Starting phenix.real_space_refine
on Sat Jan 18 21:14:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wjn_32546/01_2025/7wjn_32546.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wjn_32546/01_2025/7wjn_32546.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wjn_32546/01_2025/7wjn_32546.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wjn_32546/01_2025/7wjn_32546.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wjn_32546/01_2025/7wjn_32546.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wjn_32546/01_2025/7wjn_32546.cif"
  }
  resolution = 3.3
  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
-------------------------------------------------------------------------------
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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       4      5.49       5
     S      74      5.16       5
     C    8458      2.51       5
     N    2170      2.21       5
     O    2346      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 13054
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 808, 6487
          Classifications: {'peptide': 808}
          Link IDs: {'PTRANS': 30, 'TRANS': 777}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 40
          Unusual residues: {' MN': 1, 'UD1': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 14.06, per 1000 atoms: 1.08
  Number of scatterers: 13054
  At special positions: 0
  Unit cell: (118.77, 112.35, 127.33, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      74     16.00
     P       4     15.00
     O    2346      8.00
     N    2170      7.00
     C    8458      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.64
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3040

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 4 sheets defined
      66.8% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 37
    Processing helix  chain 'A' and resid 66 through 74
      removed outlier: 3.835A  pdb=" N   ASP A  70 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 3.764A  pdb=" N   SER A  80 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 110
    Processing helix  chain 'A' and resid 112 through 134
      removed outlier: 4.146A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ARG A 133 " --> pdb=" O   ASN A 129 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN A 134 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 163
    Processing helix  chain 'A' and resid 194 through 199
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 221 through 227
    Processing helix  chain 'A' and resid 242 through 262
      removed outlier: 3.940A  pdb=" N   LEU A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 282
    Processing helix  chain 'A' and resid 297 through 307
    Processing helix  chain 'A' and resid 311 through 319
    Processing helix  chain 'A' and resid 357 through 374
    Processing helix  chain 'A' and resid 390 through 403
      removed outlier: 3.560A  pdb=" N   HIS A 403 " --> pdb=" O   PHE A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 447
      removed outlier: 3.562A  pdb=" N   SER A 427 " --> pdb=" O   ASN A 423 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   PHE A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 479
      removed outlier: 5.156A  pdb=" N   THR A 476 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   LEU A 477 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 3.666A  pdb=" N   LEU A 484 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 493
      removed outlier: 3.695A  pdb=" N   GLY A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 505
    Processing helix  chain 'A' and resid 528 through 554
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 564 through 587
      removed outlier: 3.650A  pdb=" N   PHE A 587 " --> pdb=" O   ALA A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 605
    Processing helix  chain 'A' and resid 621 through 646
      removed outlier: 4.235A  pdb=" N   VAL A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 681
    Processing helix  chain 'A' and resid 684 through 706
      removed outlier: 5.302A  pdb=" N   VAL A 697 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   TYR A 698 " --> pdb=" O   THR A 694 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE A 699 " --> pdb=" O   VAL A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 720
      removed outlier: 5.368A  pdb=" N   THR A 716 " --> pdb=" O   PHE A 712 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   HIS A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 735
    Processing helix  chain 'A' and resid 764 through 819
      removed outlier: 3.581A  pdb=" N   PHE A 818 " --> pdb=" O   PHE A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 853
    Processing helix  chain 'A' and resid 854 through 858
      removed outlier: 3.779A  pdb=" N   GLY A 857 " --> pdb=" O   GLY A 854 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ARG A 858 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 854 through 858'
    Processing helix  chain 'B' and resid 24 through 37
    Processing helix  chain 'B' and resid 66 through 74
      removed outlier: 3.835A  pdb=" N   ASP B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 89
      removed outlier: 3.763A  pdb=" N   SER B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 110
    Processing helix  chain 'B' and resid 112 through 134
      removed outlier: 4.145A  pdb=" N   GLU B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ARG B 133 " --> pdb=" O   ASN B 129 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN B 134 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 163
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 210 through 214
    Processing helix  chain 'B' and resid 221 through 227
    Processing helix  chain 'B' and resid 242 through 262
      removed outlier: 3.941A  pdb=" N   LEU B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 282
    Processing helix  chain 'B' and resid 297 through 307
    Processing helix  chain 'B' and resid 311 through 319
    Processing helix  chain 'B' and resid 357 through 374
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.561A  pdb=" N   HIS B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 447
      removed outlier: 3.561A  pdb=" N   SER B 427 " --> pdb=" O   ASN B 423 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   PHE B 447 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 479
      removed outlier: 5.156A  pdb=" N   THR B 476 " --> pdb=" O   ALA B 472 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   LEU B 477 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 485
      removed outlier: 3.665A  pdb=" N   LEU B 484 " --> pdb=" O   GLU B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 493
      removed outlier: 3.694A  pdb=" N   GLY B 489 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 505
    Processing helix  chain 'B' and resid 528 through 554
    Processing helix  chain 'B' and resid 555 through 560
    Processing helix  chain 'B' and resid 564 through 587
      removed outlier: 3.650A  pdb=" N   PHE B 587 " --> pdb=" O   ALA B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 605
    Processing helix  chain 'B' and resid 621 through 646
      removed outlier: 4.235A  pdb=" N   VAL B 626 " --> pdb=" O   LEU B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 652 through 681
    Processing helix  chain 'B' and resid 684 through 706
      removed outlier: 5.301A  pdb=" N   VAL B 697 " --> pdb=" O   LEU B 693 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   TYR B 698 " --> pdb=" O   THR B 694 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE B 699 " --> pdb=" O   VAL B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 720
      removed outlier: 5.367A  pdb=" N   THR B 716 " --> pdb=" O   PHE B 712 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   HIS B 717 " --> pdb=" O   MET B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 735
    Processing helix  chain 'B' and resid 764 through 819
      removed outlier: 3.580A  pdb=" N   PHE B 818 " --> pdb=" O   PHE B 814 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 824 through 853
    Processing helix  chain 'B' and resid 854 through 858
      removed outlier: 3.779A  pdb=" N   GLY B 857 " --> pdb=" O   GLY B 854 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ARG B 858 " --> pdb=" O   LEU B 855 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 854 through 858'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
      removed outlier: 6.049A  pdb=" N   HIS B 175 " --> pdb=" O   PRO B 205 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   ARG B 200 " --> pdb=" O   THR B 332 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   THR B 332 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   GLN B 346 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LYS B 352 " --> pdb=" O   ALA B 290 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU B 232 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   CYS B 287 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ILE B 234 " --> pdb=" O   CYS B 287 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   VAL B 289 " --> pdb=" O   ILE B 234 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE B 236 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   MET B 233 " --> pdb=" O   ALA B 379 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   MET B 381 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   CYS B 235 " --> pdb=" O   MET B 381 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG B 461 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   GLY B 406 " --> pdb=" O   ARG B 461 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   HIS B 514 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ALA B 408 " --> pdb=" O   HIS B 514 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   VAL B 516 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   GLY B 410 " --> pdb=" O   VAL B 516 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   ASP B 518 " --> pdb=" O   GLY B 410 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   LEU B 412 " --> pdb=" O   ASP B 518 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   VAL B 520 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
      removed outlier: 9.251A  pdb=" N   VAL B 414 " --> pdb=" O   VAL B 520 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ARG B 522 " --> pdb=" O   VAL B 414 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 387
      removed outlier: 7.645A  pdb=" N   HIS A 514 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ALA A 408 " --> pdb=" O   HIS A 514 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   VAL A 516 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   GLY A 410 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   ASP A 518 " --> pdb=" O   GLY A 410 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   LEU A 412 " --> pdb=" O   ASP A 518 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   VAL A 520 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
      removed outlier: 9.251A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 520 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ARG A 522 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   GLY A 406 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG A 461 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   MET A 233 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   MET A 381 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   CYS A 235 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU A 232 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   CYS A 287 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ILE A 234 " --> pdb=" O   CYS A 287 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   VAL A 289 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE A 236 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   GLN A 346 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LYS A 352 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   THR A 332 " --> pdb=" O   ARG A 200 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   ARG A 200 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   HIS A 175 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   VAL A 174 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   SER B  55 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   LYS A 176 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337
    Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337

    855 hydrogen bonds defined for protein.
    2517 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: 4.46

  Time building geometry restraints manager: 4.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4088
        1.34 -     1.46: 2260
        1.46 -     1.57: 6932
        1.57 -     1.69: 6
        1.69 -     1.81: 118
  Bond restraints: 13404
  Sorted by residual:
  bond pdb=" O1' UD1 A1001 "
       pdb=" PB  UD1 A1001 "
    ideal  model  delta    sigma   weight residual
    1.658  1.563  0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" O1' UD1 B1001 "
       pdb=" PB  UD1 B1001 "
    ideal  model  delta    sigma   weight residual
    1.658  1.563  0.095 2.00e-02 2.50e+03 2.25e+01
  bond pdb=" O5B UD1 B1001 "
       pdb=" PA  UD1 B1001 "
    ideal  model  delta    sigma   weight residual
    1.645  1.582  0.063 2.00e-02 2.50e+03 1.00e+01
  bond pdb=" O5B UD1 A1001 "
       pdb=" PA  UD1 A1001 "
    ideal  model  delta    sigma   weight residual
    1.645  1.582  0.063 2.00e-02 2.50e+03 9.81e+00
  bond pdb=" O3A UD1 B1001 "
       pdb=" PA  UD1 B1001 "
    ideal  model  delta    sigma   weight residual
    1.642  1.586  0.056 2.00e-02 2.50e+03 7.89e+00
  ... (remaining 13399 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.84: 18154
        3.84 -     7.69: 46
        7.69 -    11.53: 2
       11.53 -    15.38: 2
       15.38 -    19.22: 2
  Bond angle restraints: 18206
  Sorted by residual:
  angle pdb=" O1' UD1 A1001 "
        pdb=" PB  UD1 A1001 "
        pdb=" O3A UD1 A1001 "
      ideal   model   delta    sigma   weight residual
      92.88  112.10  -19.22 3.00e+00 1.11e-01 4.10e+01
  angle pdb=" O1' UD1 B1001 "
        pdb=" PB  UD1 B1001 "
        pdb=" O3A UD1 B1001 "
      ideal   model   delta    sigma   weight residual
      92.88  112.10  -19.22 3.00e+00 1.11e-01 4.10e+01
  angle pdb=" PA  UD1 B1001 "
        pdb=" O3A UD1 B1001 "
        pdb=" PB  UD1 B1001 "
      ideal   model   delta    sigma   weight residual
     122.84  137.31  -14.47 3.00e+00 1.11e-01 2.33e+01
  angle pdb=" PA  UD1 A1001 "
        pdb=" O3A UD1 A1001 "
        pdb=" PB  UD1 A1001 "
      ideal   model   delta    sigma   weight residual
     122.84  137.29  -14.45 3.00e+00 1.11e-01 2.32e+01
  angle pdb=" C   SER A 615 "
        pdb=" N   GLU A 616 "
        pdb=" CA  GLU A 616 "
      ideal   model   delta    sigma   weight residual
     121.71  116.60    5.11 1.39e+00 5.18e-01 1.35e+01
  ... (remaining 18201 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.93: 7316
       14.93 -    29.86: 467
       29.86 -    44.80: 89
       44.80 -    59.73: 18
       59.73 -    74.66: 6
  Dihedral angle restraints: 7896
    sinusoidal: 3162
      harmonic: 4734
  Sorted by residual:
  dihedral pdb=" CA  GLN A 602 "
           pdb=" C   GLN A 602 "
           pdb=" N   GLY A 603 "
           pdb=" CA  GLY A 603 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  GLN B 602 "
           pdb=" C   GLN B 602 "
           pdb=" N   GLY B 603 "
           pdb=" CA  GLY B 603 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  ASN A 607 "
           pdb=" CB  ASN A 607 "
           pdb=" CG  ASN A 607 "
           pdb=" OD1 ASN A 607 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -153.48   63.48     2      2.00e+01 2.50e-03 9.61e+00
  ... (remaining 7893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1623
       0.047 -    0.095: 314
       0.095 -    0.142: 63
       0.142 -    0.189: 0
       0.189 -    0.237: 2
  Chirality restraints: 2002
  Sorted by residual:
  chirality pdb=" C1B UD1 A1001 "
            pdb=" C2B UD1 A1001 "
            pdb=" N1  UD1 A1001 "
            pdb=" O4B UD1 A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.44   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" C1B UD1 B1001 "
            pdb=" C2B UD1 B1001 "
            pdb=" N1  UD1 B1001 "
            pdb=" O4B UD1 B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.44   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C1' UD1 A1001 "
            pdb=" C2' UD1 A1001 "
            pdb=" O1' UD1 A1001 "
            pdb=" O5' UD1 A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.21   -2.34    0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 1999 not shown)

  Planarity restraints: 2292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 437 "   -0.012 2.00e-02 2.50e+03   2.50e-02 6.23e+00
        pdb=" C   ASN A 437 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ASN A 437 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE A 438 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 437 "    0.012 2.00e-02 2.50e+03   2.48e-02 6.17e+00
        pdb=" C   ASN B 437 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   ASN B 437 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE B 438 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 598 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.09e+00
        pdb=" C   PHE A 598 "    0.039 2.00e-02 2.50e+03
        pdb=" O   PHE A 598 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE A 599 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2289 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2328
        2.77 -     3.30: 12056
        3.30 -     3.83: 21093
        3.83 -     4.37: 22778
        4.37 -     4.90: 42685
  Nonbonded interactions: 100940
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" OE2 GLU B 225 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OD1 ASN A 109 "
            pdb=" NH2 ARG A 171 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OD1 ASN B 109 "
            pdb=" NH2 ARG B 171 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   GLU A 241 "
            pdb=" OG1 THR A 300 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   GLU B 241 "
            pdb=" OG1 THR B 300 "
     model   vdw
     2.303 3.040
  ... (remaining 100935 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: 0.06
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:             1.170
  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:          0.430
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     37.950
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
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   0.095  13404  Z= 0.229
  Angle     :  0.586  19.220  18206  Z= 0.286
  Chirality :  0.039   0.237   2002
  Planarity :  0.004   0.043   2292
  Dihedral  : 10.438  74.658   4856
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.33 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.22), residues: 1604
  helix:  2.65 (0.17), residues: 1006
  sheet: -0.26 (0.41), residues: 166
  loop : -1.19 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 804 
 HIS   0.002   0.001   HIS B 578 
 PHE   0.012   0.001   PHE A 601 
 TYR   0.008   0.001   TYR A 365 
 ARG   0.003   0.000   ARG B 608 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 250
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.6085 (mt)
REVERT: A  327 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8239 (m-70)
REVERT: A  738 GLN cc_start: 0.8155 (pm20) cc_final: 0.7368 (pm20)
REVERT: A  785 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7020 (ttp80)
REVERT: B  183 ASN cc_start: 0.7150 (m-40) cc_final: 0.6804 (p0)
REVERT: B  403 HIS cc_start: 0.6931 (t-90) cc_final: 0.6641 (t-90)
REVERT: B  552 TRP cc_start: 0.7593 (t-100) cc_final: 0.5244 (m-10)
REVERT: B  790 LYS cc_start: 0.8149 (tttt) cc_final: 0.7920 (tttp)
  outliers start: 8
  outliers final: 5
  residues processed: 258
  average time/residue: 0.2657
  time to fit residues: 97.7582
Evaluate side-chains
  157 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 1.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  617 TYR
Chi-restraints excluded: chain B residue  651 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    0.6980
   chunk 121 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 93 optimal weight:    8.9990
   chunk 145 optimal weight:    1.9990
   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 129 ASN
A 478 ASN
A 607 ASN
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 372 GLN
B 607 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.150145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116256 restraints weight = 15611.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.93
r_work: 0.3182 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13404  Z= 0.188
  Angle     :  0.501   7.674  18206  Z= 0.264
  Chirality :  0.038   0.135   2002
  Planarity :  0.004   0.045   2292
  Dihedral  :  6.803  59.305   1898
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  9.37 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.22), residues: 1604
  helix:  2.61 (0.17), residues: 1012
  sheet: -0.39 (0.42), residues: 170
  loop : -0.98 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 804 
 HIS   0.002   0.001   HIS A 578 
 PHE   0.014   0.001   PHE A 601 
 TYR   0.008   0.001   TYR A 732 
 ARG   0.005   0.000   ARG B 199 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 160
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.6249 (OUTLIER) cc_final: 0.5828 (mt)
REVERT: A   71 MET cc_start: 0.0935 (ttm) cc_final: 0.0350 (mtt)
REVERT: A  738 GLN cc_start: 0.8420 (pm20) cc_final: 0.7567 (pm20)
REVERT: A  785 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7057 (ttp80)
REVERT: B   75 MET cc_start: 0.3361 (mpp) cc_final: 0.2869 (tpt)
REVERT: B  183 ASN cc_start: 0.7339 (m-40) cc_final: 0.6991 (p0)
REVERT: B  229 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7538 (mtm-85)
REVERT: B  552 TRP cc_start: 0.7824 (t-100) cc_final: 0.5006 (m-10)
REVERT: B  666 MET cc_start: 0.8423 (ttp) cc_final: 0.8178 (ttm)
REVERT: B  780 ARG cc_start: 0.7449 (mtm110) cc_final: 0.7013 (ptp-110)
REVERT: B  790 LYS cc_start: 0.8271 (tttt) cc_final: 0.8042 (tttp)
  outliers start: 27
  outliers final: 10
  residues processed: 183
  average time/residue: 0.2655
  time to fit residues: 70.8454
Evaluate side-chains
  154 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  294 GLU
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  313 ASP
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  651 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 138 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
B 263 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.112760 restraints weight = 16062.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.99
r_work: 0.3073 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13404  Z= 0.289
  Angle     :  0.550  10.941  18206  Z= 0.290
  Chirality :  0.040   0.137   2002
  Planarity :  0.005   0.052   2292
  Dihedral  :  6.829  65.357   1894
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.30 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 10.66 %
    Favored  : 86.67 %
  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:  1.80 (0.22), residues: 1604
  helix:  2.36 (0.17), residues: 1010
  sheet: -0.42 (0.42), residues: 170
  loop : -1.04 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 804 
 HIS   0.004   0.001   HIS A 578 
 PHE   0.024   0.001   PHE B 397 
 TYR   0.012   0.001   TYR A 365 
 ARG   0.007   0.001   ARG A 199 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 1.462 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.5818 (mt)
REVERT: A  161 ILE cc_start: 0.8421 (tp) cc_final: 0.8104 (tt)
REVERT: A  229 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7666 (mtm-85)
REVERT: A  713 MET cc_start: 0.8489 (mmt) cc_final: 0.7919 (mpp)
REVERT: B   75 MET cc_start: 0.3634 (mpp) cc_final: 0.3379 (tpt)
REVERT: B  183 ASN cc_start: 0.7430 (m-40) cc_final: 0.7123 (p0)
REVERT: B  229 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7551 (mtm-85)
REVERT: B  371 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8497 (mm-30)
  outliers start: 37
  outliers final: 28
  residues processed: 174
  average time/residue: 0.2794
  time to fit residues: 70.6250
Evaluate side-chains
  169 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain A residue  294 GLU
Chi-restraints excluded: chain A residue  403 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  263 GLN
Chi-restraints excluded: chain B residue  313 ASP
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  403 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 119 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 118 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9980
   chunk 132 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 263 GLN
B 263 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.143408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.109922 restraints weight = 15852.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.97
r_work: 0.3039 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  13404  Z= 0.372
  Angle     :  0.582   9.784  18206  Z= 0.308
  Chirality :  0.042   0.139   2002
  Planarity :  0.005   0.054   2292
  Dihedral  :  6.819  63.787   1892
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.80 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 11.31 %
    Favored  : 85.66 %
  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:  1.56 (0.22), residues: 1604
  helix:  2.22 (0.17), residues: 998
  sheet: -0.56 (0.42), residues: 174
  loop : -1.14 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 804 
 HIS   0.004   0.001   HIS A 363 
 PHE   0.018   0.002   PHE B 397 
 TYR   0.014   0.001   TYR A 365 
 ARG   0.006   0.001   ARG B 199 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 1.349 
Fit side-chains
REVERT: A  161 ILE cc_start: 0.8417 (tp) cc_final: 0.8094 (tt)
REVERT: A  229 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7667 (mtm-85)
REVERT: B   75 MET cc_start: 0.3733 (mpp) cc_final: 0.3330 (tpt)
REVERT: B  183 ASN cc_start: 0.7503 (m-40) cc_final: 0.7201 (p0)
REVERT: B  229 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7591 (mtm-85)
REVERT: B  299 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8158 (mptt)
REVERT: B  780 ARG cc_start: 0.7499 (mtm110) cc_final: 0.6966 (ptp-110)
  outliers start: 42
  outliers final: 32
  residues processed: 176
  average time/residue: 0.2762
  time to fit residues: 70.2968
Evaluate side-chains
  173 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  294 GLU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   29 MET
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  313 ASP
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 115 optimal weight:    0.8980
   chunk 138 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 157 optimal weight:    0.8980
   chunk 4 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.0982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.145764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.112125 restraints weight = 15905.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.99
r_work: 0.3059 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13404  Z= 0.250
  Angle     :  0.526   9.927  18206  Z= 0.278
  Chirality :  0.039   0.138   2002
  Planarity :  0.004   0.055   2292
  Dihedral  :  6.635  63.029   1892
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.42 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.68 %
    Favored  : 84.80 %
  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 (0.22), residues: 1604
  helix:  2.32 (0.17), residues: 1000
  sheet: -0.51 (0.42), residues: 174
  loop : -1.11 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 804 
 HIS   0.003   0.001   HIS B 578 
 PHE   0.017   0.001   PHE B 397 
 TYR   0.012   0.001   TYR B 239 
 ARG   0.007   0.000   ARG B 199 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 147
  time to evaluate  : 1.489 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.6169 (OUTLIER) cc_final: 0.5586 (mt)
REVERT: A   71 MET cc_start: 0.1604 (ttm) cc_final: 0.0826 (tpp)
REVERT: A  162 GLU cc_start: 0.6691 (tp30) cc_final: 0.6365 (tm-30)
REVERT: A  229 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7659 (mtm-85)
REVERT: A  238 MET cc_start: 0.9068 (ttp) cc_final: 0.8754 (ptm)
REVERT: A  299 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8205 (mptt)
REVERT: A  721 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8818 (mp)
REVERT: B   75 MET cc_start: 0.3755 (mpp) cc_final: 0.3212 (tpt)
REVERT: B  183 ASN cc_start: 0.7528 (m-40) cc_final: 0.7202 (p0)
REVERT: B  229 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7557 (mtm-85)
REVERT: B  299 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8126 (mptt)
REVERT: B  721 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8846 (mp)
REVERT: B  780 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7202 (mtm110)
  outliers start: 35
  outliers final: 22
  residues processed: 174
  average time/residue: 0.2695
  time to fit residues: 67.6954
Evaluate side-chains
  171 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   29 MET
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 135 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 110 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 106 optimal weight:    0.3980
   chunk 132 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
B 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.143499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.109815 restraints weight = 16192.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.01
r_work: 0.3022 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  13404  Z= 0.340
  Angle     :  0.572  10.339  18206  Z= 0.302
  Chirality :  0.041   0.133   2002
  Planarity :  0.004   0.056   2292
  Dihedral  :  6.666  62.002   1892
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.86 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.68 %
    Favored  : 84.29 %
  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:  1.53 (0.22), residues: 1604
  helix:  2.22 (0.17), residues: 1000
  sheet: -0.63 (0.41), residues: 174
  loop : -1.19 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 804 
 HIS   0.003   0.001   HIS A 363 
 PHE   0.015   0.002   PHE A 601 
 TYR   0.012   0.001   TYR B 239 
 ARG   0.007   0.001   ARG B 199 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 148
  time to evaluate  : 1.364 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.6719 (tp30) cc_final: 0.6415 (tm-30)
REVERT: A  229 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7594 (mtm-85)
REVERT: A  299 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8173 (mptt)
REVERT: A  721 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8797 (mp)
REVERT: A  733 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8213 (m)
REVERT: A  785 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7342 (ttp80)
REVERT: B   75 MET cc_start: 0.3661 (mpp) cc_final: 0.3333 (tpt)
REVERT: B  183 ASN cc_start: 0.7453 (m-40) cc_final: 0.7155 (p0)
REVERT: B  229 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7556 (mtm-85)
REVERT: B  299 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8131 (mptt)
REVERT: B  667 MET cc_start: 0.8074 (tpp) cc_final: 0.7730 (tpt)
REVERT: B  721 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8805 (mp)
REVERT: B  733 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8205 (m)
  outliers start: 42
  outliers final: 31
  residues processed: 179
  average time/residue: 0.2748
  time to fit residues: 71.1250
Evaluate side-chains
  176 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  294 GLU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  733 SER
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   29 MET
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  208 CYS
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  733 SER
Chi-restraints excluded: chain B residue  850 ILE
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 120 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0070
   chunk 89 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 149 optimal weight:    0.7980
   chunk 113 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
B 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.148224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.114910 restraints weight = 15922.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.92
r_work: 0.3106 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13404  Z= 0.173
  Angle     :  0.499   9.250  18206  Z= 0.262
  Chirality :  0.038   0.130   2002
  Planarity :  0.004   0.053   2292
  Dihedral  :  6.460  61.777   1892
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.76 %
    Favored  : 84.01 %
  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:  1.81 (0.22), residues: 1604
  helix:  2.45 (0.17), residues: 1000
  sheet: -0.57 (0.42), residues: 174
  loop : -1.08 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 804 
 HIS   0.002   0.001   HIS A 327 
 PHE   0.017   0.001   PHE B 487 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.008   0.000   ARG B 780 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 1.553 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.5931 (mt)
REVERT: A  162 GLU cc_start: 0.6510 (tp30) cc_final: 0.6241 (tm-30)
REVERT: A  229 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7577 (mtm-85)
REVERT: A  238 MET cc_start: 0.8992 (ttp) cc_final: 0.8687 (ptm)
REVERT: A  299 LYS cc_start: 0.8375 (mmtt) cc_final: 0.8060 (mmtm)
REVERT: A  721 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8787 (mp)
REVERT: A  785 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7444 (ttp80)
REVERT: B   75 MET cc_start: 0.3742 (mpp) cc_final: 0.3179 (tpt)
REVERT: B  183 ASN cc_start: 0.7530 (m-40) cc_final: 0.7245 (p0)
REVERT: B  229 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7588 (mtm-85)
REVERT: B  299 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8133 (mptt)
REVERT: B  721 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8823 (mp)
  outliers start: 31
  outliers final: 23
  residues processed: 169
  average time/residue: 0.2735
  time to fit residues: 66.7971
Evaluate side-chains
  168 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  617 TYR
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   29 MET
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  617 TYR
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  851 HIS
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0570
   chunk 114 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 136 optimal weight:    0.5980
   chunk 115 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 130 optimal weight:    0.5980
   chunk 125 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8300

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

Flipped N/Q/H residues before XYZ refinement:
B 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.114049 restraints weight = 16018.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.00
r_work: 0.3093 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13404  Z= 0.206
  Angle     :  0.513  10.476  18206  Z= 0.270
  Chirality :  0.038   0.130   2002
  Planarity :  0.004   0.053   2292
  Dihedral  :  6.433  61.024   1892
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.98 %
    Favored  : 83.65 %
  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:  1.80 (0.22), residues: 1604
  helix:  2.44 (0.17), residues: 1004
  sheet: -0.65 (0.42), residues: 174
  loop : -1.09 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 202 
 HIS   0.003   0.001   HIS B 327 
 PHE   0.014   0.001   PHE B 545 
 TYR   0.011   0.001   TYR B 239 
 ARG   0.007   0.000   ARG A 199 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 1.452 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.6518 (OUTLIER) cc_final: 0.6056 (mt)
REVERT: A  162 GLU cc_start: 0.6409 (tp30) cc_final: 0.6158 (tm-30)
REVERT: A  229 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7580 (mtm-85)
REVERT: A  299 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8091 (mmtm)
REVERT: A  721 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8792 (mp)
REVERT: A  785 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7431 (ttp80)
REVERT: B   75 MET cc_start: 0.3540 (mpp) cc_final: 0.3174 (tpt)
REVERT: B  183 ASN cc_start: 0.7588 (m-40) cc_final: 0.7285 (p0)
REVERT: B  229 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7603 (mtm-85)
REVERT: B  299 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8146 (mptt)
REVERT: B  667 MET cc_start: 0.7986 (tpp) cc_final: 0.7702 (tpt)
REVERT: B  721 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8826 (mp)
REVERT: B  787 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7711 (tm-30)
  outliers start: 33
  outliers final: 25
  residues processed: 172
  average time/residue: 0.2567
  time to fit residues: 64.2509
Evaluate side-chains
  169 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 1.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  617 TYR
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   29 MET
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  617 TYR
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 153 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 134 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 263 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.145051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112202 restraints weight = 15801.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.93
r_work: 0.3064 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13404  Z= 0.226
  Angle     :  0.522   9.066  18206  Z= 0.274
  Chirality :  0.039   0.131   2002
  Planarity :  0.004   0.053   2292
  Dihedral  :  6.425  60.407   1892
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.27 %
    Favored  : 83.21 %
  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:  1.79 (0.22), residues: 1604
  helix:  2.45 (0.17), residues: 1000
  sheet: -0.68 (0.41), residues: 174
  loop : -1.09 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 804 
 HIS   0.003   0.001   HIS B 578 
 PHE   0.014   0.001   PHE B 601 
 TYR   0.011   0.001   TYR A 239 
 ARG   0.007   0.000   ARG A 199 

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 1.367 
Fit side-chains
REVERT: A   37 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.6061 (mt)
REVERT: A  162 GLU cc_start: 0.6399 (tp30) cc_final: 0.6169 (tm-30)
REVERT: A  229 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7605 (mtm-85)
REVERT: A  299 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8101 (mmtt)
REVERT: A  721 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8799 (mp)
REVERT: A  785 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7462 (ttp80)
REVERT: B   75 MET cc_start: 0.3492 (mpp) cc_final: 0.3189 (tpt)
REVERT: B  183 ASN cc_start: 0.7578 (m-40) cc_final: 0.7287 (p0)
REVERT: B  229 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7631 (mtm-85)
REVERT: B  299 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8138 (mptt)
REVERT: B  667 MET cc_start: 0.8030 (tpp) cc_final: 0.7709 (tpt)
REVERT: B  721 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8841 (mp)
  outliers start: 35
  outliers final: 30
  residues processed: 169
  average time/residue: 0.2712
  time to fit residues: 66.3390
Evaluate side-chains
  173 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 138
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain A residue  229 ARG
Chi-restraints excluded: chain A residue  327 HIS
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  564 THR
Chi-restraints excluded: chain A residue  651 HIS
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  671 SER
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  850 ILE
Chi-restraints excluded: chain A residue  851 HIS
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain B residue   29 MET
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  313 ASP
Chi-restraints excluded: chain B residue  327 HIS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  564 THR
Chi-restraints excluded: chain B residue  617 TYR
Chi-restraints excluded: chain B residue  651 HIS
Chi-restraints excluded: chain B residue  671 SER
Chi-restraints excluded: chain B residue  721 LEU
Chi-restraints excluded: chain B residue  851 HIS
Chi-restraints excluded: chain B residue  852 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 54.4382 > 50:
  distance: 93 - 96:   4.962
  distance: 96 - 97:  15.774
  distance: 97 - 98:  15.853
  distance: 97 - 100:  34.573
  distance: 98 - 99:  25.461
  distance: 98 - 104:  19.112
  distance: 99 - 125:  16.977
  distance: 100 - 101:  12.300
  distance: 101 - 102:   8.393
  distance: 101 - 103:   7.473
  distance: 104 - 105:  10.296
  distance: 105 - 106:  14.194
  distance: 105 - 108:  16.620
  distance: 106 - 107:  18.940
  distance: 106 - 112:   4.412
  distance: 107 - 136:  28.071
  distance: 108 - 109:  17.360
  distance: 108 - 110:  43.021
  distance: 109 - 111:  36.469
  distance: 112 - 113:   5.206
  distance: 112 - 118:  15.349
  distance: 113 - 114:   5.076
  distance: 113 - 116:  16.475
  distance: 114 - 115:  20.085
  distance: 114 - 119:  13.350
  distance: 115 - 143:  27.499
  distance: 116 - 117:   4.454
  distance: 117 - 118:  12.584
  distance: 119 - 120:  10.259
  distance: 120 - 121:  14.043
  distance: 120 - 123:  12.397
  distance: 121 - 122:   4.217
  distance: 121 - 125:   7.966
  distance: 122 - 151:  16.228
  distance: 123 - 124:   8.848
  distance: 125 - 126:  12.920
  distance: 126 - 127:  10.056
  distance: 126 - 129:   9.325
  distance: 127 - 128:  10.921
  distance: 127 - 136:  11.399
  distance: 128 - 159:  12.706
  distance: 129 - 130:   7.687
  distance: 130 - 131:   3.057
  distance: 130 - 132:   4.699
  distance: 132 - 134:   6.761
  distance: 133 - 135:   7.958
  distance: 134 - 135:   8.024
  distance: 137 - 138:   8.696
  distance: 137 - 140:   8.531
  distance: 138 - 139:  12.583
  distance: 138 - 143:   6.739
  distance: 139 - 170:  18.009
  distance: 140 - 141:   5.149
  distance: 140 - 142:  15.851
  distance: 143 - 144:   8.188
  distance: 144 - 145:   5.011
  distance: 145 - 146:   3.404
  distance: 145 - 151:   6.600
  distance: 146 - 177:   9.837
  distance: 148 - 149:   5.561
  distance: 148 - 150:   8.913
  distance: 152 - 153:   6.242
  distance: 153 - 154:   9.823
  distance: 153 - 159:   6.507
  distance: 154 - 185:  15.117
  distance: 155 - 156:   7.067
  distance: 155 - 157:   6.449
  distance: 156 - 158:   3.872
  distance: 159 - 160:   5.156
  distance: 160 - 161:   3.074
  distance: 160 - 163:   7.424
  distance: 161 - 162:   7.141
  distance: 161 - 170:   4.706
  distance: 162 - 190:  16.400
  distance: 163 - 164:   9.037
  distance: 164 - 165:   6.666
  distance: 164 - 166:   4.726
  distance: 165 - 167:  16.172
  distance: 166 - 168:   7.100
  distance: 167 - 169:  12.350
  distance: 168 - 169:  16.010
  distance: 171 - 172:   3.429
  distance: 171 - 174:   7.771
  distance: 172 - 173:   8.158
  distance: 172 - 177:   5.781
  distance: 173 - 195:  13.026
  distance: 174 - 175:   6.018
  distance: 174 - 176:  15.436