Starting phenix.real_space_refine
on Thu Sep 26 05:05:01 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/09_2024/7tym_26185_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/09_2024/7tym_26185.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/09_2024/7tym_26185.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/09_2024/7tym_26185.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/09_2024/7tym_26185_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tym_26185/09_2024/7tym_26185_neut.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      70      5.16       5
     C    7670      2.51       5
     N    2160      2.21       5
     O    2212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 12112
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 771, 6056
          Classifications: {'peptide': 771}
          Link IDs: {'PTRANS': 40, 'TRANS': 730}
          Chain breaks: 7
  Restraints were copied for chains:
    B
  Time building chain proxies: 12.63, per 1000 atoms: 1.04
  Number of scatterers: 12112
  At special positions: 0
  Unit cell: (122.04, 154.44, 154.44, 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      70     16.00
     O    2212      8.00
     N    2160      7.00
     C    7670      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 122 " - pdb=" SG  CYS A 150 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS A 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 188 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 190 " - pdb=" SG  CYS A 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 207 " - pdb=" SG  CYS A 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 223 " - pdb=" SG  CYS A 232 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 254 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 302 " - pdb=" SG  CYS A 321 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 631 " - pdb=" SG  CYS A 838 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 764 " - pdb=" SG  CYS A 773 " 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: 2.75
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2860

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 26 sheets defined
      11.2% alpha, 26.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 20
      removed outlier: 3.510A  pdb=" N   GLN A  18 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A  19 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 139
      removed outlier: 3.831A  pdb=" N   ALA A 138 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN A 139 " --> pdb=" O   PRO A 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 135 through 139'
    Processing helix  chain 'A' and resid 146 through 150
      removed outlier: 3.580A  pdb=" N   CYS A 150 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 220
      removed outlier: 3.636A  pdb=" N   CYS A 220 " --> pdb=" O   PRO A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 258
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.916A  pdb=" N   GLY A 272 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 4.268A  pdb=" N   GLN A 316 " --> pdb=" O   GLN A 313 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ASP A 317 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LEU A 318 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   VAL A 319 " --> pdb=" O   GLN A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 346
      removed outlier: 3.806A  pdb=" N   SER A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 4.136A  pdb=" N   ILE A 427 " --> pdb=" O   CYS A 423 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 693
    Processing helix  chain 'A' and resid 841 through 848
      removed outlier: 3.899A  pdb=" N   PHE A 847 " --> pdb=" O   ARG A 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 20
      removed outlier: 3.510A  pdb=" N   GLN B  18 " --> pdb=" O   GLU B  15 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU B  19 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 139
      removed outlier: 3.831A  pdb=" N   ALA B 138 " --> pdb=" O   ALA B 135 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASN B 139 " --> pdb=" O   PRO B 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 135 through 139'
    Processing helix  chain 'B' and resid 146 through 150
      removed outlier: 3.581A  pdb=" N   CYS B 150 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 220
      removed outlier: 3.637A  pdb=" N   CYS B 220 " --> pdb=" O   PRO B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 258
    Processing helix  chain 'B' and resid 269 through 273
      removed outlier: 3.915A  pdb=" N   GLY B 272 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 319
      removed outlier: 4.267A  pdb=" N   GLN B 316 " --> pdb=" O   GLN B 313 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ASP B 317 " --> pdb=" O   ALA B 314 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 315 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   VAL B 319 " --> pdb=" O   GLN B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 346
      removed outlier: 3.806A  pdb=" N   SER B 345 " --> pdb=" O   GLN B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 435
      removed outlier: 4.136A  pdb=" N   ILE B 427 " --> pdb=" O   CYS B 423 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLY B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 693
    Processing helix  chain 'B' and resid 841 through 848
      removed outlier: 3.899A  pdb=" N   PHE B 847 " --> pdb=" O   ARG B 843 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9
      removed outlier: 8.186A  pdb=" N   GLN A  30 " --> pdb=" O   PRO A   5 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU A   7 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   LEU A  32 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ILE A   9 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   MET A  34 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 9
      removed outlier: 8.186A  pdb=" N   GLN A  30 " --> pdb=" O   PRO A   5 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   LEU A   7 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   LEU A  32 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ILE A   9 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   MET A  34 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   LEU A  58 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU A  29 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   PHE A  60 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ILE A  31 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   VAL A  62 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   LEU A  33 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   PHE A  92 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LEU A  59 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ARG A 114 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL A  90 " --> pdb=" O   ARG A 114 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   GLU A 116 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   PHE A  92 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL A 113 " --> pdb=" O   HIS A 140 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 168
      removed outlier: 3.689A  pdb=" N   THR A 168 " --> pdb=" O   ASP A 175 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ASP A 175 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228
    Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243
      removed outlier: 3.551A  pdb=" N   ARG A 247 " --> pdb=" O   TYR A 243 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 309
      removed outlier: 3.840A  pdb=" N   VAL A 304 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   SER A 327 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   THR A 306 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ILE A 329 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   THR A 308 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 309
      removed outlier: 3.840A  pdb=" N   VAL A 304 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   SER A 327 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   THR A 306 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ILE A 329 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   THR A 308 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 8.622A  pdb=" N   LYS A 357 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   LEU A 328 " --> pdb=" O   LYS A 357 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   LYS A 359 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU A 330 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   LEU A 388 " --> pdb=" O   TYR A 415 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 463 through 468
      removed outlier: 6.581A  pdb=" N   ARG A 476 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ASN A 466 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU A 474 " --> pdb=" O   ASN A 466 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   THR A 468 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ARG A 472 " --> pdb=" O   THR A 468 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 518 through 522
    Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 588
      removed outlier: 5.669A  pdb=" N   ASP A 584 " --> pdb=" O   LYS A 600 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LYS A 600 " --> pdb=" O   ASP A 584 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 737 through 741
      removed outlier: 3.567A  pdb=" N   VAL A 614 " --> pdb=" O   ASP A 739 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR A 611 " --> pdb=" O   CYS A 764 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLU A 756 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 797 through 801
      removed outlier: 3.848A  pdb=" N   SER A 805 " --> pdb=" O   SER A 801 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 834 through 840
      removed outlier: 3.650A  pdb=" N   TYR A 827 " --> pdb=" O   THR A 835 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS A 822 " --> pdb=" O   THR A 867 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 9
      removed outlier: 8.185A  pdb=" N   GLN B  30 " --> pdb=" O   PRO B   5 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LEU B   7 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ILE B   9 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   MET B  34 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 5 through 9
      removed outlier: 8.185A  pdb=" N   GLN B  30 " --> pdb=" O   PRO B   5 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LEU B   7 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ILE B   9 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   MET B  34 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
      removed outlier: 8.453A  pdb=" N   LEU B  58 " --> pdb=" O   GLY B  27 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU B  29 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   PHE B  60 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ILE B  31 " --> pdb=" O   PHE B  60 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   VAL B  62 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   LEU B  33 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   PHE B  92 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LEU B  59 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   ARG B 114 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL B  90 " --> pdb=" O   ARG B 114 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   GLU B 116 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   PHE B  92 " --> pdb=" O   GLU B 116 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 113 " --> pdb=" O   HIS B 140 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 167 through 168
      removed outlier: 3.690A  pdb=" N   THR B 168 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ASP B 175 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 226 through 228
    Processing sheet with id=AB9, first strand: chain 'B' and resid 240 through 243
      removed outlier: 3.552A  pdb=" N   ARG B 247 " --> pdb=" O   TYR B 243 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 301 through 309
      removed outlier: 3.839A  pdb=" N   VAL B 304 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   SER B 327 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   THR B 306 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ILE B 329 " --> pdb=" O   THR B 306 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   THR B 308 " --> pdb=" O   ILE B 329 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 301 through 309
      removed outlier: 3.839A  pdb=" N   VAL B 304 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   SER B 327 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   THR B 306 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ILE B 329 " --> pdb=" O   THR B 306 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   THR B 308 " --> pdb=" O   ILE B 329 " (cutoff:3.500A)
      removed outlier: 8.621A  pdb=" N   LYS B 357 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   LEU B 328 " --> pdb=" O   LYS B 357 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   LYS B 359 " --> pdb=" O   LEU B 328 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU B 330 " --> pdb=" O   LYS B 359 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   LEU B 388 " --> pdb=" O   TYR B 415 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 463 through 468
      removed outlier: 6.580A  pdb=" N   ARG B 476 " --> pdb=" O   VAL B 464 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ASN B 466 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU B 474 " --> pdb=" O   ASN B 466 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   THR B 468 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   ARG B 472 " --> pdb=" O   THR B 468 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 518 through 522
    Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 588
      removed outlier: 5.669A  pdb=" N   ASP B 584 " --> pdb=" O   LYS B 600 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LYS B 600 " --> pdb=" O   ASP B 584 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 737 through 741
      removed outlier: 3.567A  pdb=" N   VAL B 614 " --> pdb=" O   ASP B 739 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR B 611 " --> pdb=" O   CYS B 764 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLU B 756 " --> pdb=" O   LEU B 619 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 797 through 801
      removed outlier: 3.847A  pdb=" N   SER B 805 " --> pdb=" O   SER B 801 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 834 through 840
      removed outlier: 3.650A  pdb=" N   TYR B 827 " --> pdb=" O   THR B 835 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS B 822 " --> pdb=" O   THR B 867 " (cutoff:3.500A)

    254 hydrogen bonds defined for protein.
    636 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.81

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4034
        1.35 -     1.48: 3074
        1.48 -     1.60: 5204
        1.60 -     1.73: 0
        1.73 -     1.86: 80
  Bond restraints: 12392
  Sorted by residual:
  bond pdb=" CB  CYS A 321 "
       pdb=" SG  CYS A 321 "
    ideal  model  delta    sigma   weight residual
    1.808  1.857 -0.049 3.30e-02 9.18e+02 2.21e+00
  bond pdb=" CB  CYS B 321 "
       pdb=" SG  CYS B 321 "
    ideal  model  delta    sigma   weight residual
    1.808  1.857 -0.049 3.30e-02 9.18e+02 2.20e+00
  bond pdb=" CA  THR B 553 "
       pdb=" CB  THR B 553 "
    ideal  model  delta    sigma   weight residual
    1.529  1.548 -0.019 1.58e-02 4.01e+03 1.40e+00
  bond pdb=" CA  THR A 553 "
       pdb=" CB  THR A 553 "
    ideal  model  delta    sigma   weight residual
    1.529  1.547 -0.018 1.58e-02 4.01e+03 1.34e+00
  bond pdb=" C   PRO A 237 "
       pdb=" N   PRO A 238 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.25e+00
  ... (remaining 12387 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 16511
        1.62 -     3.24: 256
        3.24 -     4.85: 53
        4.85 -     6.47: 8
        6.47 -     8.09: 6
  Bond angle restraints: 16834
  Sorted by residual:
  angle pdb=" CA  CYS B 302 "
        pdb=" CB  CYS B 302 "
        pdb=" SG  CYS B 302 "
      ideal   model   delta    sigma   weight residual
     114.40  122.07   -7.67 2.30e+00 1.89e-01 1.11e+01
  angle pdb=" CA  CYS A 302 "
        pdb=" CB  CYS A 302 "
        pdb=" SG  CYS A 302 "
      ideal   model   delta    sigma   weight residual
     114.40  122.04   -7.64 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" CA  THR B 553 "
        pdb=" CB  THR B 553 "
        pdb=" CG2 THR B 553 "
      ideal   model   delta    sigma   weight residual
     110.50  114.63   -4.13 1.70e+00 3.46e-01 5.91e+00
  angle pdb=" CA  THR A 553 "
        pdb=" CB  THR A 553 "
        pdb=" CG2 THR A 553 "
      ideal   model   delta    sigma   weight residual
     110.50  114.63   -4.13 1.70e+00 3.46e-01 5.90e+00
  angle pdb=" C   PHE A 370 "
        pdb=" N   LYS A 371 "
        pdb=" CA  LYS A 371 "
      ideal   model   delta    sigma   weight residual
     120.54  123.82   -3.28 1.35e+00 5.49e-01 5.89e+00
  ... (remaining 16829 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 6335
       16.79 -    33.58: 804
       33.58 -    50.38: 217
       50.38 -    67.17: 32
       67.17 -    83.96: 16
  Dihedral angle restraints: 7404
    sinusoidal: 2964
      harmonic: 4440
  Sorted by residual:
  dihedral pdb=" CB  CYS A 165 "
           pdb=" SG  CYS A 165 "
           pdb=" SG  CYS A 184 "
           pdb=" CB  CYS A 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.76  -83.76     1      1.00e+01 1.00e-02 8.56e+01
  dihedral pdb=" CB  CYS A 122 "
           pdb=" SG  CYS A 122 "
           pdb=" SG  CYS A 150 "
           pdb=" CB  CYS A 150 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -25.46  -60.54     1      1.00e+01 1.00e-02 4.88e+01
  dihedral pdb=" CB  CYS A 154 "
           pdb=" SG  CYS A 154 "
           pdb=" SG  CYS A 178 "
           pdb=" CB  CYS A 178 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.87   58.13     1      1.00e+01 1.00e-02 4.53e+01
  ... (remaining 7401 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1394
       0.041 -    0.082: 308
       0.082 -    0.122: 160
       0.122 -    0.163: 16
       0.163 -    0.204: 2
  Chirality restraints: 1880
  Sorted by residual:
  chirality pdb=" CA  PHE B 418 "
            pdb=" N   PHE B 418 "
            pdb=" C   PHE B 418 "
            pdb=" CB  PHE B 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  PHE A 418 "
            pdb=" N   PHE A 418 "
            pdb=" C   PHE A 418 "
            pdb=" CB  PHE A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  THR A 553 "
            pdb=" CA  THR A 553 "
            pdb=" OG1 THR A 553 "
            pdb=" CG2 THR A 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.59e-01
  ... (remaining 1877 not shown)

  Planarity restraints: 2176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 778 "    0.013 2.00e-02 2.50e+03   1.69e-02 5.03e+00
        pdb=" CG  PHE B 778 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 778 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 778 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 778 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 778 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 778 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 778 "    0.012 2.00e-02 2.50e+03   1.69e-02 4.99e+00
        pdb=" CG  PHE A 778 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 778 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 778 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 778 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 778 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 778 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 418 "   -0.023 2.00e-02 2.50e+03   1.52e-02 4.03e+00
        pdb=" CG  PHE B 418 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 418 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 418 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 418 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 418 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 418 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 2173 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 120
        2.60 -     3.18: 9664
        3.18 -     3.75: 17794
        3.75 -     4.33: 24220
        4.33 -     4.90: 41511
  Nonbonded interactions: 93309
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 188 "
            pdb=" SG  CYS B 196 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS B 223 "
            pdb=" SG  CYS B 232 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 207 "
            pdb=" SG  CYS B 220 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B   4 "
            pdb=" SG  CYS B  22 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 236 "
            pdb=" SG  CYS B 248 "
     model   vdw
     2.030 3.760
  ... (remaining 93304 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.720
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
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      :  0.002   0.049  12392  Z= 0.153
  Angle     :  0.541   8.091  16834  Z= 0.280
  Chirality :  0.043   0.204   1880
  Planarity :  0.004   0.040   2176
  Dihedral  : 15.938  83.961   4502
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.09 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.87 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.22), residues: 1510
  helix:  1.00 (0.53), residues: 112
  sheet: -0.10 (0.26), residues: 376
  loop : -1.52 (0.19), residues: 1022

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 402 
 HIS   0.004   0.001   HIS A 762 
 PHE   0.039   0.001   PHE B 778 
 TYR   0.009   0.001   TYR B 176 
 ARG   0.011   0.000   ARG B 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.655 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2589
  time to fit residues: 31.0621
Evaluate side-chains
  77 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    0.0970
   chunk 116 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 120 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 89 optimal weight:    5.9990
   chunk 139 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 271 GLN
A 617 GLN
B 183 HIS
B 271 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.0747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12392  Z= 0.168
  Angle     :  0.514   6.082  16834  Z= 0.266
  Chirality :  0.043   0.141   1880
  Planarity :  0.004   0.044   2176
  Dihedral  :  4.164  24.716   1688
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.89 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.21), residues: 1510
  helix:  1.02 (0.52), residues: 112
  sheet: -0.04 (0.26), residues: 376
  loop : -1.52 (0.19), residues: 1022

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 234 
 HIS   0.005   0.001   HIS A 762 
 PHE   0.026   0.001   PHE B 418 
 TYR   0.008   0.001   TYR B  56 
 ARG   0.006   0.000   ARG B 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 1.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7652 (mmt180)
REVERT: A  229 GLN cc_start: 0.8074 (mt0) cc_final: 0.7872 (mm110)
REVERT: A  307 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7408 (tttp)
REVERT: A  377 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7349 (mtm110)
REVERT: A  402 TRP cc_start: 0.7310 (OUTLIER) cc_final: 0.5917 (p-90)
REVERT: B  199 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7669 (mmt180)
REVERT: B  236 CYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6973 (m)
REVERT: B  307 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7300 (tttp)
REVERT: B  377 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7347 (mtm110)
REVERT: B  402 TRP cc_start: 0.7305 (OUTLIER) cc_final: 0.5878 (p-90)
REVERT: B  631 CYS cc_start: 0.8726 (m) cc_final: 0.7992 (m)
  outliers start: 28
  outliers final: 12
  residues processed: 121
  average time/residue: 0.2144
  time to fit residues: 39.1275
Evaluate side-chains
  107 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain B residue  199 ARG
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  236 CYS
Chi-restraints excluded: chain B residue  271 GLN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  825 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0470
   chunk 116 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 140 optimal weight:    4.9990
   chunk 151 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9990
   chunk 138 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
A 617 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.0889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12392  Z= 0.156
  Angle     :  0.504   9.396  16834  Z= 0.257
  Chirality :  0.042   0.172   1880
  Planarity :  0.004   0.042   2176
  Dihedral  :  4.122  23.282   1688
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.43 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.21), residues: 1510
  helix:  1.58 (0.54), residues: 100
  sheet: -0.04 (0.26), residues: 376
  loop : -1.50 (0.19), residues: 1034

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 599 
 HIS   0.005   0.001   HIS B 762 
 PHE   0.019   0.001   PHE B 418 
 TYR   0.008   0.001   TYR A  56 
 ARG   0.002   0.000   ARG B 743 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 1.294 
Fit side-chains
REVERT: A  199 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7712 (mmp80)
REVERT: A  307 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7401 (tttp)
REVERT: A  377 ARG cc_start: 0.7682 (mtm110) cc_final: 0.7467 (mtm110)
REVERT: A  402 TRP cc_start: 0.7450 (OUTLIER) cc_final: 0.6030 (p-90)
REVERT: B  199 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7738 (mmp80)
REVERT: B  307 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7287 (tttp)
REVERT: B  377 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7465 (mtm110)
REVERT: B  402 TRP cc_start: 0.7449 (OUTLIER) cc_final: 0.6031 (p-90)
REVERT: B  631 CYS cc_start: 0.8768 (m) cc_final: 0.8091 (m)
  outliers start: 34
  outliers final: 11
  residues processed: 125
  average time/residue: 0.2437
  time to fit residues: 44.2636
Evaluate side-chains
  102 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  199 ARG
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  199 ARG
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  480 TYR
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  774 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 138 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 140 optimal weight:    4.9990
   chunk 148 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 133 optimal weight:    0.0570
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.1700

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
B 419 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12392  Z= 0.238
  Angle     :  0.541   7.365  16834  Z= 0.279
  Chirality :  0.044   0.197   1880
  Planarity :  0.004   0.042   2176
  Dihedral  :  4.372  23.717   1688
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.20 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.21), residues: 1510
  helix:  1.49 (0.54), residues: 100
  sheet: -0.19 (0.26), residues: 378
  loop : -1.56 (0.19), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 599 
 HIS   0.005   0.001   HIS B 762 
 PHE   0.045   0.001   PHE B 418 
 TYR   0.010   0.001   TYR B 630 
 ARG   0.002   0.000   ARG A 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 88
  time to evaluate  : 1.461 
Fit side-chains
REVERT: A    7 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (pp)
REVERT: A  307 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7523 (tttp)
REVERT: A  402 TRP cc_start: 0.7673 (OUTLIER) cc_final: 0.6262 (p-90)
REVERT: B  631 CYS cc_start: 0.8810 (m) cc_final: 0.8152 (m)
  outliers start: 34
  outliers final: 20
  residues processed: 118
  average time/residue: 0.2090
  time to fit residues: 38.2425
Evaluate side-chains
  104 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 LEU
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  480 TYR
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  836 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 123 optimal weight:    0.2980
   chunk 84 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 110 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 127 optimal weight:    4.9990
   chunk 102 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 133 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 337 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12392  Z= 0.194
  Angle     :  0.521   6.792  16834  Z= 0.267
  Chirality :  0.043   0.186   1880
  Planarity :  0.004   0.041   2176
  Dihedral  :  4.331  23.489   1688
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 21.34 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.21), residues: 1510
  helix:  1.46 (0.54), residues: 100
  sheet: -0.18 (0.26), residues: 374
  loop : -1.57 (0.19), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 599 
 HIS   0.005   0.001   HIS B 762 
 PHE   0.034   0.001   PHE B 418 
 TYR   0.008   0.001   TYR B 630 
 ARG   0.004   0.000   ARG B 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 89
  time to evaluate  : 1.468 
Fit side-chains
REVERT: A  307 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7425 (tttp)
REVERT: A  402 TRP cc_start: 0.7626 (OUTLIER) cc_final: 0.6396 (p-90)
REVERT: B  213 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7377 (mm-40)
REVERT: B  307 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7335 (tttp)
REVERT: B  402 TRP cc_start: 0.7628 (OUTLIER) cc_final: 0.6405 (p-90)
REVERT: B  631 CYS cc_start: 0.8731 (m) cc_final: 0.8085 (m)
  outliers start: 35
  outliers final: 25
  residues processed: 119
  average time/residue: 0.2374
  time to fit residues: 42.3697
Evaluate side-chains
  114 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  402 TRP
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  480 TYR
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  774 SER
Chi-restraints excluded: chain B residue  825 ILE
Chi-restraints excluded: chain B residue  836 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 134 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 149 optimal weight:    3.9990
   chunk 123 optimal weight:    0.7980
   chunk 68 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
A 337 ASN
B  28 HIS
B 337 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12392  Z= 0.374
  Angle     :  0.613   7.466  16834  Z= 0.316
  Chirality :  0.046   0.205   1880
  Planarity :  0.004   0.044   2176
  Dihedral  :  4.941  27.498   1688
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.88 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.21), residues: 1510
  helix:  1.30 (0.54), residues: 100
  sheet: -0.48 (0.25), residues: 378
  loop : -1.73 (0.19), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 599 
 HIS   0.006   0.001   HIS B 762 
 PHE   0.031   0.002   PHE B 418 
 TYR   0.013   0.002   TYR B 630 
 ARG   0.008   0.000   ARG B 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 80
  time to evaluate  : 1.347 
Fit side-chains
REVERT: A  377 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6877 (ttp-110)
REVERT: B  194 MET cc_start: 0.7069 (mmm) cc_final: 0.6780 (mtp)
REVERT: B  307 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7458 (tttp)
REVERT: B  631 CYS cc_start: 0.8822 (m) cc_final: 0.8117 (m)
  outliers start: 38
  outliers final: 30
  residues processed: 114
  average time/residue: 0.2077
  time to fit residues: 36.3782
Evaluate side-chains
  112 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  270 HIS
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  480 TYR
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  774 SER
Chi-restraints excluded: chain B residue  796 VAL
Chi-restraints excluded: chain B residue  825 ILE
Chi-restraints excluded: chain B residue  836 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 143 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 108 optimal weight:    6.9990
   chunk 125 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 148 optimal weight:    4.9990
   chunk 92 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 617 GLN
B 337 ASN
B 617 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12392  Z= 0.194
  Angle     :  0.536   6.706  16834  Z= 0.276
  Chirality :  0.044   0.194   1880
  Planarity :  0.004   0.040   2176
  Dihedral  :  4.643  28.230   1688
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 22.71 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.21), residues: 1510
  helix:  1.32 (0.54), residues: 100
  sheet: -0.50 (0.25), residues: 384
  loop : -1.68 (0.19), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 599 
 HIS   0.005   0.001   HIS A 762 
 PHE   0.013   0.001   PHE B 418 
 TYR   0.009   0.001   TYR B  56 
 ARG   0.003   0.000   ARG B 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 82
  time to evaluate  : 1.361 
Fit side-chains
REVERT: B  631 CYS cc_start: 0.8775 (m) cc_final: 0.8111 (m)
  outliers start: 30
  outliers final: 28
  residues processed: 109
  average time/residue: 0.2321
  time to fit residues: 38.0049
Evaluate side-chains
  107 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  462 ARG
Chi-restraints excluded: chain B residue  480 TYR
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  774 SER
Chi-restraints excluded: chain B residue  796 VAL
Chi-restraints excluded: chain B residue  825 ILE
Chi-restraints excluded: chain B residue  836 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0670
   chunk 101 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 116 optimal weight:    0.2980
   chunk 135 optimal weight:    3.9990
   overall best weight:    1.0720

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

Flipped N/Q/H residues before XYZ refinement:
A 617 GLN
B 337 ASN
B 617 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12392  Z= 0.213
  Angle     :  0.543   7.145  16834  Z= 0.279
  Chirality :  0.044   0.200   1880
  Planarity :  0.004   0.041   2176
  Dihedral  :  4.593  29.401   1688
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 22.18 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.21), residues: 1510
  helix:  1.30 (0.54), residues: 100
  sheet: -0.51 (0.25), residues: 384
  loop : -1.68 (0.19), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 599 
 HIS   0.006   0.001   HIS B 762 
 PHE   0.018   0.001   PHE B 418 
 TYR   0.009   0.001   TYR B 630 
 ARG   0.012   0.000   ARG B 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 83
  time to evaluate  : 1.144 
Fit side-chains
REVERT: A  307 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7386 (tttp)
REVERT: B  316 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7399 (mp10)
REVERT: B  377 ARG cc_start: 0.7484 (mtm110) cc_final: 0.6815 (ttp-110)
REVERT: B  631 CYS cc_start: 0.8809 (m) cc_final: 0.8165 (m)
  outliers start: 37
  outliers final: 29
  residues processed: 118
  average time/residue: 0.1869
  time to fit residues: 34.5914
Evaluate side-chains
  106 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 75
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  270 HIS
Chi-restraints excluded: chain B residue  316 GLN
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  480 TYR
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  774 SER
Chi-restraints excluded: chain B residue  796 VAL
Chi-restraints excluded: chain B residue  825 ILE
Chi-restraints excluded: chain B residue  836 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 142 optimal weight:    0.9990
   chunk 129 optimal weight:    0.3980
   chunk 138 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 108 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 124 optimal weight:    0.7980
   chunk 130 optimal weight:    4.9990
   chunk 137 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0770
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 617 GLN
B 337 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12392  Z= 0.159
  Angle     :  0.537  10.663  16834  Z= 0.273
  Chirality :  0.044   0.229   1880
  Planarity :  0.004   0.040   2176
  Dihedral  :  4.483  32.894   1688
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 22.71 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.21), residues: 1510
  helix:  1.32 (0.54), residues: 100
  sheet: -0.42 (0.25), residues: 384
  loop : -1.63 (0.19), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 179 
 HIS   0.005   0.001   HIS B 762 
 PHE   0.014   0.001   PHE B 418 
 TYR   0.008   0.001   TYR A 415 
 ARG   0.009   0.000   ARG B 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 77
  time to evaluate  : 1.370 
Fit side-chains
REVERT: A  307 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7342 (tttp)
REVERT: B  316 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7368 (mp10)
REVERT: B  402 TRP cc_start: 0.7762 (OUTLIER) cc_final: 0.6564 (p-90)
REVERT: B  631 CYS cc_start: 0.8727 (m) cc_final: 0.8074 (m)
  outliers start: 38
  outliers final: 31
  residues processed: 112
  average time/residue: 0.2063
  time to fit residues: 35.8472
Evaluate side-chains
  109 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 75
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  270 HIS
Chi-restraints excluded: chain B residue  316 GLN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  462 ARG
Chi-restraints excluded: chain B residue  480 TYR
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  774 SER
Chi-restraints excluded: chain B residue  825 ILE
Chi-restraints excluded: chain B residue  836 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 153 optimal weight:    3.9990
   chunk 141 optimal weight:    0.6980
   chunk 122 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 617 GLN
B 337 ASN
** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12392  Z= 0.266
  Angle     :  0.572  10.929  16834  Z= 0.291
  Chirality :  0.045   0.207   1880
  Planarity :  0.004   0.041   2176
  Dihedral  :  4.653  32.568   1688
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.74 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 22.64 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.21), residues: 1510
  helix:  1.26 (0.54), residues: 100
  sheet: -0.49 (0.25), residues: 384
  loop : -1.68 (0.19), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 599 
 HIS   0.006   0.001   HIS B 762 
 PHE   0.022   0.001   PHE B 418 
 TYR   0.010   0.001   TYR B 630 
 ARG   0.013   0.000   ARG B 377 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 77
  time to evaluate  : 1.319 
Fit side-chains
REVERT: A  316 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7349 (mp10)
REVERT: B  316 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7401 (mp10)
REVERT: B  377 ARG cc_start: 0.7457 (mtm110) cc_final: 0.6818 (ttp-110)
REVERT: B  402 TRP cc_start: 0.7856 (OUTLIER) cc_final: 0.6485 (p-90)
REVERT: B  631 CYS cc_start: 0.8821 (m) cc_final: 0.8154 (m)
  outliers start: 35
  outliers final: 30
  residues processed: 110
  average time/residue: 0.2006
  time to fit residues: 34.7871
Evaluate side-chains
  108 residues out of total 1312 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 75
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  188 CYS
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  480 TYR
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  535 THR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  643 ASP
Chi-restraints excluded: chain A residue  774 SER
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  836 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  270 HIS
Chi-restraints excluded: chain B residue  316 GLN
Chi-restraints excluded: chain B residue  402 TRP
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  480 TYR
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  535 THR
Chi-restraints excluded: chain B residue  580 THR
Chi-restraints excluded: chain B residue  643 ASP
Chi-restraints excluded: chain B residue  774 SER
Chi-restraints excluded: chain B residue  825 ILE
Chi-restraints excluded: chain B residue  836 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    0.0770
   chunk 37 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 125 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.9142

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

Flipped N/Q/H residues before XYZ refinement:
** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.128184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.100992 restraints weight = 19139.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 3.30
r_work: 0.3087 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12392  Z= 0.194
  Angle     :  0.555  10.911  16834  Z= 0.281
  Chirality :  0.044   0.205   1880
  Planarity :  0.004   0.040   2176
  Dihedral  :  4.559  32.291   1688
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 22.71 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.21), residues: 1510
  helix:  1.33 (0.54), residues: 100
  sheet: -0.45 (0.25), residues: 384
  loop : -1.66 (0.19), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 599 
 HIS   0.005   0.001   HIS B 762 
 PHE   0.018   0.001   PHE B 418 
 TYR   0.008   0.001   TYR A 415 
 ARG   0.013   0.000   ARG A 377 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2372.20 seconds
wall clock time: 44 minutes 33.82 seconds (2673.82 seconds total)