Starting phenix.real_space_refine
on Mon Jul 22 04:59:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/07_2024/8x5i_38070_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/07_2024/8x5i_38070.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/07_2024/8x5i_38070.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/07_2024/8x5i_38070.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/07_2024/8x5i_38070_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5i_38070/07_2024/8x5i_38070_neut.cif"
  }
  resolution = 3.01
  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=   0.001 sd=   0.023
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
     P      12      5.49       5
     Mg      4      5.21       5
     S      55      5.16       5
     C   10851      2.51       5
     N    2808      2.21       5
     O    3276      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  315": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  471": "OE1" <-> "OE2"
    Residue "A ASP  472": "OD1" <-> "OD2"
    Residue "B ARG   12": "NH1" <-> "NH2"
    Residue "B PHE   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  216": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  315": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  315": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  285": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  493": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 17006
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 477, 3904
          Classifications: {'peptide': 477}
          Link IDs: {'PTRANS': 8, 'TRANS': 468}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 555, 4537
          Classifications: {'peptide': 555}
          Link IDs: {'PTRANS': 8, 'TRANS': 546}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3888
          Classifications: {'peptide': 474}
          Link IDs: {'PTRANS': 8, 'TRANS': 465}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 4549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4549
          Classifications: {'peptide': 557}
          Link IDs: {'PTRANS': 10, 'TRANS': 546}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 10.36, per 1000 atoms: 0.61
  Number of scatterers: 17006
  At special positions: 0
  Unit cell: (87.36, 112.56, 193.2, 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)
     S      55     16.00
     P      12     15.00
     Mg      4     11.99
     O    3276      8.00
     N    2808      7.00
     C   10851      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 6.12
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3896

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 20 sheets defined
      45.2% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 46
      removed outlier: 3.573A  pdb=" N   LEU A  39 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 52
      removed outlier: 3.529A  pdb=" N   ARG A  51 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 64
      removed outlier: 3.635A  pdb=" N   HIS A  63 " --> pdb=" O   TYR A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 94
      removed outlier: 4.102A  pdb=" N   LYS A  87 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   VAL A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 97
      No H-bonds generated for 'chain 'A' and resid 95 through 97'
    Processing helix  chain 'A' and resid 98 through 102
    Processing helix  chain 'A' and resid 143 through 147
      removed outlier: 3.525A  pdb=" N   ASN A 147 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 277
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.533A  pdb=" N   GLN A 309 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 326
      removed outlier: 3.920A  pdb=" N   TYR A 326 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 370
      removed outlier: 3.674A  pdb=" N   SER A 368 " --> pdb=" O   LYS A 364 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 394
      removed outlier: 3.604A  pdb=" N   LYS A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 423
      removed outlier: 3.643A  pdb=" N   LEU A 423 " --> pdb=" O   THR A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 458
    Processing helix  chain 'A' and resid 475 through 493
      removed outlier: 3.943A  pdb=" N   LYS A 479 " --> pdb=" O   GLY A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 503
      removed outlier: 3.610A  pdb=" N   GLU A 503 " --> pdb=" O   GLU A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 529
      removed outlier: 3.933A  pdb=" N   ASP A 515 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A 519 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   GLU A 522 " --> pdb=" O   SER A 518 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   SER A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 538
      removed outlier: 3.755A  pdb=" N   GLN A 538 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 550
      removed outlier: 3.507A  pdb=" N   MET A 545 " --> pdb=" O   LYS A 541 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   VAL A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 562
    Processing helix  chain 'A' and resid 566 through 574
      removed outlier: 4.186A  pdb=" N   LYS A 570 " --> pdb=" O   PHE A 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 47
      removed outlier: 3.835A  pdb=" N   LEU B  42 " --> pdb=" O   PHE B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 60 through 64
      removed outlier: 3.651A  pdb=" N   HIS B  63 " --> pdb=" O   TYR B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 91
      removed outlier: 4.121A  pdb=" N   LYS B  87 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 97
      removed outlier: 4.287A  pdb=" N   ARG B  97 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 177
      removed outlier: 4.394A  pdb=" N   LEU B 163 " --> pdb=" O   ASP B 159 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLN B 166 " --> pdb=" O   LYS B 162 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LYS B 169 " --> pdb=" O   ALA B 165 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   PHE B 172 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 194
    Processing helix  chain 'B' and resid 202 through 217
      removed outlier: 3.824A  pdb=" N   PHE B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   THR B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 277
      removed outlier: 3.628A  pdb=" N   SER B 268 " --> pdb=" O   MET B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 281
      removed outlier: 3.529A  pdb=" N   LYS B 281 " --> pdb=" O   TYR B 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 278 through 281'
    Processing helix  chain 'B' and resid 295 through 308
    Processing helix  chain 'B' and resid 321 through 326
      removed outlier: 3.699A  pdb=" N   LEU B 324 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   TYR B 326 " --> pdb=" O   GLU B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 357
      No H-bonds generated for 'chain 'B' and resid 355 through 357'
    Processing helix  chain 'B' and resid 358 through 370
      removed outlier: 4.610A  pdb=" N   SER B 368 " --> pdb=" O   LYS B 364 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ALA B 369 " --> pdb=" O   ALA B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 394
      removed outlier: 3.612A  pdb=" N   LYS B 384 " --> pdb=" O   GLY B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 402
      removed outlier: 3.548A  pdb=" N   ASN B 401 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 402 " --> pdb=" O   TYR B 398 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 397 through 402'
    Processing helix  chain 'B' and resid 412 through 423
      removed outlier: 4.027A  pdb=" N   TYR B 416 " --> pdb=" O   TYR B 412 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU B 423 " --> pdb=" O   THR B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 457
      removed outlier: 3.719A  pdb=" N   LEU B 457 " --> pdb=" O   CYS B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 493
      removed outlier: 3.639A  pdb=" N   GLU B 480 " --> pdb=" O   LYS B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 503
    Processing helix  chain 'B' and resid 511 through 529
      removed outlier: 3.884A  pdb=" N   ASP B 515 " --> pdb=" O   ASP B 511 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   GLU B 522 " --> pdb=" O   SER B 518 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   SER B 523 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 538
      removed outlier: 3.599A  pdb=" N   TYR B 536 " --> pdb=" O   ASP B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 550
      removed outlier: 3.518A  pdb=" N   GLU B 547 " --> pdb=" O   PHE B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 562
      removed outlier: 3.595A  pdb=" N   CYS B 557 " --> pdb=" O   SER B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 574
      removed outlier: 4.165A  pdb=" N   LYS B 570 " --> pdb=" O   PHE B 566 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY B 574 " --> pdb=" O   LYS B 570 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 47
      removed outlier: 3.519A  pdb=" N   LEU C  42 " --> pdb=" O   PHE C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 52
    Processing helix  chain 'C' and resid 60 through 64
      removed outlier: 3.684A  pdb=" N   HIS C  63 " --> pdb=" O   TYR C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 94
      removed outlier: 4.305A  pdb=" N   LYS C  87 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   VAL C  92 " --> pdb=" O   LYS C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 262 through 278
      removed outlier: 3.661A  pdb=" N   TYR C 270 " --> pdb=" O   SER C 266 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TYR C 278 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 308
    Processing helix  chain 'C' and resid 321 through 326
      removed outlier: 3.767A  pdb=" N   LEU C 324 " --> pdb=" O   SER C 321 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   TYR C 326 " --> pdb=" O   GLU C 323 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 370
      removed outlier: 4.695A  pdb=" N   SER C 368 " --> pdb=" O   LYS C 364 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA C 369 " --> pdb=" O   ALA C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 394
      removed outlier: 3.695A  pdb=" N   LYS C 384 " --> pdb=" O   GLY C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 413 through 424
      removed outlier: 3.555A  pdb=" N   VAL C 417 " --> pdb=" O   PHE C 413 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 458
      removed outlier: 4.274A  pdb=" N   LEU C 456 " --> pdb=" O   ARG C 452 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LEU C 457 " --> pdb=" O   CYS C 453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 493
      removed outlier: 3.688A  pdb=" N   GLU C 480 " --> pdb=" O   LYS C 476 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 493 through 503
    Processing helix  chain 'C' and resid 511 through 520
      removed outlier: 3.681A  pdb=" N   ASP C 515 " --> pdb=" O   ASP C 511 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 521 through 529
      removed outlier: 3.644A  pdb=" N   LYS C 525 " --> pdb=" O   GLY C 521 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 532 through 538
      removed outlier: 3.802A  pdb=" N   TYR C 536 " --> pdb=" O   ASP C 532 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 540 through 551
      removed outlier: 3.617A  pdb=" N   MET C 545 " --> pdb=" O   LYS C 541 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   VAL C 546 " --> pdb=" O   LEU C 542 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASN C 551 " --> pdb=" O   GLU C 547 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 562
    Processing helix  chain 'C' and resid 563 through 565
      No H-bonds generated for 'chain 'C' and resid 563 through 565'
    Processing helix  chain 'C' and resid 566 through 574
      removed outlier: 4.172A  pdb=" N   LYS C 570 " --> pdb=" O   PHE C 566 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 47
      removed outlier: 3.746A  pdb=" N   LEU D  42 " --> pdb=" O   PHE D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 52
      removed outlier: 3.554A  pdb=" N   ARG D  51 " --> pdb=" O   ASP D  47 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LYS D  52 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 47 through 52'
    Processing helix  chain 'D' and resid 60 through 64
      removed outlier: 3.953A  pdb=" N   ASP D  64 " --> pdb=" O   HIS D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 91
      removed outlier: 4.256A  pdb=" N   LYS D  87 " --> pdb=" O   ASP D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 145 through 147
      No H-bonds generated for 'chain 'D' and resid 145 through 147'
    Processing helix  chain 'D' and resid 159 through 168
    Processing helix  chain 'D' and resid 181 through 192
    Processing helix  chain 'D' and resid 205 through 211
    Processing helix  chain 'D' and resid 260 through 277
      removed outlier: 3.608A  pdb=" N   MET D 264 " --> pdb=" O   GLY D 260 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER D 266 " --> pdb=" O   ARG D 262 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 295 through 308
    Processing helix  chain 'D' and resid 321 through 326
      removed outlier: 3.742A  pdb=" N   LEU D 324 " --> pdb=" O   SER D 321 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TYR D 326 " --> pdb=" O   GLU D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 358 through 370
      removed outlier: 4.637A  pdb=" N   SER D 368 " --> pdb=" O   LYS D 364 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ALA D 369 " --> pdb=" O   ALA D 365 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 380 through 394
      removed outlier: 3.638A  pdb=" N   LYS D 384 " --> pdb=" O   GLY D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 412 through 423
      removed outlier: 3.895A  pdb=" N   TYR D 416 " --> pdb=" O   TYR D 412 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL D 417 " --> pdb=" O   PHE D 413 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU D 423 " --> pdb=" O   THR D 419 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 457
      removed outlier: 3.519A  pdb=" N   LEU D 457 " --> pdb=" O   CYS D 453 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 475 through 493
    Processing helix  chain 'D' and resid 493 through 503
      removed outlier: 3.796A  pdb=" N   GLU D 503 " --> pdb=" O   GLU D 499 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 511 through 529
      removed outlier: 3.989A  pdb=" N   ASP D 515 " --> pdb=" O   ASP D 511 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA D 519 " --> pdb=" O   ASP D 515 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   GLU D 522 " --> pdb=" O   SER D 518 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   SER D 523 " --> pdb=" O   ALA D 519 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU D 529 " --> pdb=" O   LYS D 525 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 532 through 540
      removed outlier: 4.163A  pdb=" N   SER D 540 " --> pdb=" O   TYR D 536 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 542 through 550
      removed outlier: 3.579A  pdb=" N   VAL D 546 " --> pdb=" O   LEU D 542 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 553 through 562
    Processing helix  chain 'D' and resid 566 through 574
      removed outlier: 4.226A  pdb=" N   LYS D 570 " --> pdb=" O   PHE D 566 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY D 574 " --> pdb=" O   LYS D 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20
      removed outlier: 3.746A  pdb=" N   ASN A   5 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   GLU A  70 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LYS A 112 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ASN A 121 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154
      removed outlier: 8.321A  pdb=" N   PHE A 316 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   TYR A 285 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
      removed outlier: 8.088A  pdb=" N   SER A 318 " --> pdb=" O   TYR A 285 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ILE A 287 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ASN A  25 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL A  26 " --> pdb=" O   ILE A 334 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   VAL A 336 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   PHE A  28 " --> pdb=" O   VAL A 336 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407
      removed outlier: 8.429A  pdb=" N   TYR A 506 " --> pdb=" O   HIS A 427 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ILE A 429 " --> pdb=" O   TYR A 506 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437
    Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 20
      removed outlier: 6.622A  pdb=" N   LYS B  16 " --> pdb=" O   LYS B   9 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LYS B   9 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ASN B  18 " --> pdb=" O   THR B   7 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   THR B   7 " --> pdb=" O   ASN B  18 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASN B  20 " --> pdb=" O   ASN B   5 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   ASN B   5 " --> pdb=" O   ASN B  20 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   THR B  74 " --> pdb=" O   SER B   4 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ILE B   6 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ILE B  72 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   ILE B   8 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   GLU B  70 " --> pdb=" O   ILE B   8 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LYS B 112 " --> pdb=" O   ASN B 121 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ASN B 121 " --> pdb=" O   LYS B 112 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154
      removed outlier: 8.256A  pdb=" N   PHE B 316 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   TYR B 285 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   SER B 318 " --> pdb=" O   TYR B 285 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ILE B 287 " --> pdb=" O   SER B 318 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LYS B  24 " --> pdb=" O   ARG B 332 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   ILE B 334 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   VAL B  26 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   VAL B 336 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   PHE B  28 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
      removed outlier: 9.016A  pdb=" N   SER B 338 " --> pdb=" O   PHE B  28 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139
      removed outlier: 3.717A  pdb=" N   ILE B 142 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 229
    Processing sheet with id=AA9, first strand: chain 'B' and resid 403 through 407
      removed outlier: 6.659A  pdb=" N   ARG B 374 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   LEU B 406 " --> pdb=" O   ARG B 374 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU B 376 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS B 430 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   TYR B 506 " --> pdb=" O   HIS B 427 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ILE B 429 " --> pdb=" O   TYR B 506 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 435 through 437
    Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 20
      removed outlier: 6.805A  pdb=" N   THR C  74 " --> pdb=" O   SER C   4 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ILE C   6 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ILE C  72 " --> pdb=" O   ILE C   6 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   ILE C   8 " --> pdb=" O   GLU C  70 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   GLU C  70 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LYS C 112 " --> pdb=" O   ASN C 121 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASN C 121 " --> pdb=" O   LYS C 112 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE C 134 " --> pdb=" O   TRP C 126 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 149 through 154
      removed outlier: 4.466A  pdb=" N   TYR C 314 " --> pdb=" O   VAL C 283 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL C  26 " --> pdb=" O   ILE C 334 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   VAL C 336 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   PHE C  28 " --> pdb=" O   VAL C 336 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 407
      removed outlier: 6.659A  pdb=" N   ARG C 374 " --> pdb=" O   PHE C 404 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   LEU C 406 " --> pdb=" O   ARG C 374 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU C 376 " --> pdb=" O   LEU C 406 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 435 through 437
    Processing sheet with id=AB6, first strand: chain 'D' and resid 14 through 20
      removed outlier: 6.622A  pdb=" N   GLU D  15 " --> pdb=" O   ASN D  10 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   THR D  74 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   ILE D   6 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   ILE D  72 " --> pdb=" O   ILE D   6 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   ILE D   8 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   GLU D  70 " --> pdb=" O   ILE D   8 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 149 through 154
      removed outlier: 8.213A  pdb=" N   PHE D 316 " --> pdb=" O   VAL D 283 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   TYR D 285 " --> pdb=" O   PHE D 316 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   SER D 318 " --> pdb=" O   TYR D 285 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE D 287 " --> pdb=" O   SER D 318 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D 332 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   ILE D 334 " --> pdb=" O   LYS D  24 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   VAL D  26 " --> pdb=" O   ILE D 334 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   VAL D 336 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   PHE D  28 " --> pdb=" O   VAL D 336 " (cutoff:3.500A)
      removed outlier: 8.932A  pdb=" N   SER D 338 " --> pdb=" O   PHE D  28 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 113 through 114
    Processing sheet with id=AB9, first strand: chain 'D' and resid 138 through 139
      removed outlier: 3.832A  pdb=" N   ILE D 142 " --> pdb=" O   ARG D 139 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 403 through 407
      removed outlier: 6.596A  pdb=" N   ARG D 374 " --> pdb=" O   PHE D 404 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   LEU D 406 " --> pdb=" O   ARG D 374 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   LEU D 376 " --> pdb=" O   LEU D 406 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LYS D 430 " --> pdb=" O   LEU D 377 " (cutoff:3.500A)
      removed outlier: 8.457A  pdb=" N   TYR D 506 " --> pdb=" O   HIS D 427 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE D 429 " --> pdb=" O   TYR D 506 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 435 through 437

    700 hydrogen bonds defined for protein.
    1983 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: 5.40

  Time building geometry restraints manager: 6.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4319
        1.33 -     1.45: 3116
        1.45 -     1.57: 9752
        1.57 -     1.69: 17
        1.69 -     1.81: 90
  Bond restraints: 17294
  Sorted by residual:
  bond pdb=" N   VAL A 358 "
       pdb=" CA  VAL A 358 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.25e-02 6.40e+03 1.15e+01
  bond pdb=" N   ILE A 467 "
       pdb=" CA  ILE A 467 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.14e-02 7.69e+03 1.10e+01
  bond pdb=" C   VAL A 358 "
       pdb=" O   VAL A 358 "
    ideal  model  delta    sigma   weight residual
    1.236  1.274 -0.037 1.19e-02 7.06e+03 9.91e+00
  bond pdb=" N   VAL D  93 "
       pdb=" CA  VAL D  93 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.59e+00
  bond pdb=" N   VAL B  93 "
       pdb=" CA  VAL B  93 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.58e+00
  ... (remaining 17289 not shown)

  Histogram of bond angle deviations from ideal:
       97.68 -   106.09: 232
      106.09 -   114.50: 10036
      114.50 -   122.91: 11303
      122.91 -   131.32: 1640
      131.32 -   139.72: 28
  Bond angle restraints: 23239
  Sorted by residual:
  angle pdb=" C   GLU C 471 "
        pdb=" N   ASP C 472 "
        pdb=" CA  ASP C 472 "
      ideal   model   delta    sigma   weight residual
     121.54  134.62  -13.08 1.91e+00 2.74e-01 4.69e+01
  angle pdb=" C   THR C 554 "
        pdb=" N   LYS C 555 "
        pdb=" CA  LYS C 555 "
      ideal   model   delta    sigma   weight residual
     121.54  133.91  -12.37 1.91e+00 2.74e-01 4.19e+01
  angle pdb=" C   PHE A 528 "
        pdb=" N   GLU A 529 "
        pdb=" CA  GLU A 529 "
      ideal   model   delta    sigma   weight residual
     122.08  131.48   -9.40 1.47e+00 4.63e-01 4.09e+01
  angle pdb=" C   ASP C  64 "
        pdb=" N   THR C  65 "
        pdb=" CA  THR C  65 "
      ideal   model   delta    sigma   weight residual
     122.61  132.44   -9.83 1.56e+00 4.11e-01 3.97e+01
  angle pdb=" N   ASP A  32 "
        pdb=" CA  ASP A  32 "
        pdb=" C   ASP A  32 "
      ideal   model   delta    sigma   weight residual
     111.52  119.96   -8.44 1.40e+00 5.10e-01 3.63e+01
  ... (remaining 23234 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 9413
       17.90 -    35.79: 966
       35.79 -    53.69: 202
       53.69 -    71.58: 35
       71.58 -    89.48: 15
  Dihedral angle restraints: 10631
    sinusoidal: 4574
      harmonic: 6057
  Sorted by residual:
  dihedral pdb=" CA  GLN B 198 "
           pdb=" C   GLN B 198 "
           pdb=" N   ILE B 199 "
           pdb=" CA  ILE B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.10   27.90     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" CA  GLU B 201 "
           pdb=" C   GLU B 201 "
           pdb=" N   MET B 202 "
           pdb=" CA  MET B 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.81   27.19     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  LYS C  35 "
           pdb=" C   LYS C  35 "
           pdb=" N   THR C  36 "
           pdb=" CA  THR C  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.58   25.42     0      5.00e+00 4.00e-02 2.58e+01
  ... (remaining 10628 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.114: 2358
       0.114 -    0.228: 177
       0.228 -    0.342: 12
       0.342 -    0.456: 3
       0.456 -    0.570: 1
  Chirality restraints: 2551
  Sorted by residual:
  chirality pdb=" CB  VAL B 549 "
            pdb=" CA  VAL B 549 "
            pdb=" CG1 VAL B 549 "
            pdb=" CG2 VAL B 549 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.06   -0.57 2.00e-01 2.50e+01 8.11e+00
  chirality pdb=" CB  ILE D 199 "
            pdb=" CA  ILE D 199 "
            pdb=" CG1 ILE D 199 "
            pdb=" CG2 ILE D 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.43 2.00e-01 2.50e+01 4.62e+00
  chirality pdb=" CA  ASP A  32 "
            pdb=" N   ASP A  32 "
            pdb=" C   ASP A  32 "
            pdb=" CB  ASP A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.44e+00
  ... (remaining 2548 not shown)

  Planarity restraints: 2940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 358 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   VAL C 358 "    0.061 2.00e-02 2.50e+03
        pdb=" O   VAL C 358 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS C 359 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D  90 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.88e+00
        pdb=" C   ILE D  90 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   ILE D  90 "    0.018 2.00e-02 2.50e+03
        pdb=" N   SER D  91 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  90 "   -0.014 2.00e-02 2.50e+03   2.80e-02 7.86e+00
        pdb=" C   ILE B  90 "    0.048 2.00e-02 2.50e+03
        pdb=" O   ILE B  90 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   SER B  91 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 2937 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 188
        2.67 -     3.23: 13731
        3.23 -     3.79: 24175
        3.79 -     4.34: 36253
        4.34 -     4.90: 58753
  Nonbonded interactions: 133100
  Sorted by model distance:
  nonbonded pdb=" O1G ATP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.113 2.170
  nonbonded pdb=" OG1 THR D  36 "
            pdb="MG    MG D 602 "
     model   vdw
     2.127 2.170
  nonbonded pdb=" OG1 THR B  36 "
            pdb="MG    MG B 602 "
     model   vdw
     2.130 2.170
  nonbonded pdb=" OG1 THR A  36 "
            pdb="MG    MG A 602 "
     model   vdw
     2.160 2.170
  nonbonded pdb=" O2B ATP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.197 2.170
  ... (remaining 133095 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 156 or resid 261 through 578 or resid 601 throug \ 
h 602))
  selection = (chain 'B' and (resid 1 through 156 or resid 261 through 578 or resid 601 throug \ 
h 602))
  selection = chain 'C'
  selection = (chain 'D' and (resid 1 through 156 or resid 261 through 578 or resid 601 throug \ 
h 602))
}

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:             3.390
  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:          0.650
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     47.040
  Find NCS groups from input model:        1.100
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
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      :  0.007   0.062  17294  Z= 0.431
  Angle     :  1.045  13.081  23239  Z= 0.595
  Chirality :  0.064   0.570   2551
  Planarity :  0.006   0.059   2940
  Dihedral  : 15.256  89.476   6735
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.79 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  0.95 %
    Favored  : 98.41 %
  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: -3.57 (0.15), residues: 2047
  helix: -3.88 (0.08), residues: 807
  sheet:  0.41 (0.26), residues: 393
  loop : -2.00 (0.18), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 126 
 HIS   0.012   0.002   HIS C 320 
 PHE   0.038   0.003   PHE C 315 
 TYR   0.021   0.002   TYR B 272 
 ARG   0.007   0.001   ARG C  51 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 322
  time to evaluate  : 2.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 GLU cc_start: 0.8163 (tt0) cc_final: 0.7821 (tp30)
REVERT: A  143 ASN cc_start: 0.8520 (p0) cc_final: 0.8312 (p0)
REVERT: A  480 GLU cc_start: 0.7159 (mp0) cc_final: 0.6626 (tp30)
REVERT: A  481 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7569 (tpp80)
REVERT: A  511 ASP cc_start: 0.7775 (m-30) cc_final: 0.7559 (m-30)
REVERT: B  132 ASN cc_start: 0.8754 (t0) cc_final: 0.8527 (t0)
REVERT: B  197 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7888 (tm-30)
REVERT: B  211 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: B  229 LYS cc_start: 0.8178 (ptpt) cc_final: 0.7944 (ptpt)
REVERT: B  232 MET cc_start: 0.8234 (ppp) cc_final: 0.7987 (ptm)
REVERT: B  422 ASP cc_start: 0.8446 (m-30) cc_final: 0.8093 (m-30)
REVERT: B  476 LYS cc_start: 0.7322 (tttt) cc_final: 0.6949 (mptt)
REVERT: B  492 GLN cc_start: 0.8152 (tt0) cc_final: 0.7929 (tt0)
REVERT: C   62 LYS cc_start: 0.8370 (mttt) cc_final: 0.7661 (mmtt)
REVERT: C   70 GLU cc_start: 0.7994 (tt0) cc_final: 0.7765 (tt0)
REVERT: C   94 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7659 (tppt)
REVERT: C  464 GLU cc_start: 0.7646 (pp20) cc_final: 0.6922 (pp20)
REVERT: C  465 ILE cc_start: 0.8434 (pt) cc_final: 0.7948 (tp)
REVERT: C  477 LYS cc_start: 0.8652 (mmmm) cc_final: 0.7733 (pttm)
REVERT: C  481 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7433 (ttp-170)
REVERT: D   67 LYS cc_start: 0.8110 (mmpt) cc_final: 0.7366 (mtmm)
REVERT: D   87 LYS cc_start: 0.8100 (mttt) cc_final: 0.7615 (mtmt)
REVERT: D  114 ASP cc_start: 0.7668 (t0) cc_final: 0.7377 (t0)
REVERT: D  278 TYR cc_start: 0.8749 (m-80) cc_final: 0.8459 (m-80)
REVERT: D  279 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: D  280 ASP cc_start: 0.7533 (m-30) cc_final: 0.7266 (m-30)
REVERT: D  434 ASP cc_start: 0.8406 (m-30) cc_final: 0.8134 (m-30)
REVERT: D  438 LYS cc_start: 0.8255 (pttm) cc_final: 0.8008 (pttm)
REVERT: D  526 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7505 (ttp-170)
  outliers start: 12
  outliers final: 2
  residues processed: 332
  average time/residue: 0.3404
  time to fit residues: 160.3347
Evaluate side-chains
  219 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 216
  time to evaluate  : 2.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain C residue   94 LYS
Chi-restraints excluded: chain C residue  103 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:    3.9990
   chunk 154 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 159 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 97 optimal weight:    5.9990
   chunk 119 optimal weight:    0.4980
   chunk 185 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 492 GLN
B 186 ASN
B 455 ASN
C  13 ASN
C  56 ASN
C 563 HIS
D 186 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  17294  Z= 0.160
  Angle     :  0.503   8.243  23239  Z= 0.275
  Chirality :  0.042   0.157   2551
  Planarity :  0.003   0.038   2940
  Dihedral  :  8.560  85.970   2378
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.66 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.93 %
    Favored  : 92.06 %
  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: -1.72 (0.16), residues: 2047
  helix: -1.34 (0.15), residues: 826
  sheet:  0.67 (0.26), residues: 384
  loop : -1.71 (0.19), residues: 837

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 126 
 HIS   0.012   0.001   HIS A 535 
 PHE   0.023   0.001   PHE C 315 
 TYR   0.013   0.001   TYR B 272 
 ARG   0.005   0.000   ARG D 139 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 234
  time to evaluate  : 1.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 GLU cc_start: 0.8257 (tt0) cc_final: 0.8012 (tp30)
REVERT: A  530 ASN cc_start: 0.7650 (t0) cc_final: 0.6841 (t0)
REVERT: B  197 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7967 (tm-30)
REVERT: B  211 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7643 (mt-10)
REVERT: B  217 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7724 (mtp85)
REVERT: B  221 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8391 (mppt)
REVERT: B  229 LYS cc_start: 0.8138 (ptpt) cc_final: 0.7924 (ptpt)
REVERT: B  232 MET cc_start: 0.8372 (ppp) cc_final: 0.8054 (ptm)
REVERT: B  446 GLU cc_start: 0.7737 (tt0) cc_final: 0.7459 (tt0)
REVERT: C   50 ILE cc_start: 0.9240 (mm) cc_final: 0.9040 (mm)
REVERT: C   70 GLU cc_start: 0.8036 (tt0) cc_final: 0.7820 (tt0)
REVERT: C   94 LYS cc_start: 0.8389 (ttpp) cc_final: 0.7521 (tppt)
REVERT: C  278 TYR cc_start: 0.7786 (m-80) cc_final: 0.7441 (m-80)
REVERT: C  464 GLU cc_start: 0.7929 (pp20) cc_final: 0.6994 (pp20)
REVERT: C  465 ILE cc_start: 0.8046 (pt) cc_final: 0.7777 (tt)
REVERT: C  480 GLU cc_start: 0.7295 (pm20) cc_final: 0.6900 (pm20)
REVERT: C  481 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7572 (ttp-170)
REVERT: D   30 MET cc_start: 0.8153 (mmt) cc_final: 0.7801 (tpt)
REVERT: D   67 LYS cc_start: 0.8112 (mmpt) cc_final: 0.7306 (mtmm)
REVERT: D   87 LYS cc_start: 0.8004 (mttt) cc_final: 0.7676 (mtmt)
REVERT: D  114 ASP cc_start: 0.7881 (t0) cc_final: 0.7573 (t0)
REVERT: D  279 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7765 (tm-30)
REVERT: D  280 ASP cc_start: 0.7505 (m-30) cc_final: 0.7233 (m-30)
REVERT: D  434 ASP cc_start: 0.8402 (m-30) cc_final: 0.8123 (m-30)
REVERT: D  438 LYS cc_start: 0.8303 (pttm) cc_final: 0.8098 (pttm)
REVERT: D  526 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.7473 (ttp-170)
REVERT: D  564 GLU cc_start: 0.7762 (tp30) cc_final: 0.7520 (tp30)
  outliers start: 19
  outliers final: 14
  residues processed: 247
  average time/residue: 0.3426
  time to fit residues: 121.5070
Evaluate side-chains
  213 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 199
  time to evaluate  : 2.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  495 ASN
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  186 ASN
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  455 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 154 optimal weight:    3.9990
   chunk 126 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 185 optimal weight:    3.9990
   chunk 200 optimal weight:    4.9990
   chunk 165 optimal weight:    1.9990
   chunk 184 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 148 optimal weight:    3.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 535 HIS
B 178 ASN
B 209 GLN
C  56 ASN
C 551 ASN
D 198 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055  17294  Z= 0.496
  Angle     :  0.686   8.216  23239  Z= 0.357
  Chirality :  0.049   0.177   2551
  Planarity :  0.004   0.041   2940
  Dihedral  :  9.093  88.877   2374
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.18 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 10.22 %
    Favored  : 87.72 %
  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: -0.95 (0.18), residues: 2047
  helix: -0.22 (0.17), residues: 818
  sheet:  0.49 (0.26), residues: 388
  loop : -1.53 (0.19), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 126 
 HIS   0.008   0.002   HIS C 320 
 PHE   0.036   0.002   PHE C 315 
 TYR   0.019   0.002   TYR C 412 
 ARG   0.005   0.001   ARG A 139 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 208
  time to evaluate  : 1.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 ASN cc_start: 0.7856 (t0) cc_final: 0.7000 (t0)
REVERT: B  106 TYR cc_start: 0.8875 (m-80) cc_final: 0.8097 (m-80)
REVERT: B  197 GLN cc_start: 0.8629 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: B  211 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7790 (mt-10)
REVERT: B  229 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7876 (ptpt)
REVERT: B  232 MET cc_start: 0.8480 (ppp) cc_final: 0.8042 (ptm)
REVERT: B  446 GLU cc_start: 0.8095 (tt0) cc_final: 0.7838 (tt0)
REVERT: C   70 GLU cc_start: 0.8016 (tt0) cc_final: 0.7805 (tt0)
REVERT: C  278 TYR cc_start: 0.7836 (m-80) cc_final: 0.7501 (m-80)
REVERT: C  439 LYS cc_start: 0.8456 (tttm) cc_final: 0.8224 (tttm)
REVERT: C  464 GLU cc_start: 0.7949 (pp20) cc_final: 0.7083 (pp20)
REVERT: C  477 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8064 (ptmm)
REVERT: C  481 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7556 (ttp-170)
REVERT: C  538 GLN cc_start: 0.8138 (mm110) cc_final: 0.7755 (mm110)
REVERT: D   30 MET cc_start: 0.8356 (mmt) cc_final: 0.7974 (tpt)
REVERT: D   67 LYS cc_start: 0.7992 (mmpt) cc_final: 0.7096 (mtmm)
REVERT: D  198 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5643 (pm20)
REVERT: D  279 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7861 (tm-30)
REVERT: D  392 ASP cc_start: 0.8375 (t0) cc_final: 0.8172 (t0)
REVERT: D  526 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7381 (ttt-90)
  outliers start: 39
  outliers final: 29
  residues processed: 237
  average time/residue: 0.3495
  time to fit residues: 117.8288
Evaluate side-chains
  218 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 188
  time to evaluate  : 2.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  495 ASN
Chi-restraints excluded: chain A residue  501 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  198 GLN
Chi-restraints excluded: chain D residue  341 LYS
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  455 ASN
Chi-restraints excluded: chain D residue  461 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 183 optimal weight:    0.7980
   chunk 139 optimal weight:    6.9990
   chunk 96 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   chunk 88 optimal weight:    6.9990
   chunk 124 optimal weight:    0.9990
   chunk 186 optimal weight:    0.4980
   chunk 197 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 176 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 132 ASN
B 147 ASN
C  13 ASN
C  56 ASN
D 198 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  17294  Z= 0.164
  Angle     :  0.479   6.916  23239  Z= 0.262
  Chirality :  0.043   0.169   2551
  Planarity :  0.003   0.030   2940
  Dihedral  :  8.078  83.656   2374
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.96 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.28 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.18), residues: 2047
  helix:  0.53 (0.18), residues: 816
  sheet:  0.53 (0.26), residues: 392
  loop : -1.32 (0.20), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 126 
 HIS   0.005   0.001   HIS C 415 
 PHE   0.020   0.001   PHE C 315 
 TYR   0.010   0.001   TYR B 272 
 ARG   0.003   0.000   ARG A 481 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 208
  time to evaluate  : 2.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 ASN cc_start: 0.7844 (t0) cc_final: 0.6970 (t0)
REVERT: B  106 TYR cc_start: 0.8843 (m-80) cc_final: 0.8193 (m-80)
REVERT: B  206 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7965 (mmtt)
REVERT: B  211 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7633 (mt-10)
REVERT: B  232 MET cc_start: 0.8450 (ppp) cc_final: 0.7933 (ptm)
REVERT: B  446 GLU cc_start: 0.8012 (tt0) cc_final: 0.7805 (tt0)
REVERT: B  481 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7889 (mmm-85)
REVERT: C   70 GLU cc_start: 0.8002 (tt0) cc_final: 0.7781 (tt0)
REVERT: C  278 TYR cc_start: 0.7838 (m-80) cc_final: 0.7506 (m-80)
REVERT: C  464 GLU cc_start: 0.8066 (pp20) cc_final: 0.7272 (pp20)
REVERT: C  477 LYS cc_start: 0.8547 (mmmm) cc_final: 0.7956 (ptmm)
REVERT: C  481 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7476 (ttp-170)
REVERT: C  499 GLU cc_start: 0.8230 (tp30) cc_final: 0.7981 (tt0)
REVERT: D   30 MET cc_start: 0.8289 (mmt) cc_final: 0.7928 (tpt)
REVERT: D   67 LYS cc_start: 0.8035 (mmpt) cc_final: 0.7085 (mtmm)
REVERT: D  198 GLN cc_start: 0.6344 (OUTLIER) cc_final: 0.5815 (pm20)
REVERT: D  279 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: D  379 GLU cc_start: 0.7738 (tp30) cc_final: 0.7335 (mp0)
REVERT: D  526 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7310 (ttt-90)
REVERT: D  564 GLU cc_start: 0.7726 (tp30) cc_final: 0.7502 (tp30)
  outliers start: 33
  outliers final: 25
  residues processed: 232
  average time/residue: 0.3490
  time to fit residues: 115.4728
Evaluate side-chains
  221 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 1.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  198 GLN
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  461 ASN
Chi-restraints excluded: chain D residue  537 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 164 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 146 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 168 optimal weight:   30.0000
   chunk 136 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 176 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 132 ASN
B 167 ASN
C  56 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  17294  Z= 0.280
  Angle     :  0.536   7.037  23239  Z= 0.286
  Chirality :  0.044   0.160   2551
  Planarity :  0.003   0.031   2940
  Dihedral  :  7.965  85.961   2372
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.79 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 12.49 %
    Favored  : 85.02 %
  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: -0.13 (0.18), residues: 2047
  helix:  0.81 (0.19), residues: 811
  sheet:  0.52 (0.26), residues: 389
  loop : -1.24 (0.20), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 126 
 HIS   0.006   0.001   HIS C 320 
 PHE   0.025   0.001   PHE C 315 
 TYR   0.011   0.001   TYR D 253 
 ARG   0.004   0.000   ARG C 526 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 201
  time to evaluate  : 2.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 ASN cc_start: 0.7894 (t0) cc_final: 0.7025 (t0)
REVERT: B  106 TYR cc_start: 0.8862 (m-80) cc_final: 0.8160 (m-80)
REVERT: B  197 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: B  211 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7730 (mt-10)
REVERT: B  232 MET cc_start: 0.8416 (ppp) cc_final: 0.7907 (ptm)
REVERT: B  379 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7838 (tp30)
REVERT: B  481 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7899 (mmm-85)
REVERT: C  278 TYR cc_start: 0.7856 (m-80) cc_final: 0.7518 (m-80)
REVERT: C  464 GLU cc_start: 0.8060 (pp20) cc_final: 0.7295 (pp20)
REVERT: C  477 LYS cc_start: 0.8551 (mmmm) cc_final: 0.7939 (ptmm)
REVERT: C  481 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7451 (ttp-170)
REVERT: C  485 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7581 (tpt170)
REVERT: C  538 GLN cc_start: 0.8160 (mm110) cc_final: 0.7861 (mm110)
REVERT: D   30 MET cc_start: 0.8358 (mmt) cc_final: 0.7989 (tpt)
REVERT: D   67 LYS cc_start: 0.7973 (mmpt) cc_final: 0.7068 (mtmm)
REVERT: D  379 GLU cc_start: 0.7849 (tp30) cc_final: 0.7420 (mp0)
REVERT: D  434 ASP cc_start: 0.8375 (m-30) cc_final: 0.7915 (m-30)
REVERT: D  526 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7364 (ttt-90)
REVERT: D  564 GLU cc_start: 0.7755 (tp30) cc_final: 0.7493 (tp30)
  outliers start: 47
  outliers final: 36
  residues processed: 236
  average time/residue: 0.3497
  time to fit residues: 118.8151
Evaluate side-chains
  230 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 193
  time to evaluate  : 2.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue  132 ASN
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  495 ASN
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  341 LYS
Chi-restraints excluded: chain D residue  343 VAL
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  461 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 177 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 197 optimal weight:    0.8980
   chunk 163 optimal weight:    2.9990
   chunk 91 optimal weight:    0.3980
   chunk 16 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 544 ASN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  17294  Z= 0.180
  Angle     :  0.490   7.073  23239  Z= 0.264
  Chirality :  0.044   0.458   2551
  Planarity :  0.003   0.033   2940
  Dihedral  :  7.539  81.609   2372
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.10 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.23 %
    Favored  : 84.22 %
  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:  0.09 (0.19), residues: 2047
  helix:  1.02 (0.19), residues: 822
  sheet:  0.55 (0.26), residues: 390
  loop : -1.13 (0.21), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 126 
 HIS   0.004   0.001   HIS C 415 
 PHE   0.020   0.001   PHE C 315 
 TYR   0.011   0.001   TYR D 253 
 ARG   0.006   0.000   ARG A 481 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 207
  time to evaluate  : 2.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 ASN cc_start: 0.7871 (t0) cc_final: 0.7013 (t0)
REVERT: B  106 TYR cc_start: 0.8847 (m-80) cc_final: 0.8190 (m-80)
REVERT: B  197 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8438 (tm-30)
REVERT: B  210 GLN cc_start: 0.8046 (mt0) cc_final: 0.7705 (mp10)
REVERT: B  211 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7615 (mt-10)
REVERT: B  221 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8597 (mppt)
REVERT: B  232 MET cc_start: 0.8390 (ppp) cc_final: 0.7905 (ptm)
REVERT: B  379 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7759 (tp30)
REVERT: C  278 TYR cc_start: 0.7848 (m-80) cc_final: 0.7518 (m-80)
REVERT: C  464 GLU cc_start: 0.8055 (pp20) cc_final: 0.7290 (pp20)
REVERT: C  476 LYS cc_start: 0.7702 (mmmm) cc_final: 0.7255 (mptt)
REVERT: C  481 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7432 (ttp-170)
REVERT: C  538 GLN cc_start: 0.8154 (mm110) cc_final: 0.7874 (mm110)
REVERT: D   30 MET cc_start: 0.8292 (mmt) cc_final: 0.7953 (tpt)
REVERT: D   67 LYS cc_start: 0.8031 (mmpt) cc_final: 0.7061 (mtmm)
REVERT: D   87 LYS cc_start: 0.7995 (mttt) cc_final: 0.7717 (mttp)
REVERT: D  379 GLU cc_start: 0.7844 (tp30) cc_final: 0.7416 (mp0)
REVERT: D  434 ASP cc_start: 0.8368 (m-30) cc_final: 0.7904 (m-30)
REVERT: D  526 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7246 (ttt-90)
REVERT: D  564 GLU cc_start: 0.7727 (tp30) cc_final: 0.7430 (tp30)
  outliers start: 48
  outliers final: 35
  residues processed: 242
  average time/residue: 0.3442
  time to fit residues: 119.1489
Evaluate side-chains
  235 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 1.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  343 VAL
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  461 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 190 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9980
   chunk 144 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 166 optimal weight:    6.9990
   chunk 110 optimal weight:    0.8980
   chunk 196 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0870
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
B 551 ASN
C  56 ASN
** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  17294  Z= 0.175
  Angle     :  0.487   7.185  23239  Z= 0.261
  Chirality :  0.043   0.405   2551
  Planarity :  0.002   0.033   2940
  Dihedral  :  7.325  82.116   2372
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.45 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.76 %
    Favored  : 83.80 %
  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:  0.22 (0.19), residues: 2047
  helix:  1.18 (0.19), residues: 822
  sheet:  0.56 (0.27), residues: 391
  loop : -1.10 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 126 
 HIS   0.004   0.001   HIS C 320 
 PHE   0.019   0.001   PHE C 315 
 TYR   0.009   0.001   TYR A 314 
 ARG   0.005   0.000   ARG A 481 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 202
  time to evaluate  : 2.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  479 LYS cc_start: 0.5828 (mptt) cc_final: 0.5510 (ttpt)
REVERT: A  530 ASN cc_start: 0.7910 (t0) cc_final: 0.7067 (t0)
REVERT: B  106 TYR cc_start: 0.8840 (m-80) cc_final: 0.8193 (m-80)
REVERT: B  129 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7138 (mp0)
REVERT: B  197 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8480 (tm-30)
REVERT: B  211 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7624 (mt-10)
REVERT: B  221 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8576 (mppt)
REVERT: B  232 MET cc_start: 0.8426 (ppp) cc_final: 0.7958 (ptm)
REVERT: B  379 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7771 (tp30)
REVERT: C  278 TYR cc_start: 0.7849 (m-80) cc_final: 0.7522 (m-80)
REVERT: C  464 GLU cc_start: 0.8045 (pp20) cc_final: 0.7318 (pp20)
REVERT: C  476 LYS cc_start: 0.7639 (mmmm) cc_final: 0.7212 (mptt)
REVERT: C  481 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7421 (ttp-170)
REVERT: C  485 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7584 (tpt170)
REVERT: C  491 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7573 (mtpp)
REVERT: C  538 GLN cc_start: 0.8144 (mm110) cc_final: 0.7877 (mm110)
REVERT: D   67 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7058 (mtmm)
REVERT: D   87 LYS cc_start: 0.8002 (mttt) cc_final: 0.7726 (mttp)
REVERT: D  246 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7720 (mtmt)
REVERT: D  379 GLU cc_start: 0.7855 (tp30) cc_final: 0.7419 (mp0)
REVERT: D  434 ASP cc_start: 0.8340 (m-30) cc_final: 0.7883 (m-30)
REVERT: D  526 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7249 (ttt-90)
REVERT: D  564 GLU cc_start: 0.7773 (tp30) cc_final: 0.7468 (tp30)
  outliers start: 46
  outliers final: 40
  residues processed: 237
  average time/residue: 0.3514
  time to fit residues: 118.8725
Evaluate side-chains
  243 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 202
  time to evaluate  : 2.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  495 ASN
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain C residue  495 ASN
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  341 LYS
Chi-restraints excluded: chain D residue  343 VAL
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  461 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 125 optimal weight:    5.9990
   chunk 133 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 154 optimal weight:    3.9990
   chunk 178 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 544 ASN
C  13 ASN
C  56 ASN
D 198 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  17294  Z= 0.311
  Angle     :  0.559   7.401  23239  Z= 0.295
  Chirality :  0.045   0.374   2551
  Planarity :  0.003   0.032   2940
  Dihedral  :  7.665  84.977   2372
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.89 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.24 %
    Favored  : 83.32 %
  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:  0.08 (0.19), residues: 2047
  helix:  1.09 (0.19), residues: 817
  sheet:  0.38 (0.26), residues: 400
  loop : -1.14 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 126 
 HIS   0.006   0.001   HIS C 320 
 PHE   0.025   0.001   PHE C 315 
 TYR   0.010   0.001   TYR A 314 
 ARG   0.005   0.000   ARG A 481 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 201
  time to evaluate  : 2.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  476 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6829 (tptm)
REVERT: A  479 LYS cc_start: 0.5828 (mptt) cc_final: 0.5528 (ttpt)
REVERT: A  530 ASN cc_start: 0.7901 (t0) cc_final: 0.7036 (t0)
REVERT: B  106 TYR cc_start: 0.8876 (m-80) cc_final: 0.8144 (m-80)
REVERT: B  197 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8500 (tm-30)
REVERT: B  211 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8002 (mt-10)
REVERT: B  221 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8572 (mppt)
REVERT: B  232 MET cc_start: 0.8398 (ppp) cc_final: 0.7983 (ptm)
REVERT: B  379 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7835 (tp30)
REVERT: B  446 GLU cc_start: 0.8082 (tt0) cc_final: 0.7871 (pt0)
REVERT: C  278 TYR cc_start: 0.7847 (m-80) cc_final: 0.7498 (m-80)
REVERT: C  464 GLU cc_start: 0.8086 (pp20) cc_final: 0.7361 (pp20)
REVERT: C  476 LYS cc_start: 0.7689 (mmmm) cc_final: 0.7270 (mptt)
REVERT: C  481 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7417 (ttp-170)
REVERT: C  491 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7578 (mtpp)
REVERT: D   67 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7047 (mtmm)
REVERT: D  198 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6483 (pm20)
REVERT: D  379 GLU cc_start: 0.7898 (tp30) cc_final: 0.7441 (mp0)
REVERT: D  434 ASP cc_start: 0.8387 (m-30) cc_final: 0.7929 (m-30)
REVERT: D  526 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7420 (ttt-90)
REVERT: D  564 GLU cc_start: 0.7812 (tp30) cc_final: 0.7502 (tp30)
  outliers start: 46
  outliers final: 40
  residues processed: 236
  average time/residue: 0.3466
  time to fit residues: 116.8254
Evaluate side-chains
  239 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 196
  time to evaluate  : 2.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  495 ASN
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  198 GLN
Chi-restraints excluded: chain D residue  246 LYS
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  341 LYS
Chi-restraints excluded: chain D residue  343 VAL
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  461 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 188 optimal weight:    1.9990
   chunk 171 optimal weight:    0.8980
   chunk 183 optimal weight:    0.8980
   chunk 110 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 143 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 165 optimal weight:    0.6980
   chunk 173 optimal weight:    0.9990
   chunk 182 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 535 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 ASN
C 147 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  17294  Z= 0.193
  Angle     :  0.508   7.423  23239  Z= 0.271
  Chirality :  0.043   0.320   2551
  Planarity :  0.003   0.032   2940
  Dihedral  :  7.407  85.692   2372
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.45 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.61 %
    Favored  : 83.01 %
  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:  0.21 (0.19), residues: 2047
  helix:  1.21 (0.19), residues: 819
  sheet:  0.48 (0.26), residues: 394
  loop : -1.11 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 126 
 HIS   0.004   0.001   HIS D 415 
 PHE   0.020   0.001   PHE C 315 
 TYR   0.024   0.001   TYR D 253 
 ARG   0.007   0.000   ARG B 485 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 201
  time to evaluate  : 2.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  476 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6870 (tptm)
REVERT: A  479 LYS cc_start: 0.5831 (mptt) cc_final: 0.5533 (ttpt)
REVERT: A  530 ASN cc_start: 0.7897 (t0) cc_final: 0.7158 (t0)
REVERT: B  106 TYR cc_start: 0.8867 (m-80) cc_final: 0.8171 (m-80)
REVERT: B  197 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8547 (tm-30)
REVERT: B  211 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7977 (mt-10)
REVERT: B  221 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8581 (mppt)
REVERT: B  232 MET cc_start: 0.8389 (ppp) cc_final: 0.7988 (ptm)
REVERT: B  379 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7771 (tp30)
REVERT: B  446 GLU cc_start: 0.8004 (tt0) cc_final: 0.7792 (pt0)
REVERT: C  278 TYR cc_start: 0.7840 (m-80) cc_final: 0.7493 (m-80)
REVERT: C  464 GLU cc_start: 0.8078 (pp20) cc_final: 0.7369 (pp20)
REVERT: C  476 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7283 (mptt)
REVERT: C  481 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7388 (ttp-170)
REVERT: C  485 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7614 (tpt170)
REVERT: C  491 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7577 (mtpp)
REVERT: D   67 LYS cc_start: 0.8026 (mmpt) cc_final: 0.7043 (mtmm)
REVERT: D   87 LYS cc_start: 0.7983 (mttt) cc_final: 0.7709 (mttp)
REVERT: D  246 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7562 (mtmt)
REVERT: D  379 GLU cc_start: 0.7852 (tp30) cc_final: 0.7403 (mp0)
REVERT: D  434 ASP cc_start: 0.8379 (m-30) cc_final: 0.7913 (m-30)
REVERT: D  526 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7400 (ttt-90)
REVERT: D  564 GLU cc_start: 0.7791 (tp30) cc_final: 0.7482 (tp30)
  outliers start: 45
  outliers final: 41
  residues processed: 235
  average time/residue: 0.3448
  time to fit residues: 115.8909
Evaluate side-chains
  240 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 196
  time to evaluate  : 1.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  246 LYS
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  341 LYS
Chi-restraints excluded: chain D residue  343 VAL
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  461 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 193 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0010
   chunk 134 optimal weight:    4.9990
   chunk 203 optimal weight:    0.9980
   chunk 187 optimal weight:    2.9990
   chunk 161 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 125 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 128 optimal weight:    0.8980
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
C  56 ASN
D 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  17294  Z= 0.209
  Angle     :  0.519   8.239  23239  Z= 0.275
  Chirality :  0.044   0.351   2551
  Planarity :  0.003   0.033   2940
  Dihedral  :  7.304  86.789   2372
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.54 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.61 %
    Favored  : 82.90 %
  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:  0.22 (0.19), residues: 2047
  helix:  1.24 (0.19), residues: 818
  sheet:  0.39 (0.26), residues: 402
  loop : -1.08 (0.21), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 126 
 HIS   0.005   0.001   HIS C 320 
 PHE   0.021   0.001   PHE C 315 
 TYR   0.022   0.001   TYR D 253 
 ARG   0.006   0.000   ARG C 526 

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 193
  time to evaluate  : 2.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 LYS cc_start: 0.7212 (tttm) cc_final: 0.6964 (tttm)
REVERT: A  476 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6868 (tptm)
REVERT: A  479 LYS cc_start: 0.5887 (mptt) cc_final: 0.5569 (ttpt)
REVERT: A  530 ASN cc_start: 0.8017 (t0) cc_final: 0.7164 (t0)
REVERT: B  106 TYR cc_start: 0.8872 (m-80) cc_final: 0.8180 (m-80)
REVERT: B  197 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8561 (tm-30)
REVERT: B  211 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7940 (mt-10)
REVERT: B  221 LYS cc_start: 0.8908 (mtmm) cc_final: 0.8588 (mppt)
REVERT: B  222 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7230 (mp0)
REVERT: B  232 MET cc_start: 0.8392 (ppp) cc_final: 0.7982 (ptm)
REVERT: B  379 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7788 (tp30)
REVERT: B  446 GLU cc_start: 0.7998 (tt0) cc_final: 0.7787 (pt0)
REVERT: C  278 TYR cc_start: 0.7841 (m-80) cc_final: 0.7498 (m-80)
REVERT: C  464 GLU cc_start: 0.8077 (pp20) cc_final: 0.7344 (pp20)
REVERT: C  476 LYS cc_start: 0.7670 (mmmm) cc_final: 0.7318 (mptt)
REVERT: C  481 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7394 (ttp-170)
REVERT: C  485 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7621 (tpt170)
REVERT: C  491 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7570 (mtpp)
REVERT: D   67 LYS cc_start: 0.8032 (mmpt) cc_final: 0.7050 (mtmm)
REVERT: D   87 LYS cc_start: 0.7987 (mttt) cc_final: 0.7717 (mttp)
REVERT: D  246 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7514 (mtmt)
REVERT: D  379 GLU cc_start: 0.7862 (tp30) cc_final: 0.7360 (mp0)
REVERT: D  434 ASP cc_start: 0.8370 (m-30) cc_final: 0.7913 (m-30)
REVERT: D  526 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7279 (ttt-90)
REVERT: D  564 GLU cc_start: 0.7790 (tp30) cc_final: 0.7484 (tp30)
  outliers start: 47
  outliers final: 42
  residues processed: 230
  average time/residue: 0.3372
  time to fit residues: 111.4453
Evaluate side-chains
  232 residues out of total 1889 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 187
  time to evaluate  : 1.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  495 ASN
Chi-restraints excluded: chain A residue  511 ASP
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  211 GLU
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  397 GLU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain C residue   23 ASN
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  320 HIS
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  357 SER
Chi-restraints excluded: chain C residue  358 VAL
Chi-restraints excluded: chain C residue  362 LEU
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  161 ASP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  246 LYS
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  341 LYS
Chi-restraints excluded: chain D residue  343 VAL
Chi-restraints excluded: chain D residue  418 CYS
Chi-restraints excluded: chain D residue  461 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 149 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 162 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 166 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 142 optimal weight:    4.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
C  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.150153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.109831 restraints weight = 21010.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.31
r_work: 0.3054 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  17294  Z= 0.254
  Angle     :  0.544   9.058  23239  Z= 0.287
  Chirality :  0.045   0.371   2551
  Planarity :  0.003   0.033   2940
  Dihedral  :  7.423  88.387   2372
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.59 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.61 %
    Favored  : 82.80 %
  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:  0.14 (0.19), residues: 2047
  helix:  1.17 (0.19), residues: 819
  sheet:  0.36 (0.26), residues: 395
  loop : -1.10 (0.21), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 126 
 HIS   0.006   0.001   HIS D 415 
 PHE   0.023   0.001   PHE C 315 
 TYR   0.021   0.001   TYR D 253 
 ARG   0.006   0.000   ARG C 526 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3944.97 seconds
wall clock time: 71 minutes 11.68 seconds (4271.68 seconds total)