Starting phenix.real_space_refine
on Wed Sep 17 10:27:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fz5_50893/09_2025/9fz5_50893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fz5_50893/09_2025/9fz5_50893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fz5_50893/09_2025/9fz5_50893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fz5_50893/09_2025/9fz5_50893.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fz5_50893/09_2025/9fz5_50893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fz5_50893/09_2025/9fz5_50893.map"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5074      2.51       5
     N    1397      2.21       5
     O    1579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8082
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 740, 6002
          Classifications: {'peptide': 740}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 710}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1169
          Classifications: {'peptide': 149}
          Link IDs: {'PTRANS': 8, 'TRANS': 140}
    Chain: "C"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 911
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 106}
  Time building chain proxies: 2.00, per 1000 atoms: 0.25
  Number of scatterers: 8082
  At special positions: 0
  Unit cell: (95.76, 85.12, 117.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1579      8.00
     N    1397      7.00
     C    5074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A 724 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 173 " - pdb=" SG  CYS A 725 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  67 " - pdb=" SG  CYS C 123 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 419.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1882

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 13 sheets defined
      9.8% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 33
      removed outlier: 3.969A  pdb=" N   LEU A  33 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 464 through 470
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 3.855A  pdb=" N   PHE A 541 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 3.534A  pdb=" N   ILE A 664 " --> pdb=" O   SER A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 673
      removed outlier: 3.547A  pdb=" N   SER A 673 " --> pdb=" O   LYS A 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 59
      removed outlier: 3.812A  pdb=" N   ARG B  52 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 147
      removed outlier: 3.928A  pdb=" N   ASP B 141 " --> pdb=" O   ASP B 137 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   MET B 142 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 158
      removed outlier: 3.893A  pdb=" N   GLU B 153 " --> pdb=" O   ASP B 149 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE B 156 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 168
      removed outlier: 3.916A  pdb=" N   ILE B 162 " --> pdb=" O   LYS B 158 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG B 163 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA B 168 " --> pdb=" O   ALA B 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 130
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55
      removed outlier: 6.567A  pdb=" N   ASP A  85 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL A  73 " --> pdb=" O   GLN A  83 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   GLN A  83 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ILE A  75 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ARG A  81 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   SER A  80 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ASP A 113 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   LEU A  82 " --> pdb=" O   HIS A 111 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   HIS A 111 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   ALA A  84 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   ASN A 109 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA A 106 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   VAL A 110 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LYS A 120 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   TYR A 112 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   ILE A 118 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 141
      removed outlier: 3.593A  pdb=" N   ARG A 148 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS A 150 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A 183 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 190
      removed outlier: 3.836A  pdb=" N   VAL A 195 " --> pdb=" O   ASP A 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 234
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 233 through 234
    current: chain 'A' and resid 412 through 419
      removed outlier: 3.682A  pdb=" N   GLN A 413 " --> pdb=" O   HIS A 431 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA A 427 " --> pdb=" O   PHE A 417 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 427 through 432
    current: chain 'A' and resid 445 through 457
      removed outlier: 3.921A  pdb=" N   LYS A 486 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LYS A 452 " --> pdb=" O   GLN A 484 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLN A 484 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET A 482 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 479 through 486
    current: chain 'A' and resid 505 through 512
      removed outlier: 3.689A  pdb=" N   THR A 505 " --> pdb=" O   TYR A 567 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLY A 561 " --> pdb=" O   ARG A 511 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   ILE A 582 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   THR A 560 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   GLY A 580 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   VAL A 562 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   SER A 578 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   SER A 564 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ASN A 576 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   ILE A 566 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ARG A 574 " --> pdb=" O   TRP A 614 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   TRP A 614 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASN A 576 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   THR A 612 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   SER A 578 " --> pdb=" O   GLY A 610 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLY A 610 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   GLY A 580 " --> pdb=" O   TRP A 608 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   TRP A 608 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ILE A 582 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR A 584 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TRP A 608 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR A 628 " --> pdb=" O   TRP A 608 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE A 626 " --> pdb=" O   GLY A 610 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   THR A 612 " --> pdb=" O   GLY A 624 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY A 624 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ARG A 623 " --> pdb=" O   SER A 641 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   SER A 641 " --> pdb=" O   ARG A 623 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLY A 625 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   THR A 637 " --> pdb=" O   GLN A 627 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER A 638 " --> pdb=" O   TYR A 658 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A 640 " --> pdb=" O   TYR A 656 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   TYR A 656 " --> pdb=" O   SER A 640 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASN A 655 " --> pdb=" O   GLY A 686 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN A 684 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA A 689 " --> pdb=" O   GLY A 701 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE A 699 " --> pdb=" O   TRP A 691 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ASP A 706 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS A 711 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 711 through 712
    current: chain 'A' and resid 726 through 730
      removed outlier: 3.624A  pdb=" N   ALA A 727 " --> pdb=" O   GLU A 757 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU A 757 " --> pdb=" O   ALA A 727 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG A 729 " --> pdb=" O   ASN A 755 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 244
      removed outlier: 3.782A  pdb=" N   PHE A 243 " --> pdb=" O   TYR A 263 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 255 through 256
      removed outlier: 3.540A  pdb=" N   ASP A 256 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ARG A 277 " --> pdb=" O   ASP A 256 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 275
      removed outlier: 4.122A  pdb=" N   LEU A 289 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 319
      removed outlier: 3.700A  pdb=" N   GLY A 319 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 363 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 359
      removed outlier: 4.152A  pdb=" N   THR A 374 " --> pdb=" O   PHE A 359 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 739
      removed outlier: 3.695A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 39
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 61 through 62
    current: chain 'B' and resid 97 through 108
      removed outlier: 3.512A  pdb=" N   MET B 102 " --> pdb=" O   VAL B 122 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL B 122 " --> pdb=" O   MET B 102 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 98
      removed outlier: 3.768A  pdb=" N   ILE C  74 " --> pdb=" O   ARG C  68 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ARG C  68 " --> pdb=" O   ILE C  74 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL C  76 " --> pdb=" O   ASP C  66 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE C  53 " --> pdb=" O   GLN C  69 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   VAL C  58 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY C  36 " --> pdb=" O   VAL C  58 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN C  39 " --> pdb=" O   GLU C 114 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLU C 114 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 101
      removed outlier: 3.804A  pdb=" N   TYR C 108 " --> pdb=" O   MET C 111 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    438 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1385
        1.30 -     1.43: 2242
        1.43 -     1.56: 4586
        1.56 -     1.69: 0
        1.69 -     1.82: 58
  Bond restraints: 8271
  Sorted by residual:
  bond pdb=" C   ASP A 422 "
       pdb=" N   ASP A 423 "
    ideal  model  delta    sigma   weight residual
    1.334  1.420 -0.087 1.30e-02 5.92e+03 4.45e+01
  bond pdb=" C   ARG A 421 "
       pdb=" N   ASP A 422 "
    ideal  model  delta    sigma   weight residual
    1.335  1.250  0.085 1.35e-02 5.49e+03 3.99e+01
  bond pdb=" C   THR A 420 "
       pdb=" N   ARG A 421 "
    ideal  model  delta    sigma   weight residual
    1.331  1.243  0.088 1.43e-02 4.89e+03 3.78e+01
  bond pdb=" C   LYS A 346 "
       pdb=" N   TYR A 347 "
    ideal  model  delta    sigma   weight residual
    1.333  1.399 -0.065 1.34e-02 5.57e+03 2.37e+01
  bond pdb=" CA  ARG A 421 "
       pdb=" C   ARG A 421 "
    ideal  model  delta    sigma   weight residual
    1.520  1.464  0.057 1.22e-02 6.72e+03 2.16e+01
  ... (remaining 8266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 11087
        2.43 -     4.86: 128
        4.86 -     7.29: 20
        7.29 -     9.72: 11
        9.72 -    12.15: 4
  Bond angle restraints: 11250
  Sorted by residual:
  angle pdb=" CA  ASP A 422 "
        pdb=" C   ASP A 422 "
        pdb=" N   ASP A 423 "
      ideal   model   delta    sigma   weight residual
     118.08  130.23  -12.15 1.30e+00 5.92e-01 8.74e+01
  angle pdb=" N   THR A 420 "
        pdb=" CA  THR A 420 "
        pdb=" C   THR A 420 "
      ideal   model   delta    sigma   weight residual
     112.93  122.71   -9.78 1.12e+00 7.97e-01 7.63e+01
  angle pdb=" CA  ASP A 422 "
        pdb=" CB  ASP A 422 "
        pdb=" CG  ASP A 422 "
      ideal   model   delta    sigma   weight residual
     112.60  120.51   -7.91 1.00e+00 1.00e+00 6.25e+01
  angle pdb=" CA  ASP A 423 "
        pdb=" C   ASP A 423 "
        pdb=" O   ASP A 423 "
      ideal   model   delta    sigma   weight residual
     119.95  111.02    8.93 1.18e+00 7.18e-01 5.73e+01
  angle pdb=" CA  ASP A 423 "
        pdb=" CB  ASP A 423 "
        pdb=" CG  ASP A 423 "
      ideal   model   delta    sigma   weight residual
     112.60  119.82   -7.22 1.00e+00 1.00e+00 5.22e+01
  ... (remaining 11245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4115
       17.84 -    35.69: 593
       35.69 -    53.53: 179
       53.53 -    71.37: 35
       71.37 -    89.22: 13
  Dihedral angle restraints: 4935
    sinusoidal: 1989
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CB  CYS A  31 "
           pdb=" SG  CYS A  31 "
           pdb=" SG  CYS A 724 "
           pdb=" CB  CYS A 724 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.10  -88.90     1      1.00e+01 1.00e-02 9.42e+01
  dihedral pdb=" CB  CYS A 173 "
           pdb=" SG  CYS A 173 "
           pdb=" SG  CYS A 725 "
           pdb=" CB  CYS A 725 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.03  -78.03     1      1.00e+01 1.00e-02 7.61e+01
  dihedral pdb=" C   ARG A 421 "
           pdb=" N   ARG A 421 "
           pdb=" CA  ARG A 421 "
           pdb=" CB  ARG A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -104.17  -18.43     0      2.50e+00 1.60e-01 5.43e+01
  ... (remaining 4932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1100
       0.089 -    0.179: 92
       0.179 -    0.268: 4
       0.268 -    0.358: 0
       0.358 -    0.447: 3
  Chirality restraints: 1199
  Sorted by residual:
  chirality pdb=" CA  ASP A 422 "
            pdb=" N   ASP A 422 "
            pdb=" C   ASP A 422 "
            pdb=" CB  ASP A 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.00e+00
  chirality pdb=" CA  THR A 420 "
            pdb=" N   THR A 420 "
            pdb=" C   THR A 420 "
            pdb=" CB  THR A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.13    0.40 2.00e-01 2.50e+01 3.92e+00
  chirality pdb=" CB  THR A 420 "
            pdb=" CA  THR A 420 "
            pdb=" OG1 THR A 420 "
            pdb=" CG2 THR A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.18    0.37 2.00e-01 2.50e+01 3.37e+00
  ... (remaining 1196 not shown)

  Planarity restraints: 1484
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 423 "   -0.012 2.00e-02 2.50e+03   2.40e-02 5.74e+00
        pdb=" C   ASP A 423 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ASP A 423 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A 424 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 341 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.52e+00
        pdb=" C   ASN A 341 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASN A 341 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP A 342 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 419 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   ASN A 419 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ASN A 419 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 420 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1481 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 104
        2.62 -     3.19: 6518
        3.19 -     3.76: 10777
        3.76 -     4.33: 14445
        4.33 -     4.90: 25264
  Nonbonded interactions: 57108
  Sorted by model distance:
  nonbonded pdb=" O   LYS B  70 "
            pdb=" OD1 ASP B  71 "
     model   vdw
     2.055 3.040
  nonbonded pdb=" O   HIS A  90 "
            pdb=" OG1 THR A 103 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ASN A 401 "
            pdb=" OD1 ASP A 402 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" N   GLU B  66 "
            pdb=" OE1 GLU B  66 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OG  SER A  80 "
            pdb=" OD1 ASP A 114 "
     model   vdw
     2.279 3.040
  ... (remaining 57103 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.270
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.020
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088   8274  Z= 0.261
  Angle     :  0.737  12.154  11256  Z= 0.438
  Chirality :  0.051   0.447   1199
  Planarity :  0.005   0.045   1484
  Dihedral  : 18.546  89.217   3044
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.84 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 30.94 %
    Favored  : 62.90 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.53 (0.24), residues: 996
  helix: -1.44 (0.50), residues: 101
  sheet: -3.26 (0.23), residues: 407
  loop : -3.04 (0.24), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 150 
 TYR   0.016   0.001   TYR C 108 
 PHE   0.006   0.001   PHE B 126 
 TRP   0.008   0.001   TRP C  33 
 HIS   0.002   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 8271)
  covalent geometry    : angle       0.73665 (11250)
  SS BOND              : bond        0.00256 (    3)
  SS BOND              : angle       0.70146 (    6)
  hydrogen bonds       : bond        0.30522 (  163)
  hydrogen bonds       : angle      10.70075 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 107
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6787 (t60) cc_final: 0.6266 (t60)
REVERT: A  343 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7986 (p90)
REVERT: A  421 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8671 (mtp180)
REVERT: A  448 ASN cc_start: 0.7672 (t0) cc_final: 0.7386 (t0)
REVERT: A  499 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6693 (tmm)
REVERT: A  581 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7948 (pp30)
REVERT: A  595 ILE cc_start: 0.8558 (mm) cc_final: 0.8237 (mt)
REVERT: A  754 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.6248 (t80)
REVERT: C   27 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7148 (ttmm)
REVERT: C   96 LEU cc_start: 0.8196 (mp) cc_final: 0.7958 (mm)
  outliers start: 54
  outliers final: 42
  residues processed: 153
  average time/residue: 0.0925
  time to fit residues: 19.6154
Evaluate side-chains
  150 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 102
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  421 ARG
Chi-restraints excluded: chain A residue  423 ASP
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  581 GLN
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  710 ASN
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain C residue   27 LYS
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  106 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 634 ASN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  69 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.154252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111960 restraints weight = 10679.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.115042 restraints weight = 5563.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.116978 restraints weight = 3780.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.118028 restraints weight = 3001.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.118832 restraints weight = 2623.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8274  Z= 0.120
  Angle     :  0.586   9.715  11256  Z= 0.308
  Chirality :  0.045   0.167   1199
  Planarity :  0.005   0.044   1484
  Dihedral  :  8.957  59.069   1220
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.63 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 29.68 %
    Favored  : 64.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.22 (0.24), residues: 996
  helix: -1.26 (0.48), residues: 108
  sheet: -3.00 (0.23), residues: 417
  loop : -2.89 (0.25), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 421 
 TYR   0.013   0.001   TYR C 108 
 PHE   0.007   0.001   PHE A 170 
 TRP   0.008   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8271)
  covalent geometry    : angle       0.58551 (11250)
  SS BOND              : bond        0.00255 (    3)
  SS BOND              : angle       0.59300 (    6)
  hydrogen bonds       : bond        0.03770 (  163)
  hydrogen bonds       : angle       6.55379 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 105
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6801 (t60) cc_final: 0.5994 (t60)
REVERT: A  142 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5124 (tmt)
REVERT: A  255 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7274 (mpp)
REVERT: A  288 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7655 (mt-10)
REVERT: A  328 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8206 (m-40)
REVERT: A  343 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8422 (p90)
REVERT: A  347 TYR cc_start: 0.8527 (m-80) cc_final: 0.8005 (m-80)
REVERT: A  448 ASN cc_start: 0.7985 (t0) cc_final: 0.7522 (t0)
REVERT: A  460 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8434 (mt0)
REVERT: A  499 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7084 (tmm)
REVERT: A  595 ILE cc_start: 0.8391 (mm) cc_final: 0.8063 (mt)
REVERT: A  711 LYS cc_start: 0.8225 (mmtt) cc_final: 0.8001 (mmtm)
REVERT: A  729 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7681 (ttp80)
REVERT: A  745 HIS cc_start: 0.6309 (OUTLIER) cc_final: 0.5810 (m90)
REVERT: A  778 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7750 (mt)
  outliers start: 52
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0836
  time to fit residues: 17.4348
Evaluate side-chains
  135 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 101
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 92 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 744 GLN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.150819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.108817 restraints weight = 10745.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.111760 restraints weight = 5762.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.113616 restraints weight = 3973.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.114646 restraints weight = 3175.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.115419 restraints weight = 2789.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8274  Z= 0.186
  Angle     :  0.637  13.702  11256  Z= 0.336
  Chirality :  0.046   0.163   1199
  Planarity :  0.005   0.049   1484
  Dihedral  :  7.489  58.633   1157
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.15 %
    Favored  : 87.65 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 30.02 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.24 (0.24), residues: 996
  helix: -1.19 (0.48), residues: 109
  sheet: -2.95 (0.24), residues: 414
  loop : -2.99 (0.24), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  68 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.010   0.001   PHE A 170 
 TRP   0.011   0.001   TRP A 311 
 HIS   0.011   0.002   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8271)
  covalent geometry    : angle       0.63746 (11250)
  SS BOND              : bond        0.00290 (    3)
  SS BOND              : angle       0.70796 (    6)
  hydrogen bonds       : bond        0.04286 (  163)
  hydrogen bonds       : angle       6.06890 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 103
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6976 (t60) cc_final: 0.6054 (t60)
REVERT: A  142 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5193 (tmt)
REVERT: A  255 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7401 (mpp)
REVERT: A  328 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8274 (m-40)
REVERT: A  343 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8556 (p90)
REVERT: A  347 TYR cc_start: 0.8651 (m-80) cc_final: 0.8410 (m-80)
REVERT: A  448 ASN cc_start: 0.8040 (t0) cc_final: 0.7523 (t0)
REVERT: A  460 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8516 (mt0)
REVERT: A  499 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6871 (tmm)
REVERT: A  595 ILE cc_start: 0.8437 (mm) cc_final: 0.8111 (mt)
REVERT: A  729 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7763 (ttp80)
REVERT: A  754 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6569 (t80)
REVERT: A  778 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7855 (mt)
  outliers start: 56
  outliers final: 29
  residues processed: 147
  average time/residue: 0.0801
  time to fit residues: 17.0243
Evaluate side-chains
  139 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 101
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 94 optimal weight:   10.0000
   chunk 80 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 129 ASN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.163367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.124771 restraints weight = 10896.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.127729 restraints weight = 9900.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.128421 restraints weight = 5393.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.128179 restraints weight = 4629.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.128442 restraints weight = 4624.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8274  Z= 0.190
  Angle     :  0.636  11.014  11256  Z= 0.338
  Chirality :  0.046   0.162   1199
  Planarity :  0.005   0.050   1484
  Dihedral  :  7.255  58.921   1151
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.75 %
    Favored  : 87.05 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 29.34 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.25 (0.24), residues: 996
  helix: -1.09 (0.49), residues: 109
  sheet: -3.01 (0.23), residues: 422
  loop : -2.96 (0.25), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  68 
 TYR   0.014   0.001   TYR A 537 
 PHE   0.010   0.001   PHE A 276 
 TRP   0.010   0.001   TRP A 311 
 HIS   0.006   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 8271)
  covalent geometry    : angle       0.63638 (11250)
  SS BOND              : bond        0.00311 (    3)
  SS BOND              : angle       0.72335 (    6)
  hydrogen bonds       : bond        0.04034 (  163)
  hydrogen bonds       : angle       5.82865 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 105
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6871 (t60) cc_final: 0.5963 (t60)
REVERT: A  142 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.5511 (tmt)
REVERT: A  255 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7669 (mpp)
REVERT: A  328 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8236 (m-40)
REVERT: A  343 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8611 (p90)
REVERT: A  448 ASN cc_start: 0.8011 (t0) cc_final: 0.7538 (t0)
REVERT: A  460 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8518 (mt0)
REVERT: A  499 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6750 (ttm)
REVERT: A  595 ILE cc_start: 0.8458 (mm) cc_final: 0.8137 (mt)
REVERT: A  711 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7819 (mmtt)
REVERT: A  729 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7810 (ttp80)
REVERT: A  754 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6613 (t80)
REVERT: A  778 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7973 (mt)
  outliers start: 62
  outliers final: 38
  residues processed: 153
  average time/residue: 0.0834
  time to fit residues: 17.9675
Evaluate side-chains
  147 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 99
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 217 GLN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.174448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.134773 restraints weight = 10772.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136673 restraints weight = 8435.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.138122 restraints weight = 4933.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138184 restraints weight = 3727.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.138430 restraints weight = 3731.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8274  Z= 0.130
  Angle     :  0.599   9.450  11256  Z= 0.312
  Chirality :  0.045   0.159   1199
  Planarity :  0.005   0.049   1484
  Dihedral  :  6.887  59.738   1150
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.84 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  7.19 %
    Allowed  : 28.54 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.10 (0.24), residues: 996
  helix: -0.87 (0.50), residues: 109
  sheet: -2.94 (0.23), residues: 411
  loop : -2.88 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 267 
 TYR   0.012   0.001   TYR C 108 
 PHE   0.009   0.001   PHE A 276 
 TRP   0.007   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8271)
  covalent geometry    : angle       0.59889 (11250)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       0.55855 (    6)
  hydrogen bonds       : bond        0.03354 (  163)
  hydrogen bonds       : angle       5.51991 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 102
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6954 (t60) cc_final: 0.5786 (t60)
REVERT: A  142 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.5377 (tmt)
REVERT: A  255 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7606 (mpp)
REVERT: A  328 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8258 (m-40)
REVERT: A  343 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8496 (p90)
REVERT: A  448 ASN cc_start: 0.7925 (t0) cc_final: 0.7414 (t0)
REVERT: A  460 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8473 (mt0)
REVERT: A  499 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6623 (ttm)
REVERT: A  595 ILE cc_start: 0.8418 (mm) cc_final: 0.8099 (mt)
REVERT: A  711 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.8008 (mmtm)
REVERT: A  717 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7714 (tt)
REVERT: A  729 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7806 (ttp80)
REVERT: A  754 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6570 (t80)
REVERT: A  778 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7888 (mt)
  outliers start: 63
  outliers final: 36
  residues processed: 152
  average time/residue: 0.0823
  time to fit residues: 17.8385
Evaluate side-chains
  145 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 98
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 97 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 98 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
B  58 ASN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.177104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.137274 restraints weight = 10596.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.140121 restraints weight = 7043.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.141214 restraints weight = 4264.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.141135 restraints weight = 3577.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.141434 restraints weight = 3518.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8274  Z= 0.109
  Angle     :  0.580  13.459  11256  Z= 0.295
  Chirality :  0.044   0.156   1199
  Planarity :  0.004   0.048   1484
  Dihedral  :  6.296  59.665   1146
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.13 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 29.22 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.94 (0.24), residues: 996
  helix: -0.72 (0.50), residues: 108
  sheet: -2.78 (0.23), residues: 413
  loop : -2.83 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 267 
 TYR   0.012   0.001   TYR C 108 
 PHE   0.008   0.001   PHE A 276 
 TRP   0.007   0.001   TRP C  33 
 HIS   0.003   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8271)
  covalent geometry    : angle       0.58032 (11250)
  SS BOND              : bond        0.00200 (    3)
  SS BOND              : angle       0.51094 (    6)
  hydrogen bonds       : bond        0.02963 (  163)
  hydrogen bonds       : angle       5.23080 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 101
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6835 (t60) cc_final: 0.5618 (t60)
REVERT: A  142 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.5202 (tmt)
REVERT: A  255 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7396 (mpp)
REVERT: A  278 TYR cc_start: 0.8367 (p90) cc_final: 0.7942 (p90)
REVERT: A  328 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8113 (m-40)
REVERT: A  448 ASN cc_start: 0.8000 (t0) cc_final: 0.7512 (t0)
REVERT: A  460 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8411 (mt0)
REVERT: A  469 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7105 (mmt180)
REVERT: A  499 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6547 (ttm)
REVERT: A  595 ILE cc_start: 0.8352 (mm) cc_final: 0.8029 (mt)
REVERT: A  711 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7933 (mmtm)
REVERT: A  717 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7720 (tt)
REVERT: A  729 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7780 (ttp80)
REVERT: A  745 HIS cc_start: 0.6250 (OUTLIER) cc_final: 0.5802 (m90)
REVERT: A  754 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6562 (t80)
REVERT: A  778 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7795 (mt)
  outliers start: 61
  outliers final: 39
  residues processed: 148
  average time/residue: 0.0831
  time to fit residues: 17.5095
Evaluate side-chains
  149 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 98
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 98 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0670
   chunk 61 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    1.1324

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
B  54 GLN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.176027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.136632 restraints weight = 10796.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.138278 restraints weight = 9840.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139127 restraints weight = 5874.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.140811 restraints weight = 4520.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.140718 restraints weight = 4008.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8274  Z= 0.130
  Angle     :  0.596  12.295  11256  Z= 0.304
  Chirality :  0.045   0.156   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  6.219  59.890   1144
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.34 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  7.53 %
    Allowed  : 28.54 %
    Favored  : 63.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.86 (0.24), residues: 996
  helix: -0.69 (0.50), residues: 108
  sheet: -2.72 (0.24), residues: 413
  loop : -2.79 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 267 
 TYR   0.013   0.001   TYR C 108 
 PHE   0.007   0.001   PHE A 276 
 TRP   0.007   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8271)
  covalent geometry    : angle       0.59564 (11250)
  SS BOND              : bond        0.00214 (    3)
  SS BOND              : angle       0.54842 (    6)
  hydrogen bonds       : bond        0.03172 (  163)
  hydrogen bonds       : angle       5.18316 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 102
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6859 (t60) cc_final: 0.5707 (t60)
REVERT: A  142 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.5441 (tmt)
REVERT: A  255 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7471 (mpp)
REVERT: A  278 TYR cc_start: 0.8351 (p90) cc_final: 0.8007 (p90)
REVERT: A  328 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8242 (m-40)
REVERT: A  448 ASN cc_start: 0.7927 (t0) cc_final: 0.7453 (t0)
REVERT: A  460 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8466 (mt0)
REVERT: A  469 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7098 (mmt180)
REVERT: A  499 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6521 (ttm)
REVERT: A  595 ILE cc_start: 0.8368 (mm) cc_final: 0.8053 (mt)
REVERT: A  598 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6204 (mp0)
REVERT: A  711 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7933 (mmtm)
REVERT: A  717 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7739 (tt)
REVERT: A  729 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7778 (ttp80)
REVERT: A  745 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.6069 (m170)
REVERT: A  754 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6570 (t80)
REVERT: A  778 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7820 (mt)
REVERT: B   35 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8679 (m)
  outliers start: 66
  outliers final: 42
  residues processed: 154
  average time/residue: 0.0834
  time to fit residues: 18.1228
Evaluate side-chains
  153 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 97
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  281 GLN
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 95 optimal weight:    0.3980
   chunk 91 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
B  54 GLN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.165146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.126322 restraints weight = 10630.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.128395 restraints weight = 10213.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.129797 restraints weight = 5813.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.129349 restraints weight = 4637.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.129716 restraints weight = 4546.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8274  Z= 0.173
  Angle     :  0.629  11.650  11256  Z= 0.325
  Chirality :  0.046   0.158   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  6.399  59.270   1144
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.45 %
    Favored  : 87.35 %
  Rotamer:
    Outliers :  7.19 %
    Allowed  : 29.00 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.91 (0.24), residues: 996
  helix: -0.72 (0.50), residues: 108
  sheet: -2.75 (0.24), residues: 413
  loop : -2.83 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  68 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.011   0.001   PHE A 276 
 TRP   0.009   0.001   TRP A 311 
 HIS   0.005   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8271)
  covalent geometry    : angle       0.62878 (11250)
  SS BOND              : bond        0.00252 (    3)
  SS BOND              : angle       0.62850 (    6)
  hydrogen bonds       : bond        0.03602 (  163)
  hydrogen bonds       : angle       5.30966 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 97
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6762 (t60) cc_final: 0.5723 (t60)
REVERT: A  142 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.5515 (tmt)
REVERT: A  255 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7603 (mpp)
REVERT: A  328 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8248 (m-40)
REVERT: A  448 ASN cc_start: 0.8012 (t0) cc_final: 0.7528 (t0)
REVERT: A  460 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8509 (mt0)
REVERT: A  469 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7115 (mmt180)
REVERT: A  499 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6469 (ttm)
REVERT: A  595 ILE cc_start: 0.8370 (mm) cc_final: 0.8062 (mt)
REVERT: A  598 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6227 (mp0)
REVERT: A  622 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7416 (tt)
REVERT: A  711 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7815 (mmtt)
REVERT: A  717 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7792 (tt)
REVERT: A  729 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7793 (ttp80)
REVERT: A  754 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6619 (t80)
REVERT: A  778 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7916 (mt)
  outliers start: 63
  outliers final: 41
  residues processed: 146
  average time/residue: 0.0815
  time to fit residues: 16.8956
Evaluate side-chains
  149 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 95
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.165053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.125732 restraints weight = 10678.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.126987 restraints weight = 10261.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.128329 restraints weight = 6176.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.128957 restraints weight = 4532.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.129193 restraints weight = 4168.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8274  Z= 0.161
  Angle     :  0.625  11.178  11256  Z= 0.324
  Chirality :  0.045   0.159   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  6.463  59.337   1144
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.94 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 29.57 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.91 (0.24), residues: 996
  helix: -0.63 (0.50), residues: 107
  sheet: -2.73 (0.24), residues: 412
  loop : -2.86 (0.24), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.013   0.001   TYR C 108 
 PHE   0.013   0.001   PHE A 276 
 TRP   0.008   0.001   TRP A 311 
 HIS   0.005   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8271)
  covalent geometry    : angle       0.62526 (11250)
  SS BOND              : bond        0.00237 (    3)
  SS BOND              : angle       0.60334 (    6)
  hydrogen bonds       : bond        0.03548 (  163)
  hydrogen bonds       : angle       5.35418 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 101
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6787 (t60) cc_final: 0.5707 (t60)
REVERT: A  142 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.5498 (tmt)
REVERT: A  255 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7598 (mpp)
REVERT: A  328 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8233 (m-40)
REVERT: A  448 ASN cc_start: 0.8050 (t0) cc_final: 0.7568 (t0)
REVERT: A  460 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8504 (mt0)
REVERT: A  469 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7118 (mmt180)
REVERT: A  499 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6460 (ttm)
REVERT: A  595 ILE cc_start: 0.8377 (mm) cc_final: 0.8068 (mt)
REVERT: A  598 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6223 (mp0)
REVERT: A  622 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7413 (tt)
REVERT: A  711 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7816 (mmtt)
REVERT: A  729 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7794 (ttp80)
REVERT: A  754 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6601 (t80)
REVERT: A  778 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7896 (mt)
  outliers start: 58
  outliers final: 38
  residues processed: 147
  average time/residue: 0.0830
  time to fit residues: 17.2899
Evaluate side-chains
  149 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 99
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 57 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.163182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.125247 restraints weight = 10768.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.127277 restraints weight = 10085.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.129107 restraints weight = 6646.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128637 restraints weight = 5423.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.128929 restraints weight = 4580.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8274  Z= 0.197
  Angle     :  0.665  10.867  11256  Z= 0.345
  Chirality :  0.046   0.160   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  6.655  58.198   1144
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 14.06 %
    Favored  : 85.74 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 30.37 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.98 (0.24), residues: 996
  helix: -0.68 (0.50), residues: 106
  sheet: -2.76 (0.24), residues: 430
  loop : -2.90 (0.25), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  68 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.014   0.001   PHE A 276 
 TRP   0.009   0.001   TRP A 311 
 HIS   0.006   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 8271)
  covalent geometry    : angle       0.66452 (11250)
  SS BOND              : bond        0.00258 (    3)
  SS BOND              : angle       0.70453 (    6)
  hydrogen bonds       : bond        0.03908 (  163)
  hydrogen bonds       : angle       5.52691 (  438)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 101
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6766 (t60) cc_final: 0.5703 (t60)
REVERT: A  142 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.5502 (tmt)
REVERT: A  255 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7689 (mpp)
REVERT: A  328 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8236 (m-40)
REVERT: A  448 ASN cc_start: 0.8125 (t0) cc_final: 0.7664 (t0)
REVERT: A  460 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8530 (mt0)
REVERT: A  469 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7105 (mmt180)
REVERT: A  499 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6339 (ttm)
REVERT: A  595 ILE cc_start: 0.8416 (mm) cc_final: 0.8119 (mt)
REVERT: A  598 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6219 (mp0)
REVERT: A  622 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7427 (tt)
REVERT: A  711 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7803 (mmtt)
REVERT: A  729 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7777 (ttp80)
REVERT: A  754 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6639 (t80)
REVERT: A  778 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7964 (mt)
  outliers start: 51
  outliers final: 36
  residues processed: 141
  average time/residue: 0.0817
  time to fit residues: 16.3763
Evaluate side-chains
  147 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 99
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 98 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.174364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.135260 restraints weight = 10680.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.135434 restraints weight = 10979.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136442 restraints weight = 7672.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.136757 restraints weight = 5639.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.139405 restraints weight = 4775.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8274  Z= 0.132
  Angle     :  0.613  10.785  11256  Z= 0.315
  Chirality :  0.045   0.158   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  6.333  58.714   1144
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.54 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 30.25 %
    Favored  : 63.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.84 (0.25), residues: 996
  helix: -0.45 (0.52), residues: 100
  sheet: -2.69 (0.24), residues: 410
  loop : -2.82 (0.24), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.013   0.001   TYR C 108 
 PHE   0.012   0.001   PHE A 485 
 TRP   0.006   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8271)
  covalent geometry    : angle       0.61340 (11250)
  SS BOND              : bond        0.00224 (    3)
  SS BOND              : angle       0.54453 (    6)
  hydrogen bonds       : bond        0.03205 (  163)
  hydrogen bonds       : angle       5.31164 (  438)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1467.98 seconds
wall clock time: 26 minutes 0.77 seconds (1560.77 seconds total)