Starting phenix.real_space_refine
on Sat Dec  9 08:35:20 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2023/7lh2_23334_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2023/7lh2_23334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2023/7lh2_23334.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2023/7lh2_23334.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2023/7lh2_23334_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2023/7lh2_23334_updated.pdb"
  }
  resolution = 3.43
  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=   0.005 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6930      2.51       5
     N    1690      2.21       5
     O    1860      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   31": "NH1" <-> "NH2"
    Residue "A PHE   76": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU   78": "OE1" <-> "OE2"
    Residue "A ARG  130": "NH1" <-> "NH2"
    Residue "A ARG  171": "NH1" <-> "NH2"
    Residue "A PHE  191": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  207": "OE1" <-> "OE2"
    Residue "A ARG  236": "NH1" <-> "NH2"
    Residue "A PHE  269": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  293": "OE1" <-> "OE2"
    Residue "A TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  391": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  399": "NH1" <-> "NH2"
    Residue "A ARG  463": "NH1" <-> "NH2"
    Residue "A ARG  502": "NH1" <-> "NH2"
    Residue "A TYR  546": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  558": "NH1" <-> "NH2"
    Residue "A TYR  578": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  686": "OD1" <-> "OD2"
    Residue "A ARG  689": "NH1" <-> "NH2"
    Residue "A GLU  694": "OE1" <-> "OE2"
    Residue "B ARG   31": "NH1" <-> "NH2"
    Residue "B PHE   76": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU   78": "OE1" <-> "OE2"
    Residue "B ARG  130": "NH1" <-> "NH2"
    Residue "B ARG  171": "NH1" <-> "NH2"
    Residue "B PHE  191": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  207": "OE1" <-> "OE2"
    Residue "B ARG  236": "NH1" <-> "NH2"
    Residue "B PHE  269": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  293": "OE1" <-> "OE2"
    Residue "B TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  391": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  399": "NH1" <-> "NH2"
    Residue "B ARG  463": "NH1" <-> "NH2"
    Residue "B ARG  502": "NH1" <-> "NH2"
    Residue "B TYR  546": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  558": "NH1" <-> "NH2"
    Residue "B TYR  578": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  686": "OD1" <-> "OD2"
    Residue "B ARG  689": "NH1" <-> "NH2"
    Residue "B GLU  694": "OE1" <-> "OE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 10528
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 680, 5226
          Classifications: {'peptide': 680}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 34, 'TRANS': 645}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "B"
      Number of atoms: 5226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 680, 5226
          Classifications: {'peptide': 680}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 34, 'TRANS': 645}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'CLR': 1, 'SAL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'CLR': 1, 'SAL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.12, per 1000 atoms: 0.58
  Number of scatterers: 10528
  At special positions: 0
  Unit cell: (102.16, 120.379, 113.872, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1860      8.00
     N    1690      7.00
     C    6930      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: 4.15
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2512

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      61.9% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 31
      removed outlier: 3.886A  pdb=" N   ARG A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 50
      removed outlier: 4.170A  pdb=" N   GLN A  48 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   ALA A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   PHE A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 44 through 50'
    Processing helix  chain 'A' and resid 54 through 64
    Processing helix  chain 'A' and resid 66 through 70
      removed outlier: 4.030A  pdb=" N   TRP A  70 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 105
      removed outlier: 5.451A  pdb=" N   LEU A  81 " --> pdb=" O   LYS A  77 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   GLY A  82 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LEU A  93 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 118 through 126
      removed outlier: 3.664A  pdb=" N   PHE A 125 " --> pdb=" O   ILE A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 151
    Processing helix  chain 'A' and resid 169 through 195
    Processing helix  chain 'A' and resid 198 through 204
      removed outlier: 3.549A  pdb=" N   ALA A 202 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE A 203 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 224
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 242 through 256
      removed outlier: 5.029A  pdb=" N   LYS A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ASN A 256 " --> pdb=" O   GLN A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 281
    Processing helix  chain 'A' and resid 292 through 307
    Processing helix  chain 'A' and resid 309 through 312
      No H-bonds generated for 'chain 'A' and resid 309 through 312'
    Processing helix  chain 'A' and resid 336 through 365
      removed outlier: 6.494A  pdb=" N   VAL A 341 " --> pdb=" O   HIS A 337 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   ASP A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 388
    Processing helix  chain 'A' and resid 397 through 405
    Processing helix  chain 'A' and resid 412 through 426
    Processing helix  chain 'A' and resid 437 through 447
    Processing helix  chain 'A' and resid 449 through 464
      removed outlier: 4.380A  pdb=" N   GLN A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   PHE A 455 " --> pdb=" O   MET A 451 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   SER A 456 " --> pdb=" O   PHE A 452 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   ASP A 457 " --> pdb=" O   MET A 453 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LEU A 458 " --> pdb=" O   GLN A 454 " (cutoff:3.500A)
      Proline residue:  A 459  - end of helix
    Processing helix  chain 'A' and resid 466 through 480
    Processing helix  chain 'A' and resid 484 through 504
      removed outlier: 3.866A  pdb=" N   LEU A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE A 489 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL A 499 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 559
    Processing helix  chain 'A' and resid 564 through 578
    Processing helix  chain 'A' and resid 627 through 632
      removed outlier: 4.008A  pdb=" N   PHE A 632 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 669
    Processing helix  chain 'A' and resid 681 through 689
    Processing helix  chain 'A' and resid 696 through 701
      removed outlier: 3.928A  pdb=" N   GLU A 700 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 724
    Processing helix  chain 'B' and resid 25 through 31
      removed outlier: 3.885A  pdb=" N   ARG B  31 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 50
      removed outlier: 4.170A  pdb=" N   GLN B  48 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   ALA B  49 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   PHE B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 44 through 50'
    Processing helix  chain 'B' and resid 54 through 64
    Processing helix  chain 'B' and resid 66 through 70
      removed outlier: 4.030A  pdb=" N   TRP B  70 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 105
      removed outlier: 5.451A  pdb=" N   LEU B  81 " --> pdb=" O   LYS B  77 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   GLY B  82 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LEU B  93 " --> pdb=" O   SER B  89 " (cutoff:3.500A)
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 109 through 114
    Processing helix  chain 'B' and resid 118 through 126
      removed outlier: 3.665A  pdb=" N   PHE B 125 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 151
    Processing helix  chain 'B' and resid 169 through 195
    Processing helix  chain 'B' and resid 198 through 204
      removed outlier: 3.549A  pdb=" N   ALA B 202 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE B 203 " --> pdb=" O   PHE B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 224
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 242 through 256
      removed outlier: 5.029A  pdb=" N   LYS B 255 " --> pdb=" O   LEU B 251 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ASN B 256 " --> pdb=" O   GLN B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 281
    Processing helix  chain 'B' and resid 292 through 307
    Processing helix  chain 'B' and resid 309 through 312
      No H-bonds generated for 'chain 'B' and resid 309 through 312'
    Processing helix  chain 'B' and resid 336 through 365
      removed outlier: 6.493A  pdb=" N   VAL B 341 " --> pdb=" O   HIS B 337 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   ASP B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 388
    Processing helix  chain 'B' and resid 397 through 405
    Processing helix  chain 'B' and resid 412 through 426
    Processing helix  chain 'B' and resid 437 through 447
    Processing helix  chain 'B' and resid 449 through 464
      removed outlier: 4.379A  pdb=" N   GLN B 454 " --> pdb=" O   GLY B 450 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   PHE B 455 " --> pdb=" O   MET B 451 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   SER B 456 " --> pdb=" O   PHE B 452 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   ASP B 457 " --> pdb=" O   MET B 453 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   LEU B 458 " --> pdb=" O   GLN B 454 " (cutoff:3.500A)
      Proline residue:  B 459  - end of helix
    Processing helix  chain 'B' and resid 466 through 480
    Processing helix  chain 'B' and resid 484 through 504
      removed outlier: 3.866A  pdb=" N   LEU B 488 " --> pdb=" O   LEU B 484 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   VAL B 499 " --> pdb=" O   ALA B 495 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ILE B 500 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 559
    Processing helix  chain 'B' and resid 564 through 578
    Processing helix  chain 'B' and resid 627 through 632
      removed outlier: 4.008A  pdb=" N   PHE B 632 " --> pdb=" O   GLU B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 669
    Processing helix  chain 'B' and resid 681 through 689
    Processing helix  chain 'B' and resid 696 through 701
      removed outlier: 3.928A  pdb=" N   GLU B 700 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 724
    Processing sheet with id=  A, first strand: chain 'A' and resid 511 through 513
    Processing sheet with id=  B, first strand: chain 'A' and resid 535 through 539
      removed outlier: 6.746A  pdb=" N   THR A 641 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   PHE A 538 " --> pdb=" O   THR A 641 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ILE A 643 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   TYR A 673 " --> pdb=" O   VAL A 642 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   LEU A 644 " --> pdb=" O   TYR A 673 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   TYR A 675 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  B
    Processing sheet with id=  C, first strand: chain 'B' and resid 511 through 513
    Processing sheet with id=  D, first strand: chain 'B' and resid 535 through 539
      removed outlier: 6.746A  pdb=" N   THR B 641 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   PHE B 538 " --> pdb=" O   THR B 641 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ILE B 643 " --> pdb=" O   PHE B 538 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   TYR B 673 " --> pdb=" O   VAL B 642 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   LEU B 644 " --> pdb=" O   TYR B 673 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   TYR B 675 " --> pdb=" O   LEU B 644 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  D

    542 hydrogen bonds defined for protein.
    1578 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: 2.99

  Time building geometry restraints manager: 4.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3242
        1.34 -     1.46: 2346
        1.46 -     1.58: 5104
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 10770
  Sorted by residual:
  bond pdb=" C1  SAL A 801 "
       pdb=" C2  SAL A 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.484 -0.075 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" C1  SAL B 801 "
       pdb=" C2  SAL B 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.484 -0.075 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" N   VAL B 402 "
       pdb=" CA  VAL B 402 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.49e+00
  bond pdb=" N   SER B 398 "
       pdb=" CA  SER B 398 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.19e-02 7.06e+03 6.66e+00
  bond pdb=" N   GLN B 403 "
       pdb=" CA  GLN B 403 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.83e+00
  ... (remaining 10765 not shown)

  Histogram of bond angle deviations from ideal:
       99.01 -   106.00: 294
      106.00 -   113.00: 5913
      113.00 -   120.00: 3689
      120.00 -   126.99: 4658
      126.99 -   133.99: 100
  Bond angle restraints: 14654
  Sorted by residual:
  angle pdb=" O   VAL B 402 "
        pdb=" C   VAL B 402 "
        pdb=" N   GLN B 403 "
      ideal   model   delta    sigma   weight residual
     121.87  124.67   -2.80 9.70e-01 1.06e+00 8.32e+00
  angle pdb=" CA  LEU A 448 "
        pdb=" CB  LEU A 448 "
        pdb=" CG  LEU A 448 "
      ideal   model   delta    sigma   weight residual
     116.30  125.79   -9.49 3.50e+00 8.16e-02 7.36e+00
  angle pdb=" CA  LEU B 448 "
        pdb=" CB  LEU B 448 "
        pdb=" CG  LEU B 448 "
      ideal   model   delta    sigma   weight residual
     116.30  125.74   -9.44 3.50e+00 8.16e-02 7.27e+00
  angle pdb=" CA  SER B 398 "
        pdb=" C   SER B 398 "
        pdb=" O   SER B 398 "
      ideal   model   delta    sigma   weight residual
     120.82  118.04    2.78 1.05e+00 9.07e-01 7.00e+00
  angle pdb=" CA  ARG B 399 "
        pdb=" C   ARG B 399 "
        pdb=" O   ARG B 399 "
      ideal   model   delta    sigma   weight residual
     120.55  117.84    2.71 1.06e+00 8.90e-01 6.52e+00
  ... (remaining 14649 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 5809
       16.06 -    32.13: 527
       32.13 -    48.19: 100
       48.19 -    64.25: 22
       64.25 -    80.32: 12
  Dihedral angle restraints: 6470
    sinusoidal: 2546
      harmonic: 3924
  Sorted by residual:
  dihedral pdb=" CA  PHE A  23 "
           pdb=" C   PHE A  23 "
           pdb=" N   SER A  24 "
           pdb=" CA  SER A  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.58   19.42     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  PHE B  23 "
           pdb=" C   PHE B  23 "
           pdb=" N   SER B  24 "
           pdb=" CA  SER B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.58   19.42     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  ASP B 686 "
           pdb=" CB  ASP B 686 "
           pdb=" CG  ASP B 686 "
           pdb=" OD1 ASP B 686 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.57   57.57     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 6467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1174
       0.039 -    0.077: 427
       0.077 -    0.116: 123
       0.116 -    0.154: 16
       0.154 -    0.193: 4
  Chirality restraints: 1744
  Sorted by residual:
  chirality pdb=" CG  LEU A 193 "
            pdb=" CB  LEU A 193 "
            pdb=" CD1 LEU A 193 "
            pdb=" CD2 LEU A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.30e-01
  chirality pdb=" CG  LEU B 193 "
            pdb=" CB  LEU B 193 "
            pdb=" CD1 LEU B 193 "
            pdb=" CD2 LEU B 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CA  VAL B 402 "
            pdb=" N   VAL B 402 "
            pdb=" C   VAL B 402 "
            pdb=" CB  VAL B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.28e-01
  ... (remaining 1741 not shown)

  Planarity restraints: 1812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 633 "   -0.035 5.00e-02 4.00e+02   5.34e-02 4.57e+00
        pdb=" N   PRO B 634 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 634 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 634 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 633 "    0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO A 634 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 634 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 634 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 198 "    0.015 2.00e-02 2.50e+03   1.47e-02 3.78e+00
        pdb=" CG  PHE B 198 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 198 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 198 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 198 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 198 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 198 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1809 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 64
        2.60 -     3.18: 9520
        3.18 -     3.75: 16221
        3.75 -     4.33: 21775
        4.33 -     4.90: 36224
  Nonbonded interactions: 83804
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 398 "
            pdb=" O2' SAL A 801 "
     model   vdw
     2.030 2.440
  nonbonded pdb=" OG  SER B  86 "
            pdb=" O   GLN B 403 "
     model   vdw
     2.164 2.440
  nonbonded pdb=" OD2 ASP A  83 "
            pdb=" OG1 THR A 410 "
     model   vdw
     2.223 2.440
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B 410 "
     model   vdw
     2.224 2.440
  nonbonded pdb=" OG1 THR B 503 "
            pdb=" OH  TYR B 545 "
     model   vdw
     2.226 2.440
  ... (remaining 83799 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'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          4.200
  Check model and map are aligned:         0.170
  Set scattering table:                    0.110
  Process input model:                     31.750
  Find NCS groups from input model:        0.610
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
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      :  0.003   0.075  10770  Z= 0.202
  Angle     :  0.558   9.493  14654  Z= 0.304
  Chirality :  0.043   0.193   1744
  Planarity :  0.004   0.053   1812
  Dihedral  : 13.017  80.315   3958
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.53 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.24), residues: 1352
  helix:  1.34 (0.18), residues: 894
  sheet:  1.90 (0.69), residues: 52
  loop : -1.07 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP B 472 
   HIS   0.002   0.001   HIS A  25 
   PHE   0.034   0.001   PHE B 198 
   TYR   0.014   0.001   TYR B 237 
   ARG   0.008   0.001   ARG B 572 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 1.276 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 146
  average time/residue: 0.1912
  time to fit residues: 42.3831
Evaluate side-chains
  104 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 1.233 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1207
  time to fit residues: 2.0408
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 103 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0370
   chunk 55 optimal weight:    7.9990
   chunk 106 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    2.6064

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

Flipped N/Q/H residues before XYZ refinement:
** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10770  Z= 0.192
  Angle     :  0.518  10.935  14654  Z= 0.251
  Chirality :  0.042   0.128   1744
  Planarity :  0.004   0.050   1812
  Dihedral  :  4.456  45.129   1588
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  7.23 %
    Favored  : 91.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1352
  helix:  1.45 (0.18), residues: 902
  sheet:  1.89 (0.68), residues: 52
  loop : -1.09 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 472 
   HIS   0.007   0.001   HIS A 704 
   PHE   0.022   0.001   PHE A 198 
   TYR   0.012   0.001   TYR A 237 
   ARG   0.004   0.000   ARG B 576 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 1.208 
Fit side-chains
  outliers start: 19
  outliers final: 17
  residues processed: 131
  average time/residue: 0.1962
  time to fit residues: 38.7240
Evaluate side-chains
  122 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 1.170 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1058
  time to fit residues: 5.1114
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 84 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 123 optimal weight:    5.9990
   chunk 133 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0370
   chunk 122 optimal weight:    0.0980
   chunk 42 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   overall best weight:    0.8062

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

Flipped N/Q/H residues before XYZ refinement:
B 504 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10770  Z= 0.119
  Angle     :  0.483   9.618  14654  Z= 0.231
  Chirality :  0.041   0.127   1744
  Planarity :  0.004   0.051   1812
  Dihedral  :  4.193  39.425   1588
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.29 %
    Favored  : 90.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.24), residues: 1352
  helix:  1.65 (0.18), residues: 890
  sheet:  2.15 (0.70), residues: 52
  loop : -0.85 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 472 
   HIS   0.003   0.001   HIS A 704 
   PHE   0.018   0.001   PHE B 198 
   TYR   0.010   0.001   TYR A 237 
   ARG   0.006   0.000   ARG B 572 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 7
  residues processed: 132
  average time/residue: 0.2080
  time to fit residues: 41.7095
Evaluate side-chains
  114 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 1.309 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1096
  time to fit residues: 2.9724
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    0.0970
   chunk 93 optimal weight:   10.0000
   chunk 64 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 124 optimal weight:   40.0000
   chunk 131 optimal weight:   10.0000
   chunk 117 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 109 optimal weight:    0.8980
   overall best weight:    3.3984

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10770  Z= 0.228
  Angle     :  0.531   8.761  14654  Z= 0.256
  Chirality :  0.042   0.129   1744
  Planarity :  0.004   0.054   1812
  Dihedral  :  4.062  34.842   1588
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.55 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.24), residues: 1352
  helix:  1.60 (0.18), residues: 900
  sheet:  1.94 (0.68), residues: 52
  loop : -0.90 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 472 
   HIS   0.004   0.001   HIS A 704 
   PHE   0.020   0.001   PHE B 198 
   TYR   0.011   0.001   TYR A 545 
   ARG   0.006   0.000   ARG B 572 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1987
  time to fit residues: 35.9356
Evaluate side-chains
  112 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.287 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1027
  time to fit residues: 3.7940
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 54 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0770
   chunk 90 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 117 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.8144

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 GLN
B 539 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10770  Z= 0.197
  Angle     :  0.502   8.654  14654  Z= 0.245
  Chirality :  0.041   0.124   1744
  Planarity :  0.004   0.056   1812
  Dihedral  :  3.930  31.532   1588
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 12.79 %
    Favored  : 86.33 %
  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:  1.37 (0.24), residues: 1352
  helix:  1.65 (0.18), residues: 894
  sheet:  2.07 (0.70), residues: 52
  loop : -0.91 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP B  70 
   HIS   0.003   0.001   HIS A 704 
   PHE   0.024   0.001   PHE B 198 
   TYR   0.012   0.001   TYR B 578 
   ARG   0.006   0.000   ARG B 572 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 4
  residues processed: 123
  average time/residue: 0.2004
  time to fit residues: 36.9803
Evaluate side-chains
  108 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 1.254 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1029
  time to fit residues: 2.4316
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 77 optimal weight:    0.4980
   chunk 32 optimal weight:    8.9990
   chunk 131 optimal weight:    9.9990
   chunk 109 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   chunk 126 optimal weight:   50.0000
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10770  Z= 0.214
  Angle     :  0.520   8.320  14654  Z= 0.251
  Chirality :  0.042   0.131   1744
  Planarity :  0.004   0.056   1812
  Dihedral  :  4.011  41.905   1588
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.14 %
    Favored  : 85.36 %
  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:  1.37 (0.24), residues: 1352
  helix:  1.64 (0.18), residues: 894
  sheet:  2.02 (0.70), residues: 52
  loop : -0.89 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP B  70 
   HIS   0.003   0.001   HIS A 704 
   PHE   0.024   0.001   PHE B 198 
   TYR   0.014   0.001   TYR B 578 
   ARG   0.009   0.000   ARG B 572 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1949
  time to fit residues: 35.3336
Evaluate side-chains
  119 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 1.232 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0987
  time to fit residues: 4.5857
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   chunk 110 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 131 optimal weight:    7.9990
   chunk 82 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10770  Z= 0.220
  Angle     :  0.527   9.383  14654  Z= 0.256
  Chirality :  0.042   0.138   1744
  Planarity :  0.004   0.056   1812
  Dihedral  :  4.078  46.180   1588
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 14.29 %
    Favored  : 85.19 %
  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:  1.42 (0.24), residues: 1352
  helix:  1.67 (0.18), residues: 890
  sheet:  2.00 (0.70), residues: 52
  loop : -0.82 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP B  70 
   HIS   0.003   0.001   HIS B 704 
   PHE   0.014   0.001   PHE B 198 
   TYR   0.022   0.001   TYR A 578 
   ARG   0.008   0.000   ARG B 572 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 109
  average time/residue: 0.2055
  time to fit residues: 33.9847
Evaluate side-chains
  104 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 1.257 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0995
  time to fit residues: 2.0674
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 83 optimal weight:   30.0000
   chunk 89 optimal weight:   10.0000
   chunk 64 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 119 optimal weight:   10.0000
   chunk 125 optimal weight:    7.9990
   chunk 114 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  10770  Z= 0.403
  Angle     :  0.636   8.990  14654  Z= 0.315
  Chirality :  0.045   0.162   1744
  Planarity :  0.005   0.055   1812
  Dihedral  :  4.500  53.827   1588
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 15.78 %
    Favored  : 83.86 %
  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:  0.90 (0.24), residues: 1352
  helix:  1.27 (0.18), residues: 906
  sheet:  2.01 (0.79), residues: 38
  loop : -1.04 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP B 699 
   HIS   0.004   0.001   HIS A 704 
   PHE   0.016   0.002   PHE A 111 
   TYR   0.021   0.002   TYR A 578 
   ARG   0.008   0.001   ARG B 576 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 1.323 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 109
  average time/residue: 0.2184
  time to fit residues: 35.9339
Evaluate side-chains
  101 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 1.294 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1047
  time to fit residues: 2.3596
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 125 optimal weight:    0.0770
   chunk 73 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 115 optimal weight:    9.9990
   chunk 121 optimal weight:    0.9980
   chunk 80 optimal weight:    0.1980
   chunk 129 optimal weight:    7.9990
   overall best weight:    0.6340

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10770  Z= 0.134
  Angle     :  0.530   8.950  14654  Z= 0.254
  Chirality :  0.041   0.128   1744
  Planarity :  0.004   0.054   1812
  Dihedral  :  4.274  56.270   1588
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 16.14 %
    Favored  : 83.33 %
  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:  1.43 (0.24), residues: 1352
  helix:  1.69 (0.18), residues: 878
  sheet:  1.87 (0.72), residues: 52
  loop : -0.74 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 472 
   HIS   0.002   0.001   HIS B 704 
   PHE   0.013   0.001   PHE A 269 
   TYR   0.015   0.001   TYR A 578 
   ARG   0.007   0.001   ARG A 576 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 1.334 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 124
  average time/residue: 0.2028
  time to fit residues: 38.8693
Evaluate side-chains
  108 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 1.314 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1023
  time to fit residues: 2.4832
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 61 optimal weight:    8.9990
   chunk 89 optimal weight:    7.9990
   chunk 135 optimal weight:    3.9990
   chunk 124 optimal weight:    6.9990
   chunk 107 optimal weight:   20.0000
   chunk 11 optimal weight:    8.9990
   chunk 83 optimal weight:   20.0000
   chunk 66 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 114 optimal weight:    9.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  10770  Z= 0.366
  Angle     :  0.635   9.235  14654  Z= 0.312
  Chirality :  0.045   0.141   1744
  Planarity :  0.004   0.055   1812
  Dihedral  :  4.496  57.293   1588
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 16.67 %
    Favored  : 83.16 %
  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 (0.24), residues: 1352
  helix:  1.30 (0.18), residues: 910
  sheet:  1.86 (0.78), residues: 38
  loop : -0.97 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP B 699 
   HIS   0.003   0.001   HIS A 704 
   PHE   0.015   0.002   PHE B 111 
   TYR   0.016   0.002   TYR A 578 
   ARG   0.012   0.001   ARG A 576 

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

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

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2704 Ramachandran restraints generated.
    1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 1.284 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 106
  average time/residue: 0.2034
  time to fit residues: 33.3071
Evaluate side-chains
  103 residues out of total 1154 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 1.288 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0978
  time to fit residues: 2.0670
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 108 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.137368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.111749 restraints weight = 16635.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.08
r_work: 0.3381 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10770  Z= 0.271
  Angle     :  0.586   9.605  14654  Z= 0.285
  Chirality :  0.043   0.128   1744
  Planarity :  0.004   0.055   1812
  Dihedral  :  4.524  59.916   1588
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 17.28 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.24), residues: 1352
  helix:  1.42 (0.18), residues: 898
  sheet:  1.83 (0.79), residues: 38
  loop : -0.91 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 472 
   HIS   0.003   0.001   HIS A 704 
   PHE   0.012   0.001   PHE A 391 
   TYR   0.015   0.001   TYR A 578 
   ARG   0.014   0.001   ARG A 576 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2251.24 seconds
wall clock time: 41 minutes 50.87 seconds (2510.87 seconds total)