Starting phenix.real_space_refine
on Thu Jul 31 07:15:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pyh_20524/07_2025/6pyh_20524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pyh_20524/07_2025/6pyh_20524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pyh_20524/07_2025/6pyh_20524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pyh_20524/07_2025/6pyh_20524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pyh_20524/07_2025/6pyh_20524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pyh_20524/07_2025/6pyh_20524.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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     102      5.16       5
     C    8342      2.51       5
     N    2285      2.21       5
     O    2458      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 71 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13187
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 793, 6360
          Classifications: {'peptide': 793}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 46, 'TRANS': 744}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 416
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 2, 'TRANS': 54}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 6411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 798, 6411
          Classifications: {'peptide': 798}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 754}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 7.80, per 1000 atoms: 0.59
  Number of scatterers: 13187
  At special positions: 0
  Unit cell: (120.91, 113.42, 171.2, 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     102     16.00
     O    2458      8.00
     N    2285      7.00
     C    8342      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=32, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   3 " - pdb=" SG  CYS A  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 120 " - pdb=" SG  CYS A 148 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 152 " - pdb=" SG  CYS A 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 185 " - pdb=" SG  CYS A 194 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 201 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 205 " - pdb=" SG  CYS A 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 221 " - pdb=" SG  CYS A 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 252 " - pdb=" SG  CYS A 273 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 277 " - pdb=" SG  CYS A 291 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 302 " - pdb=" SG  CYS A 324 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 426 " - pdb=" SG  CYS A 459 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 671 " - pdb=" SG  CYS D 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 777 " - pdb=" SG  CYS A 786 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   6 " - pdb=" SG  CYS B  48 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  18 " - pdb=" SG  CYS B  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  47 " - pdb=" SG  CYS B  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   3 " - pdb=" SG  CYS D  22 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 120 " - pdb=" SG  CYS D 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 152 " - pdb=" SG  CYS D 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 162 " - pdb=" SG  CYS D 181 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 185 " - pdb=" SG  CYS D 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 189 " - pdb=" SG  CYS D 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 201 " - pdb=" SG  CYS D 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 205 " - pdb=" SG  CYS D 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 221 " - pdb=" SG  CYS D 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 234 " - pdb=" SG  CYS D 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 252 " - pdb=" SG  CYS D 273 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 302 " - pdb=" SG  CYS D 324 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 777 " - pdb=" SG  CYS D 786 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.36
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3204 Ramachandran restraints generated.
    1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3098

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 30 sheets defined
      13.3% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 20
    Processing helix  chain 'A' and resid 133 through 137
    Processing helix  chain 'A' and resid 248 through 254
      removed outlier: 4.594A  pdb=" N   CYS A 252 " --> pdb=" O   ASP A 248 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA A 253 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 322
      removed outlier: 3.767A  pdb=" N   ALA A 318 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   MET A 320 " --> pdb=" O   SER A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 350
      removed outlier: 4.526A  pdb=" N   GLU A 344 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 373
      removed outlier: 4.489A  pdb=" N   PHE A 372 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 438
      removed outlier: 3.854A  pdb=" N   ILE A 430 " --> pdb=" O   CYS A 426 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ARG A 432 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   MET A 433 " --> pdb=" O   GLU A 429 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   GLU A 434 " --> pdb=" O   ILE A 430 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   GLU A 435 " --> pdb=" O   TYR A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 702
      removed outlier: 4.013A  pdb=" N   ALA A 682 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A 685 " --> pdb=" O   GLN A 681 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU A 686 " --> pdb=" O   ALA A 682 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A 687 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 697 " --> pdb=" O   PHE A 693 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   HIS A 698 " --> pdb=" O   GLU A 694 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A 702 " --> pdb=" O   HIS A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 857
    Processing helix  chain 'B' and resid 6 through 19
      removed outlier: 3.965A  pdb=" N   VAL B  11 " --> pdb=" O   GLY B   7 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP B  12 " --> pdb=" O   ALA B   8 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ALA B  13 " --> pdb=" O   GLU B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 48
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'D' and resid 12 through 20
    Processing helix  chain 'D' and resid 133 through 137
    Processing helix  chain 'D' and resid 144 through 148
    Processing helix  chain 'D' and resid 248 through 254
      removed outlier: 3.613A  pdb=" N   CYS D 252 " --> pdb=" O   ASP D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 314 through 320
    Processing helix  chain 'D' and resid 340 through 350
      removed outlier: 4.025A  pdb=" N   GLU D 344 " --> pdb=" O   ASN D 340 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 369 through 373
      removed outlier: 4.235A  pdb=" N   PHE D 372 " --> pdb=" O   SER D 369 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 385 through 389
    Processing helix  chain 'D' and resid 428 through 437
    Processing helix  chain 'D' and resid 625 through 631
      removed outlier: 3.966A  pdb=" N   TYR D 629 " --> pdb=" O   ASP D 625 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 676 through 699
      removed outlier: 3.523A  pdb=" N   LYS D 680 " --> pdb=" O   THR D 676 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE D 696 " --> pdb=" O   VAL D 692 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   LEU D 697 " --> pdb=" O   PHE D 693 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASN D 699 " --> pdb=" O   ASN D 695 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 853 through 860
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25
      removed outlier: 3.534A  pdb=" N   THR A  52 " --> pdb=" O   ILE A  25 " (cutoff:3.500A)
      removed outlier: 11.262A  pdb=" N   VAL A  50 " --> pdb=" O   ARG A  77 " (cutoff:3.500A)
      removed outlier: 10.184A  pdb=" N   TRP A  79 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 8.614A  pdb=" N   THR A  52 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32
      removed outlier: 6.539A  pdb=" N   ILE A  31 " --> pdb=" O   PHE A  58 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU A  55 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   PHE A  90 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   LEU A  57 " --> pdb=" O   PHE A  90 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU A 114 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
      removed outlier: 8.785A  pdb=" N   VAL A 140 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE A 113 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166
      removed outlier: 3.629A  pdb=" N   ASN A 172 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 209
      removed outlier: 7.098A  pdb=" N   SER A 208 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268
    Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 284
      removed outlier: 4.693A  pdb=" N   TYR A 290 " --> pdb=" O   ASN A 284 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302
    Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312
      removed outlier: 5.668A  pdb=" N   LEU A 331 " --> pdb=" O   LYS A 360 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   ARG A 362 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   ILE A 333 " --> pdb=" O   ARG A 362 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL A 359 " --> pdb=" O   TYR A 392 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   LEU A 394 " --> pdb=" O   VAL A 359 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   TYR A 418 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   TYR A 392 " --> pdb=" O   TYR A 418 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   ALA A 420 " --> pdb=" O   TYR A 392 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LEU A 394 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 379
    Processing sheet with id=AB1, first strand: chain 'A' and resid 462 through 463
      removed outlier: 6.425A  pdb=" N   ASP A 462 " --> pdb=" O   LYS A 569 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 568 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 555 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 493 " --> pdb=" O   VAL A 555 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463
      removed outlier: 6.425A  pdb=" N   ASP A 462 " --> pdb=" O   LYS A 569 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 568 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 466 through 472
    Processing sheet with id=AB4, first strand: chain 'A' and resid 586 through 594
      removed outlier: 4.550A  pdb=" N   VAL A 588 " --> pdb=" O   LYS A 601 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   LYS A 601 " --> pdb=" O   VAL A 588 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   SER A 590 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ILE A 599 " --> pdb=" O   SER A 590 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   SER A 592 " --> pdb=" O   GLN A 597 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   GLN A 597 " --> pdb=" O   SER A 592 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR A 759 " --> pdb=" O   VAL A 600 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 753
      removed outlier: 3.534A  pdb=" N   VAL A 617 " --> pdb=" O   SER A 751 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN A 620 " --> pdb=" O   ARG A 771 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 818 through 820
    Processing sheet with id=AB7, first strand: chain 'A' and resid 847 through 852
    Processing sheet with id=AB8, first strand: chain 'A' and resid 847 through 852
      removed outlier: 7.136A  pdb=" N   THR A 879 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 2 through 3
      removed outlier: 3.848A  pdb=" N   ILE D  76 " --> pdb=" O   ASN D 105 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 10
      removed outlier: 5.931A  pdb=" N   ILE D   7 " --> pdb=" O   HIS D  30 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   LEU D  32 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   ILE D   9 " --> pdb=" O   LEU D  32 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ILE D  34 " --> pdb=" O   ILE D   9 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   VAL D  60 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   LEU D  55 " --> pdb=" O   VAL D  88 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   PHE D  90 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LEU D  57 " --> pdb=" O   PHE D  90 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG D 112 " --> pdb=" O   LEU D  87 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE D  89 " --> pdb=" O   ARG D 112 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU D 114 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 239 through 241
    Processing sheet with id=AC3, first strand: chain 'D' and resid 267 through 269
    Processing sheet with id=AC4, first strand: chain 'D' and resid 281 through 284
      removed outlier: 5.949A  pdb=" N   TYR D 290 " --> pdb=" O   ASN D 284 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 312
      removed outlier: 6.269A  pdb=" N   LEU D 331 " --> pdb=" O   LYS D 360 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   ARG D 362 " --> pdb=" O   LEU D 331 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ILE D 333 " --> pdb=" O   ARG D 362 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL D 359 " --> pdb=" O   TYR D 392 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   LEU D 394 " --> pdb=" O   VAL D 359 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ILE D 361 " --> pdb=" O   LEU D 394 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 354 through 355
      removed outlier: 3.530A  pdb=" N   VAL D 355 " --> pdb=" O   LEU D 378 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ILE D 379 " --> pdb=" O   THR D 411 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'D' and resid 466 through 468
    Processing sheet with id=AC8, first strand: chain 'D' and resid 524 through 525
    Processing sheet with id=AC9, first strand: chain 'D' and resid 586 through 594
      removed outlier: 5.630A  pdb=" N   ASP D 587 " --> pdb=" O   ASN D 603 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   ASN D 603 " --> pdb=" O   ASP D 587 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ASN D 593 " --> pdb=" O   GLN D 597 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   GLN D 597 " --> pdb=" O   ASN D 593 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 612 through 621
    Processing sheet with id=AD2, first strand: chain 'D' and resid 810 through 812
      removed outlier: 3.767A  pdb=" N   LEU D 864 " --> pdb=" O   ILE D 819 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'D' and resid 847 through 851
      removed outlier: 3.733A  pdb=" N   MET D 835 " --> pdb=" O   THR D 879 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL D 895 " --> pdb=" O   GLY D 870 " (cutoff:3.500A)

    265 hydrogen bonds defined for protein.
    642 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.53

  Time building geometry restraints manager: 3.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.56: 13366
        1.56 -     1.91: 126
        1.91 -     2.25: 0
        2.25 -     2.59: 0
        2.59 -     2.94: 1
  Bond restraints: 13493
  Sorted by residual:
  bond pdb=" C   PRO A 798 "
       pdb=" N   ALA A 799 "
    ideal  model  delta    sigma   weight residual
    1.329  2.936 -1.607 1.40e-02 5.10e+03 1.32e+04
  bond pdb=" C   ALA A 501 "
       pdb=" N   PRO A 502 "
    ideal  model  delta    sigma   weight residual
    1.334  1.308  0.025 8.40e-03 1.42e+04 9.18e+00
  bond pdb=" CB  TRP A 405 "
       pdb=" CG  TRP A 405 "
    ideal  model  delta    sigma   weight residual
    1.498  1.442  0.056 3.10e-02 1.04e+03 3.21e+00
  bond pdb=" C   ALA D 117 "
       pdb=" N   ASP D 118 "
    ideal  model  delta    sigma   weight residual
    1.332  1.308  0.024 1.40e-02 5.10e+03 3.00e+00
  bond pdb=" CA  PRO A 144 "
       pdb=" C   PRO A 144 "
    ideal  model  delta    sigma   weight residual
    1.517  1.501  0.016 9.30e-03 1.16e+04 2.88e+00
  ... (remaining 13488 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.83: 18295
       14.83 -    29.65: 0
       29.65 -    44.48: 0
       44.48 -    59.30: 0
       59.30 -    74.13: 1
  Bond angle restraints: 18296
  Sorted by residual:
  angle pdb=" O   PRO A 798 "
        pdb=" C   PRO A 798 "
        pdb=" N   ALA A 799 "
      ideal   model   delta    sigma   weight residual
     122.89   48.76   74.13 1.25e+00 6.40e-01 3.52e+03
  angle pdb=" CA  PRO A 798 "
        pdb=" C   PRO A 798 "
        pdb=" N   ALA A 799 "
      ideal   model   delta    sigma   weight residual
     115.12  126.49  -11.37 1.25e+00 6.40e-01 8.28e+01
  angle pdb=" C   PRO A 798 "
        pdb=" N   ALA A 799 "
        pdb=" CA  ALA A 799 "
      ideal   model   delta    sigma   weight residual
     121.70  109.37   12.33 1.80e+00 3.09e-01 4.69e+01
  angle pdb=" N   GLN A 843 "
        pdb=" CA  GLN A 843 "
        pdb=" C   GLN A 843 "
      ideal   model   delta    sigma   weight residual
     114.75  108.87    5.88 1.26e+00 6.30e-01 2.18e+01
  angle pdb=" C   MET A 184 "
        pdb=" N   CYS A 185 "
        pdb=" CA  CYS A 185 "
      ideal   model   delta    sigma   weight residual
     120.94  113.03    7.91 1.90e+00 2.77e-01 1.73e+01
  ... (remaining 18291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 7198
       17.90 -    35.79: 806
       35.79 -    53.69: 150
       53.69 -    71.58: 26
       71.58 -    89.48: 9
  Dihedral angle restraints: 8189
    sinusoidal: 3379
      harmonic: 4810
  Sorted by residual:
  dihedral pdb=" CA  GLU D 816 "
           pdb=" C   GLU D 816 "
           pdb=" N   ASN D 817 "
           pdb=" CA  ASN D 817 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.16  -49.84     0      5.00e+00 4.00e-02 9.94e+01
  dihedral pdb=" CB  CYS D 189 "
           pdb=" SG  CYS D 189 "
           pdb=" SG  CYS D 200 "
           pdb=" CB  CYS D 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    3.52   89.48     1      1.00e+01 1.00e-02 9.51e+01
  dihedral pdb=" CB  CYS D 777 "
           pdb=" SG  CYS D 777 "
           pdb=" SG  CYS D 786 "
           pdb=" CB  CYS D 786 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.98   81.98     1      1.00e+01 1.00e-02 8.26e+01
  ... (remaining 8186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1125
       0.036 -    0.072: 538
       0.072 -    0.108: 239
       0.108 -    0.143: 67
       0.143 -    0.179: 9
  Chirality restraints: 1978
  Sorted by residual:
  chirality pdb=" CA  ILE A 575 "
            pdb=" N   ILE A 575 "
            pdb=" C   ILE A 575 "
            pdb=" CB  ILE A 575 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" CB  ILE D 448 "
            pdb=" CA  ILE D 448 "
            pdb=" CG1 ILE D 448 "
            pdb=" CG2 ILE D 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CA  PRO A 153 "
            pdb=" N   PRO A 153 "
            pdb=" C   PRO A 153 "
            pdb=" CB  PRO A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 6.81e-01
  ... (remaining 1975 not shown)

  Planarity restraints: 2373
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 798 "    0.198 2.00e-02 2.50e+03   2.81e-01 7.87e+02
        pdb=" C   PRO A 798 "   -0.460 2.00e-02 2.50e+03
        pdb=" O   PRO A 798 "    0.254 2.00e-02 2.50e+03
        pdb=" N   ALA A 799 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D   4 "   -0.035 5.00e-02 4.00e+02   5.28e-02 4.47e+00
        pdb=" N   PRO D   5 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO D   5 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D   5 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 814 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO D 815 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO D 815 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 815 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2370 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 416
        2.64 -     3.21: 13832
        3.21 -     3.77: 20389
        3.77 -     4.34: 27182
        4.34 -     4.90: 41536
  Nonbonded interactions: 103355
  Sorted by model distance:
  nonbonded pdb=" O   SER D 776 "
            pdb=" OG  SER D 787 "
     model   vdw
     2.079 3.040
  nonbonded pdb=" O   LEU A 607 "
            pdb=" ND2 ASN A 609 "
     model   vdw
     2.121 3.120
  nonbonded pdb=" OD1 ASN D  84 "
            pdb=" OG  SER D 314 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" ND2 ASN D 339 "
            pdb=" OD1 ASN D 340 "
     model   vdw
     2.133 3.120
  nonbonded pdb=" OG  SER D 461 "
            pdb=" O   GLY D 567 "
     model   vdw
     2.144 3.040
  ... (remaining 103350 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 153 or resid 162 through 186 or (resid 187 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 188 through 189 or  \ 
resid 193 through 256 or resid 265 through 294 or resid 298 or resid 306 through \ 
 510 or resid 515 through 526 or resid 532 through 558 or resid 562 through 704  \ 
or resid 746 through 897))
  selection = (chain 'D' and (resid 1 through 35 or resid 41 through 210 or resid 212 through  \ 
256 or resid 265 through 294 or resid 302 or resid 306 through 625 or resid 671  \ 
through 897))
}

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 group one per residue
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:             1.470
  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:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.140
  Process input model:                     32.050
  Find NCS groups from input model:        0.560
  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:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
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      :  0.016   1.607  13525  Z= 1.049
  Angle     :  1.053  74.130  18360  Z= 0.676
  Chirality :  0.050   0.179   1978
  Planarity :  0.008   0.281   2373
  Dihedral  : 14.643  87.364   4995
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 28.75
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 18.16 %
    Favored  : 81.65 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.95 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -5.21 (0.17), residues: 1602
  helix: -4.27 (0.21), residues: 162
  sheet: -3.01 (0.24), residues: 346
  loop : -3.74 (0.16), residues: 1094

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 403 
 HIS   0.007   0.001   HIS D 540 
 PHE   0.025   0.002   PHE D 793 
 TYR   0.026   0.002   TYR D 224 
 ARG   0.006   0.001   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24984 (  258)
  hydrogen bonds       : angle      10.10773 (  642)
  SS BOND              : bond        0.00486 (   32)
  SS BOND              : angle       1.51294 (   64)
  covalent geometry    : bond        0.01573 (13493)
  covalent geometry    : angle       1.05069 (18296)

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

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

  3204 Ramachandran restraints generated.
    1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3204 Ramachandran restraints generated.
    1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.9108 (mmm) cc_final: 0.8387 (mmt)
REVERT: A  222 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.7980 (ttt180)
REVERT: A  557 LEU cc_start: 0.8616 (mt) cc_final: 0.8280 (mt)
REVERT: B   59 MET cc_start: 0.9015 (mtt) cc_final: 0.8311 (mtt)
REVERT: D  100 LEU cc_start: 0.8614 (mt) cc_final: 0.8273 (mt)
REVERT: D  176 TRP cc_start: 0.7309 (m100) cc_final: 0.6466 (m-10)
REVERT: D  373 LEU cc_start: 0.9062 (mt) cc_final: 0.8848 (mp)
REVERT: D  509 TYR cc_start: 0.6952 (m-80) cc_final: 0.6616 (m-80)
REVERT: D  835 MET cc_start: 0.8655 (ptm) cc_final: 0.7491 (ptm)
REVERT: D  851 VAL cc_start: 0.8411 (t) cc_final: 0.7655 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 96
  average time/residue: 0.2676
  time to fit residues: 38.1772
Evaluate side-chains
  65 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:   10.0000
   chunk 123 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 127 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   chunk 95 optimal weight:    0.8980
   chunk 148 optimal weight:   10.0000
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  11 ASN
A  14 GLN
A  72 ASN
A 169 ASN
A 198 ASN
A 287 GLN
A 334 ASN
A 363 HIS
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 443 GLN
A 609 ASN
A 763 ASN
** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  11 ASN
D 275 GLN
D 365 HIS
** D 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 578 ASN
** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 624 GLN
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 763 ASN
D 817 ASN
D 830 ASN
D 877 GLN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.059633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.046663 restraints weight = 76406.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.047247 restraints weight = 46190.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.047693 restraints weight = 38591.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  13525  Z= 0.276
  Angle     :  0.786  16.287  18360  Z= 0.416
  Chirality :  0.049   0.246   1978
  Planarity :  0.006   0.048   2373
  Dihedral  :  7.043  50.267   1814
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 17.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.97 %
    Favored  : 87.03 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  6.59 %
    Favored  : 93.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -4.37 (0.18), residues: 1604
  helix: -3.19 (0.29), residues: 165
  sheet: -2.64 (0.23), residues: 365
  loop : -3.13 (0.17), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 403 
 HIS   0.009   0.001   HIS A 269 
 PHE   0.031   0.002   PHE A 893 
 TYR   0.025   0.002   TYR D 224 
 ARG   0.008   0.001   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05849 (  258)
  hydrogen bonds       : angle       7.76491 (  642)
  SS BOND              : bond        0.00491 (   32)
  SS BOND              : angle       1.45338 (   64)
  covalent geometry    : bond        0.00618 (13493)
  covalent geometry    : angle       0.78243 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 1.655 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.9551 (mm) cc_final: 0.9225 (mm)
REVERT: A  268 ILE cc_start: 0.7781 (mp) cc_final: 0.7407 (mp)
REVERT: A  522 MET cc_start: 0.8309 (ptm) cc_final: 0.8085 (ptm)
REVERT: A  557 LEU cc_start: 0.8649 (mt) cc_final: 0.8314 (mt)
REVERT: D  100 LEU cc_start: 0.8753 (mt) cc_final: 0.8454 (mt)
REVERT: D  176 TRP cc_start: 0.7182 (m100) cc_final: 0.5968 (m-10)
REVERT: D  313 ASP cc_start: 0.9171 (p0) cc_final: 0.8858 (p0)
REVERT: D  835 MET cc_start: 0.8718 (ptm) cc_final: 0.7927 (ppp)
  outliers start: 3
  outliers final: 1
  residues processed: 86
  average time/residue: 0.2144
  time to fit residues: 30.0378
Evaluate side-chains
  54 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 1.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 83 optimal weight:    0.2980
   chunk 24 optimal weight:    7.9990
   chunk 90 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 112 optimal weight:   10.0000
   chunk 99 optimal weight:   20.0000
   chunk 66 optimal weight:    3.9990
   chunk 143 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 162 optimal weight:   10.0000
   chunk 95 optimal weight:    2.9990
   overall best weight:    3.0588

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN
A 564 HIS
** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 102 ASN
** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 830 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.060451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.047515 restraints weight = 77083.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.048369 restraints weight = 47311.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.048462 restraints weight = 38003.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  13525  Z= 0.201
  Angle     :  0.691  10.399  18360  Z= 0.367
  Chirality :  0.047   0.187   1978
  Planarity :  0.005   0.047   2373
  Dihedral  :  6.609  48.910   1814
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.47 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.29 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.80 (0.19), residues: 1604
  helix: -2.71 (0.32), residues: 166
  sheet: -2.19 (0.25), residues: 359
  loop : -2.78 (0.18), residues: 1079

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 403 
 HIS   0.009   0.001   HIS A 481 
 PHE   0.023   0.002   PHE A 893 
 TYR   0.028   0.002   TYR D 224 
 ARG   0.005   0.000   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04763 (  258)
  hydrogen bonds       : angle       7.01837 (  642)
  SS BOND              : bond        0.00405 (   32)
  SS BOND              : angle       1.53361 (   64)
  covalent geometry    : bond        0.00450 (13493)
  covalent geometry    : angle       0.68623 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 1.610 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.9541 (mm) cc_final: 0.9120 (mm)
REVERT: A  268 ILE cc_start: 0.7904 (mp) cc_final: 0.7254 (mp)
REVERT: A  349 MET cc_start: 0.8356 (mtp) cc_final: 0.8141 (ttm)
REVERT: A  522 MET cc_start: 0.8305 (ptm) cc_final: 0.7988 (ptm)
REVERT: A  557 LEU cc_start: 0.8645 (mt) cc_final: 0.8350 (mt)
REVERT: D  100 LEU cc_start: 0.8736 (mt) cc_final: 0.8511 (mt)
REVERT: D  176 TRP cc_start: 0.7079 (m100) cc_final: 0.6744 (m100)
REVERT: D  313 ASP cc_start: 0.9105 (p0) cc_final: 0.8777 (p0)
REVERT: D  797 MET cc_start: 0.8125 (mtt) cc_final: 0.7888 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2196
  time to fit residues: 30.8065
Evaluate side-chains
  54 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 138 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 109 optimal weight:    6.9990
   chunk 130 optimal weight:    8.9990
   chunk 6 optimal weight:    0.6980
   chunk 135 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN
D 102 ASN
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 830 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.060210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.047065 restraints weight = 77099.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.047869 restraints weight = 48637.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.048113 restraints weight = 37930.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  13525  Z= 0.222
  Angle     :  0.695  10.522  18360  Z= 0.365
  Chirality :  0.047   0.185   1978
  Planarity :  0.005   0.047   2373
  Dihedral  :  6.526  49.333   1814
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.53 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.56 (0.19), residues: 1604
  helix: -2.55 (0.32), residues: 167
  sheet: -2.09 (0.25), residues: 374
  loop : -2.57 (0.18), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 472 
 HIS   0.005   0.001   HIS D 540 
 PHE   0.019   0.002   PHE A 893 
 TYR   0.017   0.002   TYR D 224 
 ARG   0.003   0.000   ARG A 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04506 (  258)
  hydrogen bonds       : angle       6.78118 (  642)
  SS BOND              : bond        0.00410 (   32)
  SS BOND              : angle       1.52171 (   64)
  covalent geometry    : bond        0.00499 (13493)
  covalent geometry    : angle       0.69058 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.9561 (mm) cc_final: 0.9254 (mm)
REVERT: A  184 MET cc_start: 0.8543 (mtt) cc_final: 0.8320 (mtt)
REVERT: A  268 ILE cc_start: 0.8365 (mp) cc_final: 0.7883 (mp)
REVERT: A  522 MET cc_start: 0.8220 (ptm) cc_final: 0.7850 (ptm)
REVERT: D  100 LEU cc_start: 0.8777 (mt) cc_final: 0.8507 (mt)
REVERT: D  176 TRP cc_start: 0.7179 (m100) cc_final: 0.6904 (m100)
REVERT: D  313 ASP cc_start: 0.9080 (p0) cc_final: 0.8741 (p0)
REVERT: D  373 LEU cc_start: 0.8971 (mt) cc_final: 0.8743 (mp)
REVERT: D  797 MET cc_start: 0.8219 (mtt) cc_final: 0.8015 (mtp)
REVERT: D  835 MET cc_start: 0.8466 (ppp) cc_final: 0.7526 (ppp)
REVERT: D  857 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8894 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.2229
  time to fit residues: 27.8038
Evaluate side-chains
  57 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 144 optimal weight:    9.9990
   chunk 120 optimal weight:    3.9990
   chunk 119 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 564 HIS
** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 830 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.060926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.047498 restraints weight = 74696.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.048741 restraints weight = 45878.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.048962 restraints weight = 32725.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13525  Z= 0.154
  Angle     :  0.644  10.151  18360  Z= 0.339
  Chirality :  0.046   0.273   1978
  Planarity :  0.004   0.047   2373
  Dihedral  :  6.165  49.022   1814
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.75 %
    Favored  : 97.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.23 (0.20), residues: 1604
  helix: -2.34 (0.33), residues: 167
  sheet: -1.85 (0.26), residues: 380
  loop : -2.35 (0.19), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 176 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.016   0.001   PHE A 893 
 TYR   0.030   0.001   TYR D 224 
 ARG   0.004   0.000   ARG A 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  258)
  hydrogen bonds       : angle       6.38350 (  642)
  SS BOND              : bond        0.00405 (   32)
  SS BOND              : angle       1.66471 (   64)
  covalent geometry    : bond        0.00349 (13493)
  covalent geometry    : angle       0.63762 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 1.488 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.9535 (mm) cc_final: 0.9181 (mm)
REVERT: A  268 ILE cc_start: 0.8392 (mp) cc_final: 0.7829 (mm)
REVERT: A  522 MET cc_start: 0.7998 (ptm) cc_final: 0.7648 (ptm)
REVERT: B   59 MET cc_start: 0.9188 (mtt) cc_final: 0.8799 (mtp)
REVERT: D  100 LEU cc_start: 0.8693 (mt) cc_final: 0.8381 (mt)
REVERT: D  176 TRP cc_start: 0.6883 (m100) cc_final: 0.6649 (m100)
REVERT: D  313 ASP cc_start: 0.9074 (p0) cc_final: 0.8726 (p0)
REVERT: D  835 MET cc_start: 0.8337 (ppp) cc_final: 0.7444 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.2253
  time to fit residues: 30.1447
Evaluate side-chains
  55 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 72 optimal weight:    0.3980
   chunk 132 optimal weight:   10.0000
   chunk 135 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 93 optimal weight:    0.3980
   chunk 136 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.062355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.048857 restraints weight = 74584.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.050003 restraints weight = 45265.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.050288 restraints weight = 33044.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  13525  Z= 0.111
  Angle     :  0.607  10.116  18360  Z= 0.320
  Chirality :  0.045   0.216   1978
  Planarity :  0.004   0.057   2373
  Dihedral  :  5.815  48.680   1814
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.21), residues: 1604
  helix: -1.83 (0.36), residues: 161
  sheet: -1.49 (0.26), residues: 381
  loop : -2.04 (0.19), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 811 
 HIS   0.005   0.001   HIS A 223 
 PHE   0.014   0.001   PHE A 893 
 TYR   0.024   0.001   TYR D 224 
 ARG   0.003   0.000   ARG D 222 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  258)
  hydrogen bonds       : angle       6.02785 (  642)
  SS BOND              : bond        0.00320 (   32)
  SS BOND              : angle       1.38060 (   64)
  covalent geometry    : bond        0.00256 (13493)
  covalent geometry    : angle       0.60205 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.9504 (mm) cc_final: 0.9149 (mm)
REVERT: A  184 MET cc_start: 0.8383 (mtt) cc_final: 0.8108 (mtt)
REVERT: A  522 MET cc_start: 0.8120 (ptm) cc_final: 0.7662 (ptm)
REVERT: B   59 MET cc_start: 0.9216 (mtt) cc_final: 0.8816 (mtp)
REVERT: D  313 ASP cc_start: 0.8948 (p0) cc_final: 0.8575 (p0)
REVERT: D  686 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8950 (tm-30)
REVERT: D  835 MET cc_start: 0.8242 (ppp) cc_final: 0.7393 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.2435
  time to fit residues: 33.9066
Evaluate side-chains
  61 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   chunk 110 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 149 optimal weight:    7.9990
   chunk 158 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 147 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 HIS
** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN
D  14 GLN
D 102 ASN
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.062484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.049298 restraints weight = 75560.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.050275 restraints weight = 46006.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.050458 restraints weight = 34892.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13525  Z= 0.116
  Angle     :  0.601   9.955  18360  Z= 0.314
  Chirality :  0.045   0.199   1978
  Planarity :  0.004   0.048   2373
  Dihedral  :  5.643  48.706   1814
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.21), residues: 1604
  helix: -1.67 (0.38), residues: 153
  sheet: -1.36 (0.26), residues: 381
  loop : -1.94 (0.19), residues: 1070

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 811 
 HIS   0.003   0.001   HIS D 775 
 PHE   0.022   0.001   PHE D 503 
 TYR   0.020   0.001   TYR A 224 
 ARG   0.004   0.000   ARG D 853 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  258)
  hydrogen bonds       : angle       5.86846 (  642)
  SS BOND              : bond        0.00349 (   32)
  SS BOND              : angle       1.35449 (   64)
  covalent geometry    : bond        0.00264 (13493)
  covalent geometry    : angle       0.59663 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.8324 (mtt) cc_final: 0.8084 (mtt)
REVERT: A  522 MET cc_start: 0.8113 (ptm) cc_final: 0.7658 (ptm)
REVERT: B   59 MET cc_start: 0.9193 (mtt) cc_final: 0.8807 (mtp)
REVERT: D  313 ASP cc_start: 0.8982 (p0) cc_final: 0.8586 (p0)
REVERT: D  686 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8934 (tm-30)
REVERT: D  835 MET cc_start: 0.8188 (ppp) cc_final: 0.7339 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.2529
  time to fit residues: 36.5292
Evaluate side-chains
  58 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 135 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 152 optimal weight:   10.0000
   chunk 117 optimal weight:    8.9990
   chunk 119 optimal weight:    0.9990
   chunk 153 optimal weight:    9.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 HIS
A 775 HIS
** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN
D 102 ASN
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.062823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.049467 restraints weight = 75203.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.050518 restraints weight = 46308.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.050750 restraints weight = 34328.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13525  Z= 0.112
  Angle     :  0.608  11.541  18360  Z= 0.317
  Chirality :  0.045   0.191   1978
  Planarity :  0.004   0.048   2373
  Dihedral  :  5.593  48.541   1814
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.55 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.21), residues: 1604
  helix: -1.55 (0.38), residues: 160
  sheet: -1.18 (0.27), residues: 372
  loop : -1.93 (0.19), residues: 1072

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 403 
 HIS   0.005   0.001   HIS D 775 
 PHE   0.014   0.001   PHE A 893 
 TYR   0.026   0.001   TYR D 224 
 ARG   0.009   0.000   ARG A 752 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03397 (  258)
  hydrogen bonds       : angle       5.80946 (  642)
  SS BOND              : bond        0.00374 (   32)
  SS BOND              : angle       2.16859 (   64)
  covalent geometry    : bond        0.00257 (13493)
  covalent geometry    : angle       0.59585 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 1.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 LEU cc_start: 0.9294 (mt) cc_final: 0.8990 (mt)
REVERT: A  522 MET cc_start: 0.7990 (ptm) cc_final: 0.7566 (ptm)
REVERT: B   59 MET cc_start: 0.9169 (mtt) cc_final: 0.8811 (mtp)
REVERT: D  176 TRP cc_start: 0.6637 (m100) cc_final: 0.5997 (m100)
REVERT: D  313 ASP cc_start: 0.8904 (p0) cc_final: 0.8488 (p0)
REVERT: D  686 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8903 (tm-30)
REVERT: D  835 MET cc_start: 0.8176 (ppp) cc_final: 0.7323 (ppp)
REVERT: D  851 VAL cc_start: 0.8349 (t) cc_final: 0.8125 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.2249
  time to fit residues: 31.5717
Evaluate side-chains
  56 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 27 optimal weight:    0.0970
   chunk 129 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 71 optimal weight:    7.9990
   chunk 135 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 132 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 154 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 156 optimal weight:    5.9990
   overall best weight:    2.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 HIS
A 384 GLN
A 388 ASN
** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN
D 102 ASN
D 365 HIS
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.048231 restraints weight = 74692.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.049177 restraints weight = 45696.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.049346 restraints weight = 35266.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13525  Z= 0.156
  Angle     :  0.632   9.832  18360  Z= 0.328
  Chirality :  0.046   0.195   1978
  Planarity :  0.004   0.048   2373
  Dihedral  :  5.687  48.799   1814
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.21), residues: 1604
  helix: -1.47 (0.39), residues: 154
  sheet: -1.23 (0.27), residues: 366
  loop : -1.88 (0.19), residues: 1084

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 403 
 HIS   0.006   0.001   HIS D 775 
 PHE   0.016   0.001   PHE D 503 
 TYR   0.024   0.001   TYR D 224 
 ARG   0.007   0.000   ARG A 752 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  258)
  hydrogen bonds       : angle       5.86484 (  642)
  SS BOND              : bond        0.00372 (   32)
  SS BOND              : angle       1.71351 (   64)
  covalent geometry    : bond        0.00354 (13493)
  covalent geometry    : angle       0.62451 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.8331 (mtt) cc_final: 0.7996 (mtt)
REVERT: A  522 MET cc_start: 0.8031 (ptm) cc_final: 0.7598 (ptm)
REVERT: B   59 MET cc_start: 0.9177 (mtt) cc_final: 0.8792 (mtp)
REVERT: D  176 TRP cc_start: 0.6671 (m100) cc_final: 0.6022 (m100)
REVERT: D  313 ASP cc_start: 0.8893 (p0) cc_final: 0.8481 (p0)
REVERT: D  686 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8958 (tm-30)
REVERT: D  835 MET cc_start: 0.8236 (ppp) cc_final: 0.7354 (ppp)
REVERT: D  851 VAL cc_start: 0.8373 (t) cc_final: 0.8133 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.2145
  time to fit residues: 24.7592
Evaluate side-chains
  53 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 161 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   chunk 14 optimal weight:    0.0670
   chunk 44 optimal weight:    6.9990
   chunk 152 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 157 optimal weight:   10.0000
   chunk 105 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   overall best weight:    2.1722

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 HIS
A 830 ASN
B  15 GLN
D 365 HIS
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.047966 restraints weight = 75493.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.049149 restraints weight = 46814.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.049524 restraints weight = 33538.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13525  Z= 0.149
  Angle     :  0.623   9.673  18360  Z= 0.323
  Chirality :  0.045   0.194   1978
  Planarity :  0.004   0.048   2373
  Dihedral  :  5.706  48.684   1814
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.27 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.21), residues: 1604
  helix: -1.48 (0.38), residues: 160
  sheet: -1.25 (0.27), residues: 371
  loop : -1.89 (0.19), residues: 1073

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 403 
 HIS   0.006   0.001   HIS D 775 
 PHE   0.015   0.001   PHE D 503 
 TYR   0.027   0.001   TYR D 224 
 ARG   0.007   0.000   ARG A 752 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03444 (  258)
  hydrogen bonds       : angle       5.83119 (  642)
  SS BOND              : bond        0.00435 (   32)
  SS BOND              : angle       1.65438 (   64)
  covalent geometry    : bond        0.00340 (13493)
  covalent geometry    : angle       0.61624 (18296)

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

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  522 MET cc_start: 0.8027 (ptm) cc_final: 0.7623 (ptm)
REVERT: B   59 MET cc_start: 0.9242 (mtt) cc_final: 0.8882 (mtp)
REVERT: D  176 TRP cc_start: 0.6659 (m100) cc_final: 0.5964 (m100)
REVERT: D  313 ASP cc_start: 0.8900 (p0) cc_final: 0.8510 (p0)
REVERT: D  686 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8951 (tm-30)
REVERT: D  835 MET cc_start: 0.8241 (ppp) cc_final: 0.7356 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2203
  time to fit residues: 24.7360
Evaluate side-chains
  50 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 87 optimal weight:    9.9990
   chunk 127 optimal weight:    7.9990
   chunk 150 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 132 optimal weight:    0.0370
   chunk 63 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.8066

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 223 HIS
B  15 GLN
D 365 HIS
** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.061762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.048416 restraints weight = 75266.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.049293 restraints weight = 45958.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.049586 restraints weight = 34866.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13525  Z= 0.133
  Angle     :  0.609   9.455  18360  Z= 0.317
  Chirality :  0.045   0.192   1978
  Planarity :  0.004   0.048   2373
  Dihedral  :  5.609  48.549   1814
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.20 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.21), residues: 1604
  helix: -1.35 (0.39), residues: 155
  sheet: -1.22 (0.27), residues: 371
  loop : -1.77 (0.19), residues: 1078

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 403 
 HIS   0.007   0.001   HIS D 775 
 PHE   0.015   0.001   PHE D 503 
 TYR   0.023   0.001   TYR D 224 
 ARG   0.007   0.000   ARG A 752 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  258)
  hydrogen bonds       : angle       5.70136 (  642)
  SS BOND              : bond        0.00376 (   32)
  SS BOND              : angle       1.52174 (   64)
  covalent geometry    : bond        0.00306 (13493)
  covalent geometry    : angle       0.60335 (18296)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3491.21 seconds
wall clock time: 61 minutes 48.48 seconds (3708.48 seconds total)