_final: 0.6516 (t)
REVERT: B  572 ASN cc_start: 0.8287 (m-40) cc_final: 0.8064 (t0)
REVERT: B  596 ASN cc_start: 0.7805 (m-40) cc_final: 0.7541 (m110)
REVERT: C   53 LEU cc_start: 0.8655 (mt) cc_final: 0.8227 (mm)
REVERT: C   56 ILE cc_start: 0.7335 (tt) cc_final: 0.7130 (tt)
REVERT: C   64 ASN cc_start: 0.7521 (p0) cc_final: 0.7316 (p0)
REVERT: C  105 TYR cc_start: 0.7488 (m-80) cc_final: 0.7207 (m-80)
REVERT: C  179 TRP cc_start: 0.8006 (m100) cc_final: 0.7772 (m100)
REVERT: C  180 TYR cc_start: 0.6957 (m-80) cc_final: 0.6584 (m-80)
REVERT: C  192 ILE cc_start: 0.8665 (mm) cc_final: 0.8456 (tp)
REVERT: C  202 ILE cc_start: 0.8641 (mm) cc_final: 0.8386 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 482
  average time/residue: 0.2774
  time to fit residues: 190.7557
Evaluate side-chains
  238 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 1.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0470
   chunk 63 optimal weight:    4.9990
   chunk 122 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 141 optimal weight:    7.9990
   overall best weight:    1.9484

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 316 HIS
** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 678 ASN
B  62 GLN
B 174 GLN
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS
B 674 HIS
B 678 ASN
C   9 GLN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 213 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  14746  Z= 0.389
  Angle     :  1.916  16.757  20452  Z= 1.175
  Chirality :  0.046   0.180   2198
  Planarity :  0.016   0.119   2335
  Dihedral  : 23.481  98.687   2899
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 12.52 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.23 (0.22), residues: 1538
  helix: -1.52 (0.55), residues: 82
  sheet: -1.32 (0.31), residues: 315
  loop : -0.60 (0.19), residues: 1141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  52 
 HIS   0.006   0.001   HIS B 548 
 PHE   0.022   0.002   PHE A 304 
 TYR   0.024   0.002   TYR A 302 
 ARG   0.004   0.001   ARG A 484 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 269
  time to evaluate  : 1.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.8538 (tp) cc_final: 0.8047 (tp)
REVERT: A  139 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8251 (mmmt)
REVERT: A  244 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7818 (tp30)
REVERT: A  393 LEU cc_start: 0.8433 (tp) cc_final: 0.8232 (tp)
REVERT: A  486 MET cc_start: 0.7999 (mmt) cc_final: 0.7635 (mmt)
REVERT: A  513 LEU cc_start: 0.8825 (mt) cc_final: 0.8457 (mt)
REVERT: A  520 ASN cc_start: 0.7946 (t0) cc_final: 0.7294 (p0)
REVERT: A  583 LYS cc_start: 0.8533 (pttt) cc_final: 0.8130 (tptp)
REVERT: B  133 ASN cc_start: 0.8072 (m-40) cc_final: 0.7654 (m-40)
REVERT: B  186 LEU cc_start: 0.7690 (mp) cc_final: 0.7468 (mp)
REVERT: B  196 ASN cc_start: 0.7345 (p0) cc_final: 0.6877 (m-40)
REVERT: B  233 LEU cc_start: 0.8459 (mt) cc_final: 0.7402 (tp)
REVERT: B  323 ASN cc_start: 0.8694 (t0) cc_final: 0.8389 (t0)
REVERT: B  388 ASN cc_start: 0.9033 (t0) cc_final: 0.8665 (t0)
REVERT: B  399 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8006 (tt0)
REVERT: B  420 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8667 (p)
REVERT: B  457 ASN cc_start: 0.7646 (m110) cc_final: 0.6725 (p0)
REVERT: B  486 MET cc_start: 0.8597 (mmm) cc_final: 0.8281 (mtp)
REVERT: B  516 ASN cc_start: 0.8034 (m-40) cc_final: 0.7507 (m110)
REVERT: B  523 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7966 (p0)
REVERT: B  525 MET cc_start: 0.8596 (tpp) cc_final: 0.8260 (tpp)
REVERT: B  571 SER cc_start: 0.7824 (t) cc_final: 0.7305 (t)
REVERT: B  596 ASN cc_start: 0.7926 (m-40) cc_final: 0.7455 (m110)
REVERT: B  683 TYR cc_start: 0.7687 (m-80) cc_final: 0.7129 (m-80)
REVERT: C   53 LEU cc_start: 0.8750 (mt) cc_final: 0.8467 (tp)
REVERT: C   64 ASN cc_start: 0.7557 (p0) cc_final: 0.7345 (p0)
REVERT: C   79 ASP cc_start: 0.6697 (t0) cc_final: 0.5989 (m-30)
REVERT: C  105 TYR cc_start: 0.8114 (m-80) cc_final: 0.7190 (m-80)
REVERT: C  180 TYR cc_start: 0.6814 (m-80) cc_final: 0.6496 (m-80)
REVERT: C  213 ASN cc_start: 0.6473 (OUTLIER) cc_final: 0.5703 (t0)
  outliers start: 43
  outliers final: 27
  residues processed: 301
  average time/residue: 0.2524
  time to fit residues: 113.6025
Evaluate side-chains
  222 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  285 ASN
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain A residue  659 ASN
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  523 ASP
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain C residue   60 SER
Chi-restraints excluded: chain C residue   90 ASN
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  213 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 117 optimal weight:    0.1980
   chunk 96 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 141 optimal weight:    9.9990
   chunk 153 optimal weight:   20.0000
   chunk 126 optimal weight:    1.9990
   chunk 140 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    1.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 140 ASN
** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN
B 441 ASN
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  64 ASN
** C  90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.6011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  14746  Z= 0.367
  Angle     :  1.826  15.726  20452  Z= 1.118
  Chirality :  0.046   0.165   2198
  Planarity :  0.017   0.119   2335
  Dihedral  : 24.005  98.862   2899
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 21.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 15.12 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.58 (0.22), residues: 1538
  helix: -2.01 (0.51), residues: 82
  sheet: -1.24 (0.31), residues: 307
  loop : -0.95 (0.19), residues: 1149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 353 
 HIS   0.008   0.001   HIS A 539 
 PHE   0.028   0.002   PHE B 212 
 TYR   0.029   0.002   TYR A 302 
 ARG   0.005   0.001   ARG C 164 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 217
  time to evaluate  : 1.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.7716 (m110) cc_final: 0.7470 (m-40)
REVERT: A  117 LYS cc_start: 0.8499 (pttt) cc_final: 0.7776 (mttp)
REVERT: A  244 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8505 (mm-30)
REVERT: A  307 TYR cc_start: 0.8043 (m-80) cc_final: 0.7843 (m-10)
REVERT: A  376 THR cc_start: 0.7902 (m) cc_final: 0.7501 (p)
REVERT: A  393 LEU cc_start: 0.8572 (tp) cc_final: 0.8324 (tp)
REVERT: A  520 ASN cc_start: 0.7893 (t0) cc_final: 0.7583 (t0)
REVERT: A  583 LYS cc_start: 0.8641 (pttt) cc_final: 0.8380 (tptp)
REVERT: A  604 SER cc_start: 0.8124 (m) cc_final: 0.7789 (p)
REVERT: B   37 CYS cc_start: 0.8126 (t) cc_final: 0.7455 (t)
REVERT: B  131 MET cc_start: 0.7428 (ttt) cc_final: 0.6765 (tmm)
REVERT: B  233 LEU cc_start: 0.8467 (mt) cc_final: 0.7403 (tp)
REVERT: B  243 LEU cc_start: 0.8165 (pp) cc_final: 0.7952 (mm)
REVERT: B  323 ASN cc_start: 0.8662 (t0) cc_final: 0.8237 (t0)
REVERT: B  388 ASN cc_start: 0.9127 (t0) cc_final: 0.8676 (t0)
REVERT: B  516 ASN cc_start: 0.8097 (m-40) cc_final: 0.7639 (m-40)
REVERT: B  523 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7803 (p0)
REVERT: B  525 MET cc_start: 0.8580 (tpp) cc_final: 0.8245 (tpp)
REVERT: B  556 TYR cc_start: 0.8849 (m-80) cc_final: 0.8315 (m-80)
REVERT: B  571 SER cc_start: 0.7963 (t) cc_final: 0.7463 (t)
REVERT: B  596 ASN cc_start: 0.7770 (m-40) cc_final: 0.7486 (m110)
REVERT: B  683 TYR cc_start: 0.7694 (m-80) cc_final: 0.7381 (m-80)
REVERT: C   73 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7612 (mtm-85)
REVERT: C  105 TYR cc_start: 0.8070 (m-80) cc_final: 0.6985 (m-80)
REVERT: C  112 ILE cc_start: 0.8604 (mt) cc_final: 0.8309 (mm)
REVERT: C  164 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8120 (tpp80)
REVERT: C  179 TRP cc_start: 0.8519 (m100) cc_final: 0.7614 (m100)
REVERT: C  180 TYR cc_start: 0.6962 (m-80) cc_final: 0.6653 (m-80)
REVERT: C  197 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7361 (tm-30)
REVERT: C  213 ASN cc_start: 0.7247 (t0) cc_final: 0.6375 (t0)
  outliers start: 59
  outliers final: 36
  residues processed: 264
  average time/residue: 0.2205
  time to fit residues: 89.8111
Evaluate side-chains
  222 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 185
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  285 ASN
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  659 ASN
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  441 ASN
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  523 ASP
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain B residue  659 ASN
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue   60 SER
Chi-restraints excluded: chain C residue  104 ARG
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 140 optimal weight:    2.9990
   chunk 106 optimal weight:    0.2980
   chunk 73 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 95 optimal weight:    0.8980
   chunk 142 optimal weight:    5.9990
   chunk 150 optimal weight:    0.7980
   chunk 74 optimal weight:   10.0000
   chunk 134 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 GLN
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 618 GLN
C  88 GLN
C  90 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.6429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14746  Z= 0.267
  Angle     :  1.761  15.486  20452  Z= 1.100
  Chirality :  0.044   0.227   2198
  Planarity :  0.016   0.122   2335
  Dihedral  : 23.930 103.386   2899
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 16.53 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.55 (0.22), residues: 1538
  helix: -1.73 (0.55), residues: 82
  sheet: -1.34 (0.30), residues: 309
  loop : -0.90 (0.19), residues: 1147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 353 
 HIS   0.004   0.001   HIS B 129 
 PHE   0.024   0.002   PHE B 212 
 TYR   0.017   0.001   TYR A 302 
 ARG   0.004   0.000   ARG C 164 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 217
  time to evaluate  : 1.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.7973 (m110) cc_final: 0.7699 (m-40)
REVERT: A  386 LEU cc_start: 0.8358 (mt) cc_final: 0.7987 (mt)
REVERT: A  393 LEU cc_start: 0.8447 (tp) cc_final: 0.8233 (tp)
REVERT: A  479 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8291 (m)
REVERT: A  520 ASN cc_start: 0.7830 (t0) cc_final: 0.7561 (t0)
REVERT: A  583 LYS cc_start: 0.8590 (pttt) cc_final: 0.8381 (tptp)
REVERT: A  604 SER cc_start: 0.8119 (m) cc_final: 0.7762 (p)
REVERT: B   40 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6845 (mm)
REVERT: B  131 MET cc_start: 0.7257 (ttt) cc_final: 0.7030 (tmm)
REVERT: B  133 ASN cc_start: 0.8097 (m-40) cc_final: 0.7583 (m-40)
REVERT: B  233 LEU cc_start: 0.8452 (mt) cc_final: 0.7417 (tp)
REVERT: B  323 ASN cc_start: 0.8552 (t0) cc_final: 0.8084 (t0)
REVERT: B  358 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7120 (pm20)
REVERT: B  388 ASN cc_start: 0.9060 (t0) cc_final: 0.8655 (t0)
REVERT: B  429 TRP cc_start: 0.8122 (m100) cc_final: 0.7858 (m100)
REVERT: B  516 ASN cc_start: 0.7908 (m-40) cc_final: 0.7109 (m110)
REVERT: B  523 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7850 (p0)
REVERT: B  525 MET cc_start: 0.8436 (tpp) cc_final: 0.8136 (tpp)
REVERT: B  556 TYR cc_start: 0.8833 (m-80) cc_final: 0.8246 (m-80)
REVERT: B  571 SER cc_start: 0.7572 (t) cc_final: 0.7017 (t)
REVERT: B  596 ASN cc_start: 0.7403 (m-40) cc_final: 0.6973 (m110)
REVERT: C   73 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7479 (mtm-85)
REVERT: C   89 LEU cc_start: 0.8868 (tp) cc_final: 0.8645 (tt)
REVERT: C  105 TYR cc_start: 0.8039 (m-80) cc_final: 0.7731 (m-80)
REVERT: C  164 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8232 (tpp80)
REVERT: C  180 TYR cc_start: 0.6907 (m-80) cc_final: 0.6526 (m-80)
REVERT: C  197 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7353 (tm-30)
  outliers start: 53
  outliers final: 35
  residues processed: 257
  average time/residue: 0.2234
  time to fit residues: 88.5249
Evaluate side-chains
  238 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 199
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  592 ASP
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain A residue  659 ASN
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 LYS
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  441 ASN
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  523 ASP
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain B residue  659 ASN
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  240 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 125 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0470
   chunk 112 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 135 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.6086

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  90 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.6994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14746  Z= 0.326
  Angle     :  1.732  15.590  20452  Z= 1.090
  Chirality :  0.045   0.246   2198
  Planarity :  0.016   0.121   2335
  Dihedral  : 24.217 103.053   2899
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 21.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.72 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.69 (0.22), residues: 1538
  helix: -1.58 (0.56), residues: 82
  sheet: -1.58 (0.29), residues: 333
  loop : -0.95 (0.19), residues: 1123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 353 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.029   0.002   PHE C 109 
 TYR   0.022   0.002   TYR A 302 
 ARG   0.005   0.000   ARG C  43 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 197
  time to evaluate  : 1.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 LEU cc_start: 0.8400 (tp) cc_final: 0.8156 (tp)
REVERT: A  479 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8308 (m)
REVERT: A  520 ASN cc_start: 0.7752 (t0) cc_final: 0.7533 (t0)
REVERT: B  113 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7893 (tp-100)
REVERT: B  131 MET cc_start: 0.7279 (ttt) cc_final: 0.7066 (tmm)
REVERT: B  133 ASN cc_start: 0.8150 (m-40) cc_final: 0.7674 (m-40)
REVERT: B  233 LEU cc_start: 0.8432 (mt) cc_final: 0.7286 (tp)
REVERT: B  276 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7987 (tp)
REVERT: B  323 ASN cc_start: 0.8547 (t0) cc_final: 0.8113 (t0)
REVERT: B  358 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7096 (pm20)
REVERT: B  388 ASN cc_start: 0.9137 (t0) cc_final: 0.8676 (t0)
REVERT: B  429 TRP cc_start: 0.8284 (m100) cc_final: 0.7963 (m100)
REVERT: B  467 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8390 (tttp)
REVERT: B  486 MET cc_start: 0.8517 (mmm) cc_final: 0.7968 (mtp)
REVERT: B  516 ASN cc_start: 0.8080 (m-40) cc_final: 0.7276 (m110)
REVERT: B  523 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8008 (p0)
REVERT: B  525 MET cc_start: 0.8471 (tpp) cc_final: 0.8150 (tpp)
REVERT: B  566 ILE cc_start: 0.8845 (mt) cc_final: 0.8481 (tt)
REVERT: B  571 SER cc_start: 0.7886 (t) cc_final: 0.7353 (t)
REVERT: B  596 ASN cc_start: 0.7557 (m-40) cc_final: 0.7145 (m110)
REVERT: C   73 ARG cc_start: 0.7959 (mtm110) cc_final: 0.7486 (mtm-85)
REVERT: C  164 ARG cc_start: 0.8864 (tpp80) cc_final: 0.8579 (tpp80)
REVERT: C  179 TRP cc_start: 0.8643 (m100) cc_final: 0.7939 (m100)
REVERT: C  197 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7377 (tm-30)
REVERT: C  202 ILE cc_start: 0.8035 (mp) cc_final: 0.7823 (mp)
REVERT: C  205 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7021 (ptp90)
  outliers start: 64
  outliers final: 42
  residues processed: 243
  average time/residue: 0.2300
  time to fit residues: 85.8402
Evaluate side-chains
  232 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 184
  time to evaluate  : 1.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  592 ASP
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  659 ASN
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 LYS
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  467 LYS
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  523 ASP
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain C residue   60 SER
Chi-restraints excluded: chain C residue   77 ASN
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  205 ARG
Chi-restraints excluded: chain C residue  220 SER
Chi-restraints excluded: chain C residue  240 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 135 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 150 optimal weight:    0.0060
   chunk 125 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  90 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.7198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14746  Z= 0.225
  Angle     :  1.696  15.514  20452  Z= 1.079
  Chirality :  0.043   0.254   2198
  Planarity :  0.016   0.119   2335
  Dihedral  : 24.363 103.221   2899
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 19.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.76 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.45 (0.22), residues: 1538
  helix: -0.94 (0.66), residues: 68
  sheet: -1.42 (0.30), residues: 327
  loop : -0.83 (0.19), residues: 1143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 353 
 HIS   0.003   0.001   HIS B 548 
 PHE   0.026   0.001   PHE B 212 
 TYR   0.012   0.001   TYR C 105 
 ARG   0.003   0.000   ARG C 104 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 212
  time to evaluate  : 1.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8303 (pt0)
REVERT: A  393 LEU cc_start: 0.8299 (tp) cc_final: 0.8095 (tp)
REVERT: A  479 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8292 (m)
REVERT: A  486 MET cc_start: 0.8048 (mmt) cc_final: 0.7738 (mmt)
REVERT: A  520 ASN cc_start: 0.7773 (t0) cc_final: 0.7539 (t0)
REVERT: A  579 VAL cc_start: 0.8983 (m) cc_final: 0.8597 (t)
REVERT: A  619 LYS cc_start: 0.8451 (mttp) cc_final: 0.8112 (ttmt)
REVERT: B  131 MET cc_start: 0.7152 (ttt) cc_final: 0.6921 (tmm)
REVERT: B  133 ASN cc_start: 0.8260 (m-40) cc_final: 0.7692 (m-40)
REVERT: B  233 LEU cc_start: 0.8379 (mt) cc_final: 0.7295 (tp)
REVERT: B  276 LEU cc_start: 0.8442 (tt) cc_final: 0.7893 (tp)
REVERT: B  278 MET cc_start: 0.4502 (ptp) cc_final: 0.4301 (ptp)
REVERT: B  323 ASN cc_start: 0.8347 (t0) cc_final: 0.7929 (t0)
REVERT: B  388 ASN cc_start: 0.9147 (t0) cc_final: 0.8700 (t0)
REVERT: B  429 TRP cc_start: 0.8216 (m100) cc_final: 0.7904 (m100)
REVERT: B  467 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8307 (tttp)
REVERT: B  525 MET cc_start: 0.8465 (tpp) cc_final: 0.8218 (tpp)
REVERT: B  566 ILE cc_start: 0.8854 (mt) cc_final: 0.8520 (mm)
REVERT: B  570 GLU cc_start: 0.6486 (mm-30) cc_final: 0.5598 (mt-10)
REVERT: B  571 SER cc_start: 0.7830 (t) cc_final: 0.7259 (t)
REVERT: B  596 ASN cc_start: 0.7461 (m-40) cc_final: 0.7091 (m-40)
REVERT: C   35 ASN cc_start: 0.8325 (m-40) cc_final: 0.7895 (m-40)
REVERT: C   39 TRP cc_start: 0.5686 (m100) cc_final: 0.5227 (m100)
REVERT: C   73 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7574 (mtm-85)
REVERT: C  197 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7451 (tm-30)
REVERT: C  213 ASN cc_start: 0.6228 (t0) cc_final: 0.5137 (t0)
  outliers start: 46
  outliers final: 30
  residues processed: 243
  average time/residue: 0.2347
  time to fit residues: 86.0248
Evaluate side-chains
  224 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 191
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  592 ASP
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain A residue  659 ASN
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 LYS
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  467 LYS
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain C residue   60 SER
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  220 SER
Chi-restraints excluded: chain C residue  240 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 145 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 110 optimal weight:    0.5980
   chunk 127 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 150 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0070
   chunk 91 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.7450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14746  Z= 0.252
  Angle     :  1.683  15.464  20452  Z= 1.074
  Chirality :  0.044   0.277   2198
  Planarity :  0.016   0.119   2335
  Dihedral  : 24.578 102.059   2899
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 19.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.11 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 (0.22), residues: 1538
  helix: -0.74 (0.66), residues: 68
  sheet: -1.37 (0.31), residues: 328
  loop : -0.85 (0.19), residues: 1142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 353 
 HIS   0.004   0.001   HIS A 108 
 PHE   0.025   0.002   PHE B 212 
 TYR   0.021   0.001   TYR C 105 
 ARG   0.005   0.000   ARG C 164 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 200
  time to evaluate  : 1.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8278 (pt0)
REVERT: A  479 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8301 (m)
REVERT: A  486 MET cc_start: 0.8067 (mmt) cc_final: 0.7670 (mmt)
REVERT: A  520 ASN cc_start: 0.7742 (t0) cc_final: 0.7509 (t0)
REVERT: A  579 VAL cc_start: 0.9040 (m) cc_final: 0.8630 (t)
REVERT: B  110 GLU cc_start: 0.7575 (pm20) cc_final: 0.7200 (pm20)
REVERT: B  131 MET cc_start: 0.7215 (ttt) cc_final: 0.6962 (tmm)
REVERT: B  133 ASN cc_start: 0.8295 (m-40) cc_final: 0.7741 (m-40)
REVERT: B  237 LEU cc_start: 0.8523 (mp) cc_final: 0.7787 (tt)
REVERT: B  243 LEU cc_start: 0.8237 (mm) cc_final: 0.8011 (pp)
REVERT: B  276 LEU cc_start: 0.8478 (tt) cc_final: 0.7953 (tp)
REVERT: B  323 ASN cc_start: 0.8333 (t0) cc_final: 0.7958 (t0)
REVERT: B  388 ASN cc_start: 0.9146 (t0) cc_final: 0.8703 (t0)
REVERT: B  429 TRP cc_start: 0.8257 (m100) cc_final: 0.7915 (m100)
REVERT: B  467 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8296 (tttp)
REVERT: B  486 MET cc_start: 0.8426 (mmm) cc_final: 0.8021 (mtp)
REVERT: B  525 MET cc_start: 0.8496 (tpp) cc_final: 0.8163 (tpp)
REVERT: B  566 ILE cc_start: 0.8909 (mt) cc_final: 0.8636 (mm)
REVERT: B  570 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5663 (mt-10)
REVERT: B  596 ASN cc_start: 0.7530 (m-40) cc_final: 0.7157 (m-40)
REVERT: C   30 ASP cc_start: 0.7514 (t0) cc_final: 0.7261 (t0)
REVERT: C   35 ASN cc_start: 0.8244 (m-40) cc_final: 0.7938 (m-40)
REVERT: C   73 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7731 (ptp-170)
REVERT: C  197 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7296 (tm-30)
REVERT: C  213 ASN cc_start: 0.6335 (t0) cc_final: 0.5297 (t0)
REVERT: C  229 ASP cc_start: 0.7874 (p0) cc_final: 0.7562 (t0)
  outliers start: 47
  outliers final: 35
  residues processed: 236
  average time/residue: 0.2276
  time to fit residues: 82.2462
Evaluate side-chains
  226 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 188
  time to evaluate  : 1.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  592 ASP
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 LYS
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  467 LYS
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  592 ASP
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain C residue   60 SER
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  220 SER
Chi-restraints excluded: chain C residue  240 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 95 optimal weight:    0.5980
   chunk 102 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 118 optimal weight:    0.9980
   chunk 136 optimal weight:    8.9990
   chunk 144 optimal weight:    0.5980
   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 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 352 GLN
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.7566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14746  Z= 0.207
  Angle     :  1.669  15.370  20452  Z= 1.071
  Chirality :  0.043   0.284   2198
  Planarity :  0.016   0.118   2335
  Dihedral  : 24.655 101.300   2899
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.46 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.29 (0.23), residues: 1538
  helix: -0.33 (0.77), residues: 54
  sheet: -1.30 (0.31), residues: 330
  loop : -0.75 (0.19), residues: 1154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 353 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.026   0.001   PHE B 212 
 TYR   0.032   0.001   TYR C 105 
 ARG   0.003   0.000   ARG C 164 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 204
  time to evaluate  : 1.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 GLU cc_start: 0.8668 (tp30) cc_final: 0.8446 (tp30)
REVERT: A  306 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8257 (pt0)
REVERT: A  479 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8310 (m)
REVERT: A  486 MET cc_start: 0.8034 (mmt) cc_final: 0.7684 (mmt)
REVERT: A  520 ASN cc_start: 0.7711 (t0) cc_final: 0.7461 (t0)
REVERT: A  579 VAL cc_start: 0.9047 (m) cc_final: 0.8601 (t)
REVERT: A  619 LYS cc_start: 0.8412 (mttp) cc_final: 0.8063 (ttmt)
REVERT: B  131 MET cc_start: 0.7185 (ttt) cc_final: 0.6951 (tmm)
REVERT: B  133 ASN cc_start: 0.8211 (m-40) cc_final: 0.7667 (m-40)
REVERT: B  237 LEU cc_start: 0.8503 (mp) cc_final: 0.7793 (tt)
REVERT: B  323 ASN cc_start: 0.8211 (t0) cc_final: 0.7904 (t0)
REVERT: B  325 ARG cc_start: 0.7621 (mtt-85) cc_final: 0.7072 (mtp-110)
REVERT: B  388 ASN cc_start: 0.9124 (t0) cc_final: 0.8694 (t0)
REVERT: B  429 TRP cc_start: 0.8202 (m100) cc_final: 0.7858 (m100)
REVERT: B  467 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8212 (tttp)
REVERT: B  525 MET cc_start: 0.8471 (tpp) cc_final: 0.8193 (tpp)
REVERT: B  570 GLU cc_start: 0.6305 (mm-30) cc_final: 0.5956 (mt-10)
REVERT: B  571 SER cc_start: 0.7705 (t) cc_final: 0.7127 (t)
REVERT: B  596 ASN cc_start: 0.7581 (m-40) cc_final: 0.7244 (m-40)
REVERT: C   35 ASN cc_start: 0.8270 (m-40) cc_final: 0.8029 (m-40)
REVERT: C   39 TRP cc_start: 0.6419 (m100) cc_final: 0.5576 (m100)
REVERT: C   73 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7938 (ptp-170)
REVERT: C  175 TYR cc_start: 0.7837 (m-80) cc_final: 0.7466 (m-80)
REVERT: C  197 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7286 (tm-30)
REVERT: C  198 ARG cc_start: 0.8238 (tmt170) cc_final: 0.7788 (ptp-170)
REVERT: C  213 ASN cc_start: 0.6258 (t0) cc_final: 0.5177 (t0)
  outliers start: 46
  outliers final: 34
  residues processed: 235
  average time/residue: 0.2435
  time to fit residues: 85.8748
Evaluate side-chains
  230 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 193
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  592 ASP
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 LYS
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  467 LYS
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  497 SER
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain B residue  649 CYS
Chi-restraints excluded: chain C residue   60 SER
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  220 SER
Chi-restraints excluded: chain C residue  240 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    8.9990
   chunk 140 optimal weight:    3.9990
   chunk 144 optimal weight:    0.8980
   chunk 84 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 126 optimal weight:    0.9980
   chunk 132 optimal weight:    3.9990
   chunk 139 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 494 ASN
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.7712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14746  Z= 0.251
  Angle     :  1.676  15.289  20452  Z= 1.072
  Chirality :  0.044   0.288   2198
  Planarity :  0.016   0.120   2335
  Dihedral  : 24.744 100.209   2899
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.31 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.39 (0.22), residues: 1538
  helix: -0.68 (0.68), residues: 68
  sheet: -1.28 (0.30), residues: 337
  loop : -0.83 (0.20), residues: 1133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 353 
 HIS   0.003   0.001   HIS A 539 
 PHE   0.025   0.001   PHE B 212 
 TYR   0.025   0.002   TYR C 105 
 ARG   0.003   0.000   ARG C 164 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 192
  time to evaluate  : 1.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8284 (pt0)
REVERT: A  479 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8310 (m)
REVERT: A  486 MET cc_start: 0.8061 (mmt) cc_final: 0.7713 (mmt)
REVERT: A  520 ASN cc_start: 0.7739 (t0) cc_final: 0.7494 (t0)
REVERT: A  579 VAL cc_start: 0.9029 (m) cc_final: 0.8561 (t)
REVERT: A  619 LYS cc_start: 0.8493 (mttp) cc_final: 0.8162 (ttmt)
REVERT: B  110 GLU cc_start: 0.7710 (pm20) cc_final: 0.7330 (pm20)
REVERT: B  133 ASN cc_start: 0.8246 (m-40) cc_final: 0.7786 (m-40)
REVERT: B  237 LEU cc_start: 0.8531 (mp) cc_final: 0.7829 (tt)
REVERT: B  323 ASN cc_start: 0.8197 (t0) cc_final: 0.7897 (t0)
REVERT: B  325 ARG cc_start: 0.7558 (mtt-85) cc_final: 0.7068 (mtp-110)
REVERT: B  388 ASN cc_start: 0.9140 (t0) cc_final: 0.8719 (t0)
REVERT: B  429 TRP cc_start: 0.8216 (m100) cc_final: 0.7867 (m100)
REVERT: B  486 MET cc_start: 0.8262 (mmm) cc_final: 0.8037 (mtp)
REVERT: B  525 MET cc_start: 0.8520 (tpp) cc_final: 0.8187 (tpp)
REVERT: B  566 ILE cc_start: 0.8829 (mt) cc_final: 0.8507 (tt)
REVERT: B  570 GLU cc_start: 0.6211 (mm-30) cc_final: 0.5708 (mt-10)
REVERT: B  596 ASN cc_start: 0.7630 (m-40) cc_final: 0.7297 (m-40)
REVERT: C   73 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7983 (ptp-170)
REVERT: C  104 ARG cc_start: 0.7673 (ttt-90) cc_final: 0.7421 (ttt90)
REVERT: C  164 ARG cc_start: 0.8560 (tpp80) cc_final: 0.7845 (tpp80)
REVERT: C  197 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7273 (tm-30)
REVERT: C  198 ARG cc_start: 0.8291 (tmt170) cc_final: 0.7817 (ptp-170)
REVERT: C  213 ASN cc_start: 0.6621 (t0) cc_final: 0.5684 (t0)
  outliers start: 39
  outliers final: 33
  residues processed: 221
  average time/residue: 0.2373
  time to fit residues: 78.9266
Evaluate side-chains
  216 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 181
  time to evaluate  : 1.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  592 ASP
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 LYS
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain B residue  649 CYS
Chi-restraints excluded: chain C residue   60 SER
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  220 SER
Chi-restraints excluded: chain C residue  240 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 148 optimal weight:    8.9990
   chunk 90 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 155 optimal weight:    0.5980
   chunk 143 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.8036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14746  Z= 0.325
  Angle     :  1.692  15.225  20452  Z= 1.077
  Chirality :  0.046   0.298   2198
  Planarity :  0.016   0.121   2335
  Dihedral  : 24.851  98.416   2899
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 21.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.66 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 (0.22), residues: 1538
  helix: -0.72 (0.67), residues: 68
  sheet: -1.46 (0.29), residues: 349
  loop : -0.93 (0.20), residues: 1121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 353 
 HIS   0.005   0.001   HIS A 539 
 PHE   0.018   0.002   PHE C  85 
 TYR   0.033   0.002   TYR A 683 
 ARG   0.003   0.000   ARG C 164 

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 188
  time to evaluate  : 1.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  479 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8358 (m)
REVERT: A  486 MET cc_start: 0.8161 (mmt) cc_final: 0.7696 (mmt)
REVERT: A  619 LYS cc_start: 0.8524 (mttp) cc_final: 0.8245 (ttmt)
REVERT: B  133 ASN cc_start: 0.8169 (m-40) cc_final: 0.7466 (m-40)
REVERT: B  237 LEU cc_start: 0.8541 (mp) cc_final: 0.7831 (tt)
REVERT: B  325 ARG cc_start: 0.7693 (mtt-85) cc_final: 0.7336 (mtm110)
REVERT: B  388 ASN cc_start: 0.9142 (t0) cc_final: 0.8698 (t0)
REVERT: B  486 MET cc_start: 0.8351 (mmm) cc_final: 0.8019 (mtm)
REVERT: B  525 MET cc_start: 0.8552 (tpp) cc_final: 0.8185 (tpp)
REVERT: B  566 ILE cc_start: 0.8953 (mt) cc_final: 0.8611 (tt)
REVERT: B  570 GLU cc_start: 0.6217 (mm-30) cc_final: 0.5709 (mt-10)
REVERT: B  596 ASN cc_start: 0.7750 (m-40) cc_final: 0.7456 (m-40)
REVERT: C  164 ARG cc_start: 0.8624 (tpp80) cc_final: 0.7877 (tpp80)
REVERT: C  167 CYS cc_start: 0.5597 (OUTLIER) cc_final: 0.5207 (t)
REVERT: C  175 TYR cc_start: 0.8043 (m-80) cc_final: 0.7605 (m-80)
REVERT: C  197 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7483 (tm-30)
REVERT: C  198 ARG cc_start: 0.8265 (tmt170) cc_final: 0.7782 (ptp-170)
REVERT: C  213 ASN cc_start: 0.6712 (t0) cc_final: 0.6006 (t0)
  outliers start: 39
  outliers final: 35
  residues processed: 221
  average time/residue: 0.2443
  time to fit residues: 80.9417
Evaluate side-chains
  214 residues out of total 1424 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 177
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  256 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  516 ASN
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  591 ILE
Chi-restraints excluded: chain A residue  592 ASP
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 LYS
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  443 ILE
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  497 SER
Chi-restraints excluded: chain B residue  642 MET
Chi-restraints excluded: chain B residue  645 ASN
Chi-restraints excluded: chain B residue  649 CYS
Chi-restraints excluded: chain C residue   60 SER
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  220 SER
Chi-restraints excluded: chain C residue  240 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 114 optimal weight:    0.5980
   chunk 18 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 123 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 127 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** 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 = 0.4124 r_free = 0.4124 target = 0.145598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.116676 restraints weight = 32104.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.118587 restraints weight = 18232.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.119352 restraints weight = 12276.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.8090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  14746  Z= 0.251
  Angle     :  1.680  15.247  20452  Z= 1.074
  Chirality :  0.044   0.301   2198
  Planarity :  0.016   0.120   2335
  Dihedral  : 24.773  97.631   2899
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 20.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 22.08 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.49 (0.22), residues: 1538
  helix: -0.59 (0.68), residues: 68
  sheet: -1.36 (0.30), residues: 345
  loop : -0.91 (0.20), residues: 1125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 353 
 HIS   0.003   0.001   HIS B 129 
 PHE   0.029   0.001   PHE B 212 
 TYR   0.031   0.002   TYR C 105 
 ARG   0.008   0.001   ARG C 104 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3003.83 seconds
wall clock time: 55 minutes 50.45 seconds (3350.45 seconds total)