Starting phenix.real_space_refine
on Tue Nov 19 10:39:24 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/11_2024/7t6k_25717.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/11_2024/7t6k_25717.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/11_2024/7t6k_25717.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/11_2024/7t6k_25717.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/11_2024/7t6k_25717.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6k_25717/11_2024/7t6k_25717.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 sd=   0.066
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     140      5.16       5
     C   12548      2.51       5
     N    3284      2.21       5
     O    3440      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 19412
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4853
          Classifications: {'peptide': 606}
          Link IDs: {'PTRANS': 24, 'TRANS': 581}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4853
          Classifications: {'peptide': 606}
          Link IDs: {'PTRANS': 24, 'TRANS': 581}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 4853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4853
          Classifications: {'peptide': 606}
          Link IDs: {'PTRANS': 24, 'TRANS': 581}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 4853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4853
          Classifications: {'peptide': 606}
          Link IDs: {'PTRANS': 24, 'TRANS': 581}
          Chain breaks: 1
  Time building chain proxies: 10.80, per 1000 atoms: 0.56
  Number of scatterers: 19412
  At special positions: 0
  Unit cell: (130.38, 130.38, 120.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     140     16.00
     O    3440      8.00
     N    3284      7.00
     C   12548      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: 4.40
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  4816 Ramachandran restraints generated.
    2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4576

  Finding SS restraints...
    Secondary structure from input PDB file:
      120 helices and 8 sheets defined
      66.0% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 46
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 57 through 66
    Processing helix  chain 'A' and resid 81 through 89
      removed outlier: 3.509A  pdb=" N   TYR A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 102
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.952A  pdb=" N   ALA A 106 " --> pdb=" O   PRO A 103 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS A 107 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 108 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 103 through 108'
    Processing helix  chain 'A' and resid 119 through 127
      removed outlier: 3.752A  pdb=" N   ILE A 123 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 139
    Processing helix  chain 'A' and resid 165 through 174
      removed outlier: 3.563A  pdb=" N   GLY A 174 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 184
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 210 through 222
      removed outlier: 4.497A  pdb=" N   GLN A 214 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   TYR A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASN A 217 " --> pdb=" O   CYS A 213 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 250
    Processing helix  chain 'A' and resid 252 through 260
    Processing helix  chain 'A' and resid 280 through 285
      removed outlier: 4.019A  pdb=" N   SER A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 298
    Processing helix  chain 'A' and resid 302 through 310
      removed outlier: 3.831A  pdb=" N   ARG A 305 " --> pdb=" O   ARG A 302 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A 307 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU A 308 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 324
      removed outlier: 3.826A  pdb=" N   LEU A 316 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 349
    Processing helix  chain 'A' and resid 379 through 410
      removed outlier: 3.688A  pdb=" N   LEU A 402 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
      Proline residue:  A 405  - end of helix
      removed outlier: 3.678A  pdb=" N   VAL A 410 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
      removed outlier: 3.619A  pdb=" N   PHE A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 445
    Processing helix  chain 'A' and resid 450 through 464
    Processing helix  chain 'A' and resid 465 through 472
      removed outlier: 3.641A  pdb=" N   ARG A 470 " --> pdb=" O   TYR A 467 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLY A 471 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 488
    Processing helix  chain 'A' and resid 488 through 512
      removed outlier: 3.961A  pdb=" N   ARG A 492 " --> pdb=" O   GLY A 488 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LEU A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   VAL A 499 " --> pdb=" O   TRP A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 524
      removed outlier: 4.468A  pdb=" N   PHE A 523 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER A 524 " --> pdb=" O   GLY A 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 520 through 524'
    Processing helix  chain 'A' and resid 525 through 538
    Processing helix  chain 'A' and resid 552 through 566
      removed outlier: 3.575A  pdb=" N   CYS A 556 " --> pdb=" O   PRO A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 605
      removed outlier: 4.710A  pdb=" N   GLN A 587 " --> pdb=" O   TRP A 583 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   GLU A 588 " --> pdb=" O   ARG A 584 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ASP A 590 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLU A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ARG A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL A 598 " --> pdb=" O   ARG A 594 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A 599 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 46
    Processing helix  chain 'B' and resid 47 through 56
    Processing helix  chain 'B' and resid 57 through 66
    Processing helix  chain 'B' and resid 81 through 89
      removed outlier: 3.508A  pdb=" N   VAL B  85 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR B  89 " --> pdb=" O   VAL B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 102
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.958A  pdb=" N   ALA B 106 " --> pdb=" O   PRO B 103 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS B 107 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU B 108 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 103 through 108'
    Processing helix  chain 'B' and resid 119 through 127
      removed outlier: 3.742A  pdb=" N   ILE B 123 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 139
    Processing helix  chain 'B' and resid 165 through 174
      removed outlier: 3.545A  pdb=" N   GLY B 174 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 184
    Processing helix  chain 'B' and resid 198 through 205
    Processing helix  chain 'B' and resid 210 through 222
      removed outlier: 4.494A  pdb=" N   GLN B 214 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TYR B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASN B 217 " --> pdb=" O   CYS B 213 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TYR B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 250
    Processing helix  chain 'B' and resid 252 through 260
    Processing helix  chain 'B' and resid 280 through 285
      removed outlier: 4.026A  pdb=" N   SER B 285 " --> pdb=" O   THR B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 298
    Processing helix  chain 'B' and resid 302 through 310
      removed outlier: 3.832A  pdb=" N   ARG B 305 " --> pdb=" O   ARG B 302 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE B 307 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU B 308 " --> pdb=" O   ARG B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 324
      removed outlier: 3.907A  pdb=" N   LEU B 316 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 349
    Processing helix  chain 'B' and resid 379 through 410
      removed outlier: 3.688A  pdb=" N   LEU B 402 " --> pdb=" O   ILE B 398 " (cutoff:3.500A)
      Proline residue:  B 405  - end of helix
      removed outlier: 3.666A  pdb=" N   VAL B 410 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
      removed outlier: 3.611A  pdb=" N   PHE B 416 " --> pdb=" O   ALA B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 445
    Processing helix  chain 'B' and resid 450 through 464
    Processing helix  chain 'B' and resid 465 through 472
      removed outlier: 3.594A  pdb=" N   ARG B 470 " --> pdb=" O   TYR B 467 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLY B 471 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE B 472 " --> pdb=" O   ALA B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 488
    Processing helix  chain 'B' and resid 489 through 512
      removed outlier: 4.125A  pdb=" N   LEU B 496 " --> pdb=" O   ARG B 492 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   VAL B 499 " --> pdb=" O   TRP B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 524
      removed outlier: 4.468A  pdb=" N   PHE B 523 " --> pdb=" O   LEU B 520 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   SER B 524 " --> pdb=" O   GLY B 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 520 through 524'
    Processing helix  chain 'B' and resid 525 through 538
    Processing helix  chain 'B' and resid 552 through 566
      removed outlier: 3.579A  pdb=" N   CYS B 556 " --> pdb=" O   PRO B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 605
      removed outlier: 4.810A  pdb=" N   GLN B 587 " --> pdb=" O   TRP B 583 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   GLU B 588 " --> pdb=" O   ARG B 584 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASP B 590 " --> pdb=" O   ALA B 586 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLU B 591 " --> pdb=" O   GLN B 587 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG B 594 " --> pdb=" O   ASP B 590 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL B 598 " --> pdb=" O   ARG B 594 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA B 599 " --> pdb=" O   ALA B 595 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 46
    Processing helix  chain 'C' and resid 47 through 56
    Processing helix  chain 'C' and resid 57 through 66
    Processing helix  chain 'C' and resid 81 through 89
      removed outlier: 3.507A  pdb=" N   TYR C  89 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 102
    Processing helix  chain 'C' and resid 103 through 108
      removed outlier: 3.950A  pdb=" N   ALA C 106 " --> pdb=" O   PRO C 103 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS C 107 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLU C 108 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 103 through 108'
    Processing helix  chain 'C' and resid 119 through 127
      removed outlier: 3.768A  pdb=" N   ILE C 123 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 139
    Processing helix  chain 'C' and resid 165 through 174
      removed outlier: 3.610A  pdb=" N   GLY C 174 " --> pdb=" O   ALA C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 184
    Processing helix  chain 'C' and resid 198 through 205
    Processing helix  chain 'C' and resid 213 through 220
      removed outlier: 3.502A  pdb=" N   ASN C 217 " --> pdb=" O   CYS C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 250
    Processing helix  chain 'C' and resid 252 through 260
    Processing helix  chain 'C' and resid 280 through 285
      removed outlier: 4.027A  pdb=" N   SER C 285 " --> pdb=" O   THR C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 298
    Processing helix  chain 'C' and resid 302 through 310
      removed outlier: 3.830A  pdb=" N   ARG C 305 " --> pdb=" O   ARG C 302 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE C 307 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU C 308 " --> pdb=" O   ARG C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 324
      removed outlier: 3.909A  pdb=" N   LEU C 316 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 324 through 349
    Processing helix  chain 'C' and resid 379 through 410
      removed outlier: 3.686A  pdb=" N   LEU C 402 " --> pdb=" O   ILE C 398 " (cutoff:3.500A)
      Proline residue:  C 405  - end of helix
      removed outlier: 3.661A  pdb=" N   VAL C 410 " --> pdb=" O   ASP C 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 418
      removed outlier: 3.613A  pdb=" N   PHE C 416 " --> pdb=" O   ALA C 412 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 445
    Processing helix  chain 'C' and resid 450 through 464
    Processing helix  chain 'C' and resid 465 through 472
      removed outlier: 3.563A  pdb=" N   ARG C 470 " --> pdb=" O   TYR C 467 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY C 471 " --> pdb=" O   PHE C 468 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 475 through 488
    Processing helix  chain 'C' and resid 488 through 512
      removed outlier: 3.978A  pdb=" N   ARG C 492 " --> pdb=" O   GLY C 488 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU C 496 " --> pdb=" O   ARG C 492 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   VAL C 499 " --> pdb=" O   TRP C 495 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 520 through 524
      removed outlier: 4.465A  pdb=" N   PHE C 523 " --> pdb=" O   LEU C 520 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER C 524 " --> pdb=" O   GLY C 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 520 through 524'
    Processing helix  chain 'C' and resid 525 through 538
    Processing helix  chain 'C' and resid 552 through 566
      removed outlier: 3.576A  pdb=" N   CYS C 556 " --> pdb=" O   PRO C 552 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 569 through 605
      removed outlier: 4.844A  pdb=" N   GLN C 587 " --> pdb=" O   TRP C 583 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   GLU C 588 " --> pdb=" O   ARG C 584 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASP C 590 " --> pdb=" O   ALA C 586 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   GLU C 591 " --> pdb=" O   GLN C 587 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG C 594 " --> pdb=" O   ASP C 590 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL C 598 " --> pdb=" O   ARG C 594 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA C 599 " --> pdb=" O   ALA C 595 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 46
    Processing helix  chain 'D' and resid 47 through 56
    Processing helix  chain 'D' and resid 57 through 66
    Processing helix  chain 'D' and resid 81 through 89
    Processing helix  chain 'D' and resid 91 through 102
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 3.951A  pdb=" N   ALA D 106 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS D 107 " --> pdb=" O   GLU D 104 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU D 108 " --> pdb=" O   LEU D 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 103 through 108'
    Processing helix  chain 'D' and resid 119 through 127
      removed outlier: 3.767A  pdb=" N   ILE D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 139
    Processing helix  chain 'D' and resid 165 through 174
      removed outlier: 3.616A  pdb=" N   GLY D 174 " --> pdb=" O   ALA D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 184
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 210 through 220
      removed outlier: 4.507A  pdb=" N   GLN D 214 " --> pdb=" O   THR D 210 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   TYR D 216 " --> pdb=" O   ALA D 212 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN D 217 " --> pdb=" O   CYS D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 242 through 250
    Processing helix  chain 'D' and resid 252 through 260
    Processing helix  chain 'D' and resid 280 through 285
      removed outlier: 4.026A  pdb=" N   SER D 285 " --> pdb=" O   THR D 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 291 through 298
    Processing helix  chain 'D' and resid 302 through 310
      removed outlier: 3.834A  pdb=" N   ARG D 305 " --> pdb=" O   ARG D 302 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE D 307 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU D 308 " --> pdb=" O   ARG D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 312 through 324
      removed outlier: 3.911A  pdb=" N   LEU D 316 " --> pdb=" O   PRO D 312 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 349
    Processing helix  chain 'D' and resid 379 through 410
      removed outlier: 3.744A  pdb=" N   LEU D 402 " --> pdb=" O   ILE D 398 " (cutoff:3.500A)
      Proline residue:  D 405  - end of helix
      removed outlier: 3.651A  pdb=" N   VAL D 410 " --> pdb=" O   ASP D 406 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 418
      removed outlier: 3.664A  pdb=" N   PHE D 416 " --> pdb=" O   ALA D 412 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN D 418 " --> pdb=" O   ARG D 414 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 422 through 445
    Processing helix  chain 'D' and resid 450 through 464
    Processing helix  chain 'D' and resid 465 through 472
      removed outlier: 3.601A  pdb=" N   ARG D 470 " --> pdb=" O   TYR D 467 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY D 471 " --> pdb=" O   PHE D 468 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE D 472 " --> pdb=" O   ALA D 469 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 475 through 488
    Processing helix  chain 'D' and resid 489 through 512
      removed outlier: 4.154A  pdb=" N   LEU D 496 " --> pdb=" O   ARG D 492 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL D 499 " --> pdb=" O   TRP D 495 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 520 through 524
      removed outlier: 4.468A  pdb=" N   PHE D 523 " --> pdb=" O   LEU D 520 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   SER D 524 " --> pdb=" O   GLY D 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 520 through 524'
    Processing helix  chain 'D' and resid 525 through 538
    Processing helix  chain 'D' and resid 552 through 566
      removed outlier: 3.578A  pdb=" N   CYS D 556 " --> pdb=" O   PRO D 552 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 569 through 605
      removed outlier: 4.827A  pdb=" N   GLN D 587 " --> pdb=" O   TRP D 583 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   GLU D 588 " --> pdb=" O   ARG D 584 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP D 590 " --> pdb=" O   ALA D 586 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLU D 591 " --> pdb=" O   GLN D 587 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ARG D 594 " --> pdb=" O   ASP D 590 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   VAL D 598 " --> pdb=" O   ARG D 594 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA D 599 " --> pdb=" O   ALA D 595 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 269
      removed outlier: 7.006A  pdb=" N   SER A 275 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   THR A 269 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   LEU A 273 " --> pdb=" O   THR A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354
    Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 269
      removed outlier: 7.005A  pdb=" N   SER B 275 " --> pdb=" O   GLN B 267 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   THR B 269 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   LEU B 273 " --> pdb=" O   THR B 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354
    Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 269
      removed outlier: 7.005A  pdb=" N   SER C 275 " --> pdb=" O   GLN C 267 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR C 269 " --> pdb=" O   LEU C 273 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LEU C 273 " --> pdb=" O   THR C 269 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354
    Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 269
      removed outlier: 7.008A  pdb=" N   SER D 275 " --> pdb=" O   GLN D 267 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   THR D 269 " --> pdb=" O   LEU D 273 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   LEU D 273 " --> pdb=" O   THR D 269 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354

    1047 hydrogen bonds defined for protein.
    3063 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: 6.31

  Time building geometry restraints manager: 5.10 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: 5960
        1.34 -     1.46: 3688
        1.46 -     1.58: 9984
        1.58 -     1.70: 0
        1.70 -     1.82: 228
  Bond restraints: 19860
  Sorted by residual:
  bond pdb=" C   ARG D 326 "
       pdb=" N   PRO D 327 "
    ideal  model  delta    sigma   weight residual
    1.336  1.365 -0.029 1.20e-02 6.94e+03 5.74e+00
  bond pdb=" C   ARG A 326 "
       pdb=" N   PRO A 327 "
    ideal  model  delta    sigma   weight residual
    1.336  1.365 -0.029 1.20e-02 6.94e+03 5.69e+00
  bond pdb=" C   ARG C 326 "
       pdb=" N   PRO C 327 "
    ideal  model  delta    sigma   weight residual
    1.336  1.365 -0.029 1.20e-02 6.94e+03 5.69e+00
  bond pdb=" C   ARG B 326 "
       pdb=" N   PRO B 327 "
    ideal  model  delta    sigma   weight residual
    1.336  1.364 -0.028 1.20e-02 6.94e+03 5.49e+00
  bond pdb=" C   THR C 311 "
       pdb=" N   PRO C 312 "
    ideal  model  delta    sigma   weight residual
    1.334  1.388 -0.054 2.34e-02 1.83e+03 5.38e+00
  ... (remaining 19855 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 25584
        2.06 -     4.12: 1041
        4.12 -     6.18: 241
        6.18 -     8.24: 66
        8.24 -    10.30: 32
  Bond angle restraints: 26964
  Sorted by residual:
  angle pdb=" C   ASP D 223 "
        pdb=" N   GLU D 224 "
        pdb=" CA  GLU D 224 "
      ideal   model   delta    sigma   weight residual
     121.54  131.33   -9.79 1.91e+00 2.74e-01 2.63e+01
  angle pdb=" C   ASP C 223 "
        pdb=" N   GLU C 224 "
        pdb=" CA  GLU C 224 "
      ideal   model   delta    sigma   weight residual
     121.54  131.28   -9.74 1.91e+00 2.74e-01 2.60e+01
  angle pdb=" C   ASP A 223 "
        pdb=" N   GLU A 224 "
        pdb=" CA  GLU A 224 "
      ideal   model   delta    sigma   weight residual
     121.54  131.25   -9.71 1.91e+00 2.74e-01 2.58e+01
  angle pdb=" C   ASP B 223 "
        pdb=" N   GLU B 224 "
        pdb=" CA  GLU B 224 "
      ideal   model   delta    sigma   weight residual
     121.54  131.21   -9.67 1.91e+00 2.74e-01 2.56e+01
  angle pdb=" C   GLU A 605 "
        pdb=" N   ARG A 606 "
        pdb=" CA  ARG A 606 "
      ideal   model   delta    sigma   weight residual
     123.91  131.48   -7.57 1.66e+00 3.63e-01 2.08e+01
  ... (remaining 26959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 10631
       17.85 -    35.69: 953
       35.69 -    53.54: 183
       53.54 -    71.38: 36
       71.38 -    89.23: 9
  Dihedral angle restraints: 11812
    sinusoidal: 4732
      harmonic: 7080
  Sorted by residual:
  dihedral pdb=" CA  MET D 485 "
           pdb=" C   MET D 485 "
           pdb=" N   ILE D 486 "
           pdb=" CA  ILE D 486 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.59   27.41     0      5.00e+00 4.00e-02 3.01e+01
  dihedral pdb=" CA  MET B 485 "
           pdb=" C   MET B 485 "
           pdb=" N   ILE B 486 "
           pdb=" CA  ILE B 486 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.86   27.14     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  MET A 485 "
           pdb=" C   MET A 485 "
           pdb=" N   ILE A 486 "
           pdb=" CA  ILE A 486 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.01   21.99     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 11809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 2894
       0.112 -    0.225: 164
       0.225 -    0.337: 11
       0.337 -    0.450: 0
       0.450 -    0.562: 3
  Chirality restraints: 3072
  Sorted by residual:
  chirality pdb=" CB  VAL B 585 "
            pdb=" CA  VAL B 585 "
            pdb=" CG1 VAL B 585 "
            pdb=" CG2 VAL B 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.89e+00
  chirality pdb=" CB  VAL D 585 "
            pdb=" CA  VAL D 585 "
            pdb=" CG1 VAL D 585 "
            pdb=" CG2 VAL D 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.71e+00
  chirality pdb=" CB  VAL C 585 "
            pdb=" CA  VAL C 585 "
            pdb=" CG1 VAL C 585 "
            pdb=" CG2 VAL C 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.08   -0.55 2.00e-01 2.50e+01 7.67e+00
  ... (remaining 3069 not shown)

  Planarity restraints: 3416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 456 "   -0.026 2.00e-02 2.50e+03   1.98e-02 6.89e+00
        pdb=" CG  PHE C 456 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 456 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 456 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 456 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 456 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 456 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 456 "   -0.026 2.00e-02 2.50e+03   1.96e-02 6.70e+00
        pdb=" CG  PHE B 456 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 456 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 456 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 456 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 456 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 456 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 456 "   -0.026 2.00e-02 2.50e+03   1.95e-02 6.69e+00
        pdb=" CG  PHE D 456 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 456 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 456 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 456 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 456 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 456 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 3413 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 5830
        2.83 -     3.35: 17302
        3.35 -     3.87: 32794
        3.87 -     4.38: 37888
        4.38 -     4.90: 65135
  Nonbonded interactions: 158949
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 525 "
            pdb=" OG1 THR B 528 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD1 ASP C 525 "
            pdb=" OG1 THR C 528 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD1 ASP D 525 "
            pdb=" OG1 THR D 528 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD1 ASP A 525 "
            pdb=" OG1 THR A 528 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   THR A 479 "
            pdb=" NE2 GLN A 483 "
     model   vdw
     2.338 3.120
  ... (remaining 158944 not shown)

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

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:             0.840
  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:             0.020
  Extract box with map and model:          0.720
  Check model and map are aligned:         0.150
  Set scattering table:                    0.180
  Process input model:                     41.990
  Find NCS groups from input model:        0.590
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
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      :  0.005   0.062  19860  Z= 0.329
  Angle     :  1.050  10.300  26964  Z= 0.560
  Chirality :  0.060   0.562   3072
  Planarity :  0.008   0.062   3416
  Dihedral  : 14.248  89.227   7236
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.43 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.04 %
  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: -3.51 (0.13), residues: 2408
  helix: -2.28 (0.10), residues: 1452
  sheet: -1.59 (0.49), residues: 88
  loop : -2.20 (0.17), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 593 
 HIS   0.009   0.001   HIS B 201 
 PHE   0.044   0.003   PHE C 456 
 TYR   0.024   0.002   TYR A 339 
 ARG   0.003   0.000   ARG C 606 

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

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

  4816 Ramachandran restraints generated.
    2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4816 Ramachandran restraints generated.
    2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 356
  time to evaluate  : 2.237 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 357
  average time/residue: 1.3264
  time to fit residues: 536.4410
Evaluate side-chains
  230 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 2.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 202 optimal weight:    0.9990
   chunk 181 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 188 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 114 optimal weight:    0.6980
   chunk 140 optimal weight:    0.6980
   chunk 217 optimal weight:    4.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 230 GLN
A 369 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 GLN
A 636 HIS
B 230 GLN
B 369 GLN
B 636 HIS
C 230 GLN
C 369 GLN
C 636 HIS
D 230 GLN
D 369 GLN
D 636 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  19860  Z= 0.201
  Angle     :  0.609   9.329  26964  Z= 0.308
  Chirality :  0.041   0.164   3072
  Planarity :  0.005   0.040   3416
  Dihedral  :  4.625  21.920   2644
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  9.40 %
    Favored  : 88.45 %
  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: -1.34 (0.16), residues: 2408
  helix: -0.34 (0.13), residues: 1464
  sheet: -1.75 (0.50), residues: 96
  loop : -1.60 (0.19), residues: 848

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 462 
 HIS   0.004   0.001   HIS C 582 
 PHE   0.022   0.001   PHE D 456 
 TYR   0.014   0.001   TYR B 222 
 ARG   0.003   0.000   ARG A 139 

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

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

  4816 Ramachandran restraints generated.
    2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4816 Ramachandran restraints generated.
    2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 258
  time to evaluate  : 2.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  300 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8072 (mtmt)
REVERT: B  486 ILE cc_start: 0.8198 (mm) cc_final: 0.7979 (mm)
REVERT: D  300 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8079 (mtmt)
REVERT: D  486 ILE cc_start: 0.8230 (mm) cc_final: 0.8016 (mm)
  outliers start: 45
  outliers final: 13
  residues processed: 279
  average time/residue: 1.4204
  time to fit residues: 444.9750
Evaluate side-chains
  233 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 218
  time to evaluate  : 2.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain B residue  126 MET
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain C residue  126 MET
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  273 LEU
Chi-restraints excluded: chain D residue  300 LYS
Chi-restraints excluded: chain D residue  427 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 121 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 181 optimal weight:    7.9990
   chunk 148 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 218 optimal weight:    0.6980
   chunk 235 optimal weight:    6.9990
   chunk 194 optimal weight:    3.9990
   chunk 216 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 175 optimal weight:    0.0770
   overall best weight:    2.1544

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 230 GLN
A 374 GLN
B 230 GLN
C 230 GLN
D 230 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2225
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: