Starting phenix.real_space_refine
on Sun May 25 03:31:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ctm_45911/05_2025/9ctm_45911.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ctm_45911/05_2025/9ctm_45911.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ctm_45911/05_2025/9ctm_45911.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ctm_45911/05_2025/9ctm_45911.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ctm_45911/05_2025/9ctm_45911.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ctm_45911/05_2025/9ctm_45911.cif"
  }
  resolution = 2.92
  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=   0.002 sd=   0.058
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: 5
    Type Number    sf(0)   Gaussians
     S      98      5.16       5
     C    8360      2.51       5
     N    2242      2.21       5
     O    2534      1.98       5
     H   13032      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 26266
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 13133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 862, 13133
          Classifications: {'peptide': 862}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 815}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1, 'SCY:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 13133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 862, 13133
          Classifications: {'peptide': 862}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 815}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1, 'SCY:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 12.60, per 1000 atoms: 0.48
  Number of scatterers: 26266
  At special positions: 0
  Unit cell: (103.88, 99.64, 189.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      98     16.00
     O    2534      8.00
     N    2242      7.00
     C    8360      6.00
     H   13032      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 6.87
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3168

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 10 sheets defined
      46.4% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 54
    Processing helix  chain 'A' and resid 69 through 73
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'A' and resid 94 through 100
    Processing helix  chain 'A' and resid 102 through 119
    Processing helix  chain 'A' and resid 122 through 127
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 4.305A  pdb=" N   THR A 144 " --> pdb=" O   ASN A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 162
      removed outlier: 3.785A  pdb=" N   HIS A 162 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 175
      removed outlier: 3.783A  pdb=" N   ASN A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE A 170 " --> pdb=" O   TYR A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 203
    Processing helix  chain 'A' and resid 219 through 228
      removed outlier: 3.568A  pdb=" N   THR A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 305
      removed outlier: 3.521A  pdb=" N   HIS A 305 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'A' and resid 325 through 337
    Processing helix  chain 'A' and resid 350 through 355
    Processing helix  chain 'A' and resid 357 through 359
      No H-bonds generated for 'chain 'A' and resid 357 through 359'
    Processing helix  chain 'A' and resid 360 through 373
    Processing helix  chain 'A' and resid 392 through 397
    Processing helix  chain 'A' and resid 454 through 468
    Processing helix  chain 'A' and resid 471 through 480
      removed outlier: 3.829A  pdb=" N   HIS A 475 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 536
    Processing helix  chain 'A' and resid 537 through 552
    Processing helix  chain 'A' and resid 553 through 555
      No H-bonds generated for 'chain 'A' and resid 553 through 555'
    Processing helix  chain 'A' and resid 557 through 564
    Processing helix  chain 'A' and resid 566 through 572
      removed outlier: 3.785A  pdb=" N   GLU A 572 " --> pdb=" O   ASP A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 595
      removed outlier: 3.738A  pdb=" N   PHE A 577 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 616
    Processing helix  chain 'A' and resid 619 through 637
    Processing helix  chain 'A' and resid 650 through 658
    Processing helix  chain 'A' and resid 679 through 693
    Processing helix  chain 'A' and resid 708 through 710
      No H-bonds generated for 'chain 'A' and resid 708 through 710'
    Processing helix  chain 'A' and resid 711 through 723
      removed outlier: 3.608A  pdb=" N   ALA A 716 " --> pdb=" O   THR A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 745
    Processing helix  chain 'A' and resid 747 through 752
      removed outlier: 4.161A  pdb=" N   THR A 752 " --> pdb=" O   GLU A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 764
    Processing helix  chain 'A' and resid 767 through 774
      removed outlier: 3.671A  pdb=" N   LYS A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 799
      removed outlier: 3.519A  pdb=" N   GLY A 799 " --> pdb=" O   LYS A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 829
      removed outlier: 3.567A  pdb=" N   VAL A 818 " --> pdb=" O   ASN A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 839
      removed outlier: 3.990A  pdb=" N   LEU A 838 " --> pdb=" O   PRO A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 859
      removed outlier: 3.688A  pdb=" N   VAL A 857 " --> pdb=" O   LEU A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 876
      removed outlier: 3.604A  pdb=" N   GLU A 876 " --> pdb=" O   GLU A 873 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 54
    Processing helix  chain 'B' and resid 69 through 73
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 94 through 100
    Processing helix  chain 'B' and resid 102 through 119
    Processing helix  chain 'B' and resid 122 through 127
    Processing helix  chain 'B' and resid 140 through 148
      removed outlier: 4.283A  pdb=" N   THR B 144 " --> pdb=" O   ASN B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 161
    Processing helix  chain 'B' and resid 164 through 175
      removed outlier: 3.711A  pdb=" N   ASN B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE B 170 " --> pdb=" O   TYR B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 203
    Processing helix  chain 'B' and resid 219 through 229
      removed outlier: 3.586A  pdb=" N   THR B 223 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   MET B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 305
      removed outlier: 3.559A  pdb=" N   HIS B 305 " --> pdb=" O   ILE B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 310
      No H-bonds generated for 'chain 'B' and resid 308 through 310'
    Processing helix  chain 'B' and resid 325 through 337
    Processing helix  chain 'B' and resid 350 through 355
    Processing helix  chain 'B' and resid 357 through 359
      No H-bonds generated for 'chain 'B' and resid 357 through 359'
    Processing helix  chain 'B' and resid 360 through 375
    Processing helix  chain 'B' and resid 391 through 395
      removed outlier: 3.533A  pdb=" N   LEU B 394 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 421
      No H-bonds generated for 'chain 'B' and resid 419 through 421'
    Processing helix  chain 'B' and resid 454 through 468
    Processing helix  chain 'B' and resid 471 through 480
      removed outlier: 3.800A  pdb=" N   HIS B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 536
    Processing helix  chain 'B' and resid 537 through 552
    Processing helix  chain 'B' and resid 553 through 555
      No H-bonds generated for 'chain 'B' and resid 553 through 555'
    Processing helix  chain 'B' and resid 557 through 565
    Processing helix  chain 'B' and resid 566 through 572
      removed outlier: 3.766A  pdb=" N   GLU B 572 " --> pdb=" O   ASP B 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 595
    Processing helix  chain 'B' and resid 607 through 615
    Processing helix  chain 'B' and resid 619 through 637
      removed outlier: 3.624A  pdb=" N   VAL B 634 " --> pdb=" O   ARG B 630 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   CYS B 637 " --> pdb=" O   ALA B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 658
      removed outlier: 3.765A  pdb=" N   ARG B 656 " --> pdb=" O   GLU B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 692
      removed outlier: 3.549A  pdb=" N   THR B 683 " --> pdb=" O   ALA B 679 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 710
      No H-bonds generated for 'chain 'B' and resid 708 through 710'
    Processing helix  chain 'B' and resid 711 through 723
    Processing helix  chain 'B' and resid 741 through 745
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 4.144A  pdb=" N   THR B 752 " --> pdb=" O   GLU B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 754 through 764
    Processing helix  chain 'B' and resid 767 through 775
      removed outlier: 3.627A  pdb=" N   LYS B 774 " --> pdb=" O   GLU B 770 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE B 775 " --> pdb=" O   GLY B 771 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 790 through 799
    Processing helix  chain 'B' and resid 814 through 829
      removed outlier: 3.544A  pdb=" N   VAL B 818 " --> pdb=" O   ASN B 814 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 834 through 839
      removed outlier: 3.778A  pdb=" N   LEU B 838 " --> pdb=" O   PRO B 835 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 853 through 859
      removed outlier: 3.693A  pdb=" N   VAL B 857 " --> pdb=" O   LEU B 853 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 871 through 876
      removed outlier: 3.610A  pdb=" N   GLU B 876 " --> pdb=" O   GLU B 873 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 213
      removed outlier: 7.734A  pdb=" N   GLY A 212 " --> pdb=" O   GLY A 132 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   TYR A 134 " --> pdb=" O   GLY A 212 " (cutoff:3.500A)
      removed outlier: 8.545A  pdb=" N   THR A 181 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   VAL A 133 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   TYR A 183 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ILE A 135 " --> pdb=" O   TYR A 183 " (cutoff:3.500A)
      removed outlier: 8.535A  pdb=" N   THR B 181 " --> pdb=" O   THR B 131 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   VAL B 133 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   TYR B 183 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ILE B 135 " --> pdb=" O   TYR B 183 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLY B 212 " --> pdb=" O   TYR B 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 401
      removed outlier: 5.968A  pdb=" N   LEU A 345 " --> pdb=" O   LYS A 400 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LYS A 313 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   GLY A 348 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   PHE A 315 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LEU A 412 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   TYR A 314 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ASN A 424 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   LEU A 276 " --> pdb=" O   ASN A 424 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   HIS A 426 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   SER A 274 " --> pdb=" O   HIS A 426 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE A 428 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   CYS A 269 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   VAL A  30 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   LEU A 257 " --> pdb=" O   CYS A  33 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   LEU A  35 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   ALA A 255 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 8.545A  pdb=" N   THR A 181 " --> pdb=" O   THR A 131 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   VAL A 133 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   TYR A 183 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ILE A 135 " --> pdb=" O   TYR A 183 " (cutoff:3.500A)
      removed outlier: 8.535A  pdb=" N   THR B 181 " --> pdb=" O   THR B 131 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   VAL B 133 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   TYR B 183 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ILE B 135 " --> pdb=" O   TYR B 183 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ALA B 255 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   LEU B  35 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU B 257 " --> pdb=" O   CYS B  33 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   VAL B  30 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   CYS B 269 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ILE B 428 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   SER B 274 " --> pdb=" O   HIS B 426 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   HIS B 426 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   LEU B 276 " --> pdb=" O   ASN B 424 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ASN B 424 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   LEU B 412 " --> pdb=" O   VAL B 312 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TYR B 314 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   LYS B 313 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   GLY B 348 " --> pdb=" O   LYS B 313 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   PHE B 315 " --> pdb=" O   GLY B 348 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   LEU B 345 " --> pdb=" O   LYS B 400 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 61
    Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 452
    Processing sheet with id=AA5, first strand: chain 'A' and resid 600 through 603
      removed outlier: 6.621A  pdb=" N   TRP A 517 " --> pdb=" O   ILE A 782 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ILE A 784 " --> pdb=" O   TRP A 517 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   VAL A 519 " --> pdb=" O   ILE A 784 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 662 through 663
      removed outlier: 4.464A  pdb=" N   MET A 644 " --> pdb=" O   VAL A 699 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 667 through 669
      removed outlier: 3.693A  pdb=" N   SER A 669 " --> pdb=" O   SER A 672 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 452
    Processing sheet with id=AA9, first strand: chain 'B' and resid 600 through 603
    Processing sheet with id=AB1, first strand: chain 'B' and resid 663 through 669
      removed outlier: 6.665A  pdb=" N   THR B 674 " --> pdb=" O   ALA B 665 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   HIS B 667 " --> pdb=" O   SER B 672 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   SER B 672 " --> pdb=" O   HIS B 667 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   MET B 644 " --> pdb=" O   VAL B 699 " (cutoff:3.500A)

    555 hydrogen bonds defined for protein.
    1545 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: 10.43

  Time building geometry restraints manager: 8.17 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12994
        1.03 -     1.23: 51
        1.23 -     1.43: 5581
        1.43 -     1.62: 7778
        1.62 -     1.82: 158
  Bond restraints: 26562
  Sorted by residual:
  bond pdb=" SG  SCY A 187 "
       pdb=" CD  SCY A 187 "
    ideal  model  delta    sigma   weight residual
    1.703  1.816 -0.113 2.00e-02 2.50e+03 3.19e+01
  bond pdb=" SG  SCY B 187 "
       pdb=" CD  SCY B 187 "
    ideal  model  delta    sigma   weight residual
    1.703  1.815 -0.112 2.00e-02 2.50e+03 3.11e+01
  bond pdb=" CD  SCY A 187 "
       pdb=" OCD SCY A 187 "
    ideal  model  delta    sigma   weight residual
    1.239  1.185  0.054 2.00e-02 2.50e+03 7.28e+00
  bond pdb=" CD  SCY B 187 "
       pdb=" OCD SCY B 187 "
    ideal  model  delta    sigma   weight residual
    1.239  1.185  0.054 2.00e-02 2.50e+03 7.17e+00
  bond pdb=" CA  SCY B 187 "
       pdb=" C   SCY B 187 "
    ideal  model  delta    sigma   weight residual
    1.575  1.530  0.045 2.00e-02 2.50e+03 5.12e+00
  ... (remaining 26557 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.26: 48047
        5.26 -    10.51: 9
       10.51 -    15.77: 1
       15.77 -    21.02: 0
       21.02 -    26.28: 3
  Bond angle restraints: 48060
  Sorted by residual:
  angle pdb=" CG2 ILE B 573 "
        pdb=" CB  ILE B 573 "
        pdb=" HB  ILE B 573 "
      ideal   model   delta    sigma   weight residual
     109.00   82.72   26.28 3.00e+00 1.11e-01 7.67e+01
  angle pdb=" CG1 ILE B 573 "
        pdb=" CB  ILE B 573 "
        pdb=" HB  ILE B 573 "
      ideal   model   delta    sigma   weight residual
     109.00   82.82   26.18 3.00e+00 1.11e-01 7.61e+01
  angle pdb=" CA  ILE B 573 "
        pdb=" CB  ILE B 573 "
        pdb=" HB  ILE B 573 "
      ideal   model   delta    sigma   weight residual
     109.00   85.58   23.42 3.00e+00 1.11e-01 6.09e+01
  angle pdb=" CG1 ILE B 573 "
        pdb=" CB  ILE B 573 "
        pdb=" CG2 ILE B 573 "
      ideal   model   delta    sigma   weight residual
     110.70  125.14  -14.44 3.00e+00 1.11e-01 2.32e+01
  angle pdb=" CA  ILE B 573 "
        pdb=" CB  ILE B 573 "
        pdb=" CG1 ILE B 573 "
      ideal   model   delta    sigma   weight residual
     110.40  116.25   -5.85 1.70e+00 3.46e-01 1.18e+01
  ... (remaining 48055 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 10963
       17.94 -    35.89: 1170
       35.89 -    53.83: 352
       53.83 -    71.77: 105
       71.77 -    89.72: 18
  Dihedral angle restraints: 12608
    sinusoidal: 6862
      harmonic: 5746
  Sorted by residual:
  dihedral pdb=" CB  GLU A 622 "
           pdb=" CG  GLU A 622 "
           pdb=" CD  GLU A 622 "
           pdb=" OE1 GLU A 622 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.82   86.82     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  MET A 711 "
           pdb=" CG  MET A 711 "
           pdb=" SD  MET A 711 "
           pdb=" CE  MET A 711 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.61   59.39     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET A 227 "
           pdb=" CG  MET A 227 "
           pdb=" SD  MET A 227 "
           pdb=" CE  MET A 227 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    0.78   59.22     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 12605 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.319: 2021
       0.319 -    0.637: 0
       0.637 -    0.956: 0
       0.956 -    1.275: 0
       1.275 -    1.593: 1
  Chirality restraints: 2022
  Sorted by residual:
  chirality pdb=" CB  ILE B 573 "
            pdb=" CA  ILE B 573 "
            pdb=" CG1 ILE B 573 "
            pdb=" CG2 ILE B 573 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.05    1.59 2.00e-01 2.50e+01 6.35e+01
  chirality pdb=" CA  SCY B 187 "
            pdb=" N   SCY B 187 "
            pdb=" C   SCY B 187 "
            pdb=" CB  SCY B 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.39    2.57   -0.18 2.00e-01 2.50e+01 8.24e-01
  chirality pdb=" CB  ILE B 635 "
            pdb=" CA  ILE B 635 "
            pdb=" CG1 ILE B 635 "
            pdb=" CG2 ILE B 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 2019 not shown)

  Planarity restraints: 4020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 656 "   -0.201 9.50e-02 1.11e+02   6.72e-02 4.93e+00
        pdb=" NE  ARG B 656 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 656 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 656 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 656 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG B 656 "    0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG B 656 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG B 656 "   -0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG B 656 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 575 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO B 576 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 576 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 576 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 682 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.82e+00
        pdb=" C   MET B 682 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   MET B 682 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR B 683 "    0.010 2.00e-02 2.50e+03
  ... (remaining 4017 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1376
        2.18 -     2.78: 52389
        2.78 -     3.39: 76159
        3.39 -     3.99: 100709
        3.99 -     4.60: 157697
  Nonbonded interactions: 388330
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 186 "
            pdb=" HG1 THR B 189 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" OE1 GLU A  89 "
            pdb=" H   GLU A  89 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" O   ASN B 139 "
            pdb=" HE2 HIS B 163 "
     model   vdw
     1.621 2.450
  nonbonded pdb="HH11 ARG A 453 "
            pdb=" O   SER A 488 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" HH  TYR A 520 "
            pdb=" OG1 THR A 588 "
     model   vdw
     1.638 2.450
  ... (remaining 388325 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.450
  Extract box with map and model:          0.930
  Check model and map are aligned:         0.190
  Set scattering table:                    0.240
  Process input model:                     55.270
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.070
  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:12.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.113  13530  Z= 0.132
  Angle     :  0.548  14.437  18334  Z= 0.269
  Chirality :  0.054   1.593   2022
  Planarity :  0.004   0.088   2390
  Dihedral  : 17.011  89.718   4978
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 25.56 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.21), residues: 1714
  helix:  1.10 (0.21), residues: 676
  sheet: -0.75 (0.39), residues: 174
  loop : -0.18 (0.22), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 651 
 HIS   0.019   0.001   HIS A 829 
 PHE   0.011   0.001   PHE A 819 
 TYR   0.011   0.001   TYR A 706 
 ARG   0.004   0.000   ARG B 621 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15947 (  553)
  hydrogen bonds       : angle       6.54100 ( 1545)
  covalent geometry    : bond        0.00288 (13530)
  covalent geometry    : angle       0.54849 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 241
  time to evaluate  : 2.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.7848 (mtt) cc_final: 0.7631 (mtp)
REVERT: A  242 GLU cc_start: 0.6695 (pt0) cc_final: 0.6425 (tm-30)
REVERT: A  245 ASP cc_start: 0.7193 (p0) cc_final: 0.6967 (p0)
REVERT: A  302 TYR cc_start: 0.7719 (m-80) cc_final: 0.7503 (m-80)
REVERT: A  523 MET cc_start: 0.7623 (mmm) cc_final: 0.7272 (mmm)
REVERT: A  669 SER cc_start: 0.8298 (t) cc_final: 0.7747 (p)
REVERT: A  695 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7544 (p)
REVERT: A  795 LYS cc_start: 0.8638 (tppt) cc_final: 0.7712 (ttmt)
REVERT: B  224 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7743 (mtpt)
REVERT: B  648 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6770 (mm-30)
REVERT: B  796 LYS cc_start: 0.7337 (ttmm) cc_final: 0.6867 (mmmt)
REVERT: B  876 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7187 (mt-10)
  outliers start: 6
  outliers final: 3
  residues processed: 246
  average time/residue: 1.7700
  time to fit residues: 498.1323
Evaluate side-chains
  172 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 1.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain B residue  637 CYS
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  801 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 145 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 134 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 156 optimal weight:   10.0000
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 140 ASN
A 328 ASN
A 356 HIS
** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 168 ASN
B 377 GLN
** B 581 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 = 0.3643 r_free = 0.3643 target = 0.132932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.098281 restraints weight = 49913.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.89
r_work: 0.3101 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  13530  Z= 0.276
  Angle     :  0.709  15.645  18334  Z= 0.370
  Chirality :  0.061   1.652   2022
  Planarity :  0.006   0.062   2390
  Dihedral  :  4.673  51.003   1841
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 23.47 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.20), residues: 1714
  helix:  0.45 (0.20), residues: 684
  sheet: -1.15 (0.39), residues: 150
  loop : -0.67 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 651 
 HIS   0.010   0.002   HIS A 829 
 PHE   0.023   0.002   PHE B 819 
 TYR   0.022   0.002   TYR B 520 
 ARG   0.009   0.001   ARG B 492 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05613 (  553)
  hydrogen bonds       : angle       5.06036 ( 1545)
  covalent geometry    : bond        0.00648 (13530)
  covalent geometry    : angle       0.70883 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 171
  time to evaluate  : 1.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7139 (tp30) cc_final: 0.6780 (tp30)
REVERT: A  669 SER cc_start: 0.8052 (t) cc_final: 0.7458 (p)
REVERT: A  671 ASP cc_start: 0.7452 (t0) cc_final: 0.7194 (t0)
REVERT: A  695 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7394 (p)
REVERT: A  744 ARG cc_start: 0.7117 (ttp80) cc_final: 0.6890 (ttp-110)
REVERT: A  752 THR cc_start: 0.6941 (OUTLIER) cc_final: 0.6349 (t)
REVERT: A  795 LYS cc_start: 0.8716 (tppt) cc_final: 0.7734 (ttmt)
REVERT: B  224 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7751 (mtpp)
REVERT: B  626 SER cc_start: 0.7788 (OUTLIER) cc_final: 0.7511 (m)
REVERT: B  648 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7025 (mm-30)
REVERT: B  680 GLN cc_start: 0.6713 (mp10) cc_final: 0.6504 (mp10)
REVERT: B  686 MET cc_start: 0.8158 (mtp) cc_final: 0.7926 (mtp)
REVERT: B  796 LYS cc_start: 0.7718 (ttmm) cc_final: 0.7136 (mmmt)
REVERT: B  831 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8480 (m)
REVERT: B  873 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7929 (mp0)
  outliers start: 50
  outliers final: 20
  residues processed: 208
  average time/residue: 2.0144
  time to fit residues: 473.6563
Evaluate side-chains
  178 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 2.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain A residue  752 THR
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  523 MET
Chi-restraints excluded: chain B residue  533 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  626 SER
Chi-restraints excluded: chain B residue  637 CYS
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  676 SER
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  828 SER
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  873 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 125 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 114 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 165 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 156 optimal weight:    7.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 507 GLN
** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.135278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.101380 restraints weight = 49347.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.83
r_work: 0.3149 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13530  Z= 0.151
  Angle     :  0.558  14.716  18334  Z= 0.280
  Chirality :  0.056   1.621   2022
  Planarity :  0.004   0.042   2390
  Dihedral  :  4.137  49.796   1839
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 25.35 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.21), residues: 1714
  helix:  0.92 (0.21), residues: 684
  sheet: -1.09 (0.36), residues: 184
  loop : -0.46 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 651 
 HIS   0.006   0.001   HIS B 667 
 PHE   0.011   0.001   PHE A 685 
 TYR   0.010   0.001   TYR A 827 
 ARG   0.003   0.000   ARG A 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04765 (  553)
  hydrogen bonds       : angle       4.73104 ( 1545)
  covalent geometry    : bond        0.00359 (13530)
  covalent geometry    : angle       0.55782 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 158
  time to evaluate  : 2.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7038 (tp30) cc_final: 0.6719 (tp30)
REVERT: A  695 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7405 (p)
REVERT: A  752 THR cc_start: 0.7007 (OUTLIER) cc_final: 0.6407 (t)
REVERT: A  795 LYS cc_start: 0.8701 (tppt) cc_final: 0.7890 (ttmm)
REVERT: B   77 MET cc_start: 0.8432 (ttm) cc_final: 0.8072 (ttm)
REVERT: B  224 LYS cc_start: 0.8285 (mtpp) cc_final: 0.7754 (mtpp)
REVERT: B  620 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6796 (ttm170)
REVERT: B  626 SER cc_start: 0.7804 (t) cc_final: 0.7307 (m)
REVERT: B  648 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7123 (mm-30)
REVERT: B  680 GLN cc_start: 0.6797 (mp10) cc_final: 0.6595 (mp10)
REVERT: B  686 MET cc_start: 0.8083 (mtp) cc_final: 0.7864 (mtp)
REVERT: B  758 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5363 (mp10)
REVERT: B  795 LYS cc_start: 0.6567 (tppt) cc_final: 0.6266 (tppt)
REVERT: B  831 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8525 (m)
  outliers start: 30
  outliers final: 12
  residues processed: 183
  average time/residue: 2.1450
  time to fit residues: 440.3710
Evaluate side-chains
  167 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 1.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain A residue  752 THR
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  523 MET
Chi-restraints excluded: chain B residue  620 ARG
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  758 GLN
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  831 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 151 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 139 optimal weight:    4.9990
   chunk 119 optimal weight:    1.9990
   chunk 125 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 162 optimal weight:    0.0770
   chunk 104 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 507 GLN
B  54 ASN
** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 758 GLN ** 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 = 0.3696 r_free = 0.3696 target = 0.135253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.101284 restraints weight = 49707.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.84
r_work: 0.3146 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.4040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13530  Z= 0.131
  Angle     :  0.535  14.392  18334  Z= 0.268
  Chirality :  0.055   1.614   2022
  Planarity :  0.004   0.043   2390
  Dihedral  :  3.968  47.664   1838
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 25.00 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.21), residues: 1714
  helix:  1.08 (0.21), residues: 684
  sheet: -0.74 (0.37), residues: 172
  loop : -0.47 (0.22), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 651 
 HIS   0.006   0.001   HIS B 667 
 PHE   0.014   0.001   PHE A 685 
 TYR   0.011   0.001   TYR B 113 
 ARG   0.002   0.000   ARG B 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  553)
  hydrogen bonds       : angle       4.52451 ( 1545)
  covalent geometry    : bond        0.00316 (13530)
  covalent geometry    : angle       0.53495 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 2.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7075 (tp30) cc_final: 0.6754 (tp30)
REVERT: A  507 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7379 (pt0)
REVERT: A  671 ASP cc_start: 0.7154 (t0) cc_final: 0.6789 (t0)
REVERT: A  695 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7329 (p)
REVERT: A  744 ARG cc_start: 0.7255 (ttp80) cc_final: 0.6967 (ttp80)
REVERT: A  752 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6534 (t)
REVERT: A  795 LYS cc_start: 0.8658 (tppt) cc_final: 0.7807 (ttmt)
REVERT: B   77 MET cc_start: 0.8373 (ttm) cc_final: 0.8043 (ttm)
REVERT: B  224 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7717 (mtpp)
REVERT: B  423 THR cc_start: 0.8759 (t) cc_final: 0.8543 (t)
REVERT: B  464 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6812 (tp30)
REVERT: B  546 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7415 (mt-10)
REVERT: B  626 SER cc_start: 0.7748 (t) cc_final: 0.7299 (m)
REVERT: B  648 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7169 (mm-30)
REVERT: B  758 GLN cc_start: 0.6303 (OUTLIER) cc_final: 0.5471 (mp10)
REVERT: B  795 LYS cc_start: 0.6645 (tppt) cc_final: 0.6326 (tppt)
REVERT: B  831 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8555 (m)
  outliers start: 33
  outliers final: 13
  residues processed: 181
  average time/residue: 2.1698
  time to fit residues: 441.4127
Evaluate side-chains
  168 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain A residue  752 THR
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  521 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  758 GLN
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  831 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 70 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 132 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 154 optimal weight:   10.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 808 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.132399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.098423 restraints weight = 49618.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.83
r_work: 0.3104 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  13530  Z= 0.194
  Angle     :  0.565  14.965  18334  Z= 0.285
  Chirality :  0.056   1.599   2022
  Planarity :  0.004   0.046   2390
  Dihedral  :  4.066  46.800   1838
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.37 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.21), residues: 1714
  helix:  0.97 (0.21), residues: 686
  sheet: -0.88 (0.38), residues: 174
  loop : -0.48 (0.22), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 651 
 HIS   0.008   0.001   HIS A 829 
 PHE   0.016   0.001   PHE A 685 
 TYR   0.011   0.001   TYR B 113 
 ARG   0.003   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04499 (  553)
  hydrogen bonds       : angle       4.54862 ( 1545)
  covalent geometry    : bond        0.00466 (13530)
  covalent geometry    : angle       0.56545 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 161
  time to evaluate  : 1.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7152 (tp30) cc_final: 0.6802 (tp30)
REVERT: A  695 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.7346 (p)
REVERT: A  744 ARG cc_start: 0.7313 (ttp80) cc_final: 0.7032 (ttp80)
REVERT: A  752 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6679 (t)
REVERT: A  795 LYS cc_start: 0.8714 (tppt) cc_final: 0.7894 (ttmt)
REVERT: B   58 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8665 (mtm)
REVERT: B  423 THR cc_start: 0.8800 (t) cc_final: 0.8591 (t)
REVERT: B  464 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6909 (tp30)
REVERT: B  533 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8282 (t)
REVERT: B  535 MET cc_start: 0.8438 (mmt) cc_final: 0.8107 (mmm)
REVERT: B  546 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7496 (mt-10)
REVERT: B  572 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5200 (mp0)
REVERT: B  626 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7322 (m)
REVERT: B  648 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7280 (mm-30)
REVERT: B  758 GLN cc_start: 0.6302 (OUTLIER) cc_final: 0.5586 (mp10)
REVERT: B  795 LYS cc_start: 0.6784 (tppt) cc_final: 0.6380 (tppt)
REVERT: B  831 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8593 (p)
  outliers start: 43
  outliers final: 17
  residues processed: 193
  average time/residue: 2.3750
  time to fit residues: 520.2299
Evaluate side-chains
  183 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 1.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain A residue  752 THR
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  523 MET
Chi-restraints excluded: chain B residue  533 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  626 SER
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  676 SER
Chi-restraints excluded: chain B residue  758 GLN
Chi-restraints excluded: chain B residue  777 SER
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  831 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 161 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 158 optimal weight:    4.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 507 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.132869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.099019 restraints weight = 49369.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.83
r_work: 0.3114 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.4742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13530  Z= 0.142
  Angle     :  0.547  14.813  18334  Z= 0.272
  Chirality :  0.055   1.610   2022
  Planarity :  0.004   0.060   2390
  Dihedral  :  3.983  44.917   1838
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 24.58 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.21), residues: 1714
  helix:  1.06 (0.21), residues: 686
  sheet: -0.86 (0.37), residues: 176
  loop : -0.45 (0.22), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 651 
 HIS   0.006   0.001   HIS B 667 
 PHE   0.009   0.001   PHE A 247 
 TYR   0.011   0.001   TYR B 113 
 ARG   0.006   0.000   ARG A 656 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  553)
  hydrogen bonds       : angle       4.47927 ( 1545)
  covalent geometry    : bond        0.00345 (13530)
  covalent geometry    : angle       0.54665 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 166
  time to evaluate  : 1.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7132 (tp30) cc_final: 0.6813 (tp30)
REVERT: A  528 VAL cc_start: 0.8226 (t) cc_final: 0.7979 (m)
REVERT: A  671 ASP cc_start: 0.7237 (t0) cc_final: 0.6923 (t0)
REVERT: A  695 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7176 (p)
REVERT: A  744 ARG cc_start: 0.7298 (ttp80) cc_final: 0.7019 (ttp80)
REVERT: A  795 LYS cc_start: 0.8641 (tppt) cc_final: 0.7876 (ttmt)
REVERT: B   58 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8620 (mtm)
REVERT: B  423 THR cc_start: 0.8774 (t) cc_final: 0.8559 (t)
REVERT: B  464 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6890 (tp30)
REVERT: B  533 SER cc_start: 0.8621 (m) cc_final: 0.8280 (t)
REVERT: B  535 MET cc_start: 0.8440 (mmt) cc_final: 0.8137 (mmm)
REVERT: B  546 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7506 (mt-10)
REVERT: B  572 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5188 (mp0)
REVERT: B  626 SER cc_start: 0.7708 (t) cc_final: 0.7289 (m)
REVERT: B  648 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7355 (mm-30)
REVERT: B  653 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7695 (mp0)
REVERT: B  758 GLN cc_start: 0.6246 (OUTLIER) cc_final: 0.5654 (mp10)
REVERT: B  795 LYS cc_start: 0.6823 (tppt) cc_final: 0.6482 (tppt)
REVERT: B  831 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8601 (p)
  outliers start: 38
  outliers final: 20
  residues processed: 195
  average time/residue: 2.0746
  time to fit residues: 455.1888
Evaluate side-chains
  188 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 2.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain B residue   58 MET
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  521 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  676 SER
Chi-restraints excluded: chain B residue  723 GLU
Chi-restraints excluded: chain B residue  758 GLN
Chi-restraints excluded: chain B residue  777 SER
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  831 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 507 GLN
B 168 ASN
B 773 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.097312 restraints weight = 49630.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.82
r_work: 0.3085 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.5017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  13530  Z= 0.185
  Angle     :  0.573  14.958  18334  Z= 0.288
  Chirality :  0.056   1.599   2022
  Planarity :  0.004   0.045   2390
  Dihedral  :  4.066  43.686   1838
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.58 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.21), residues: 1714
  helix:  0.97 (0.21), residues: 688
  sheet: -0.66 (0.37), residues: 188
  loop : -0.49 (0.22), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 527 
 HIS   0.006   0.001   HIS B 667 
 PHE   0.011   0.001   PHE A 247 
 TYR   0.011   0.001   TYR A 113 
 ARG   0.008   0.000   ARG A 656 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04408 (  553)
  hydrogen bonds       : angle       4.51978 ( 1545)
  covalent geometry    : bond        0.00452 (13530)
  covalent geometry    : angle       0.57251 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 172
  time to evaluate  : 2.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7140 (tp30) cc_final: 0.6806 (tp30)
REVERT: A  528 VAL cc_start: 0.8297 (t) cc_final: 0.8048 (m)
REVERT: A  671 ASP cc_start: 0.7216 (t0) cc_final: 0.6982 (t0)
REVERT: A  695 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7135 (p)
REVERT: B   58 MET cc_start: 0.9026 (mtp) cc_final: 0.8812 (mtm)
REVERT: B  423 THR cc_start: 0.8789 (t) cc_final: 0.8578 (t)
REVERT: B  464 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6930 (tp30)
REVERT: B  533 SER cc_start: 0.8603 (m) cc_final: 0.8337 (t)
REVERT: B  545 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7398 (mp0)
REVERT: B  546 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7677 (mt-10)
REVERT: B  572 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5306 (mp0)
REVERT: B  625 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6698 (mp)
REVERT: B  626 SER cc_start: 0.7724 (t) cc_final: 0.7235 (m)
REVERT: B  648 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7371 (mm-30)
REVERT: B  719 LYS cc_start: 0.7034 (ttmt) cc_final: 0.6669 (tptt)
REVERT: B  751 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7945 (mm110)
REVERT: B  758 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.5830 (mp10)
REVERT: B  795 LYS cc_start: 0.6942 (tppt) cc_final: 0.6673 (tppt)
REVERT: B  831 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8629 (p)
  outliers start: 43
  outliers final: 24
  residues processed: 205
  average time/residue: 2.2714
  time to fit residues: 519.1113
Evaluate side-chains
  195 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 2.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain A residue  767 LEU
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  521 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  625 LEU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  676 SER
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  758 GLN
Chi-restraints excluded: chain B residue  777 SER
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  831 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 165 optimal weight:    4.9990
   chunk 151 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 136 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 153 optimal weight:    8.9990
   chunk 141 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 158 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
B 168 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.125901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.091254 restraints weight = 49701.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.88
r_work: 0.2974 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.5275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13530  Z= 0.184
  Angle     :  0.576  14.886  18334  Z= 0.290
  Chirality :  0.056   1.608   2022
  Planarity :  0.005   0.068   2390
  Dihedral  :  4.091  41.873   1838
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.79 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.21), residues: 1714
  helix:  0.97 (0.21), residues: 688
  sheet: -0.64 (0.37), residues: 188
  loop : -0.49 (0.22), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 527 
 HIS   0.004   0.001   HIS B 667 
 PHE   0.013   0.001   PHE B 685 
 TYR   0.011   0.001   TYR A 113 
 ARG   0.005   0.000   ARG B 435 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  553)
  hydrogen bonds       : angle       4.51278 ( 1545)
  covalent geometry    : bond        0.00449 (13530)
  covalent geometry    : angle       0.57638 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 169
  time to evaluate  : 1.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7293 (tp30) cc_final: 0.6978 (tp30)
REVERT: A  528 VAL cc_start: 0.8372 (t) cc_final: 0.8154 (m)
REVERT: A  671 ASP cc_start: 0.7296 (t0) cc_final: 0.7089 (t0)
REVERT: A  695 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7317 (p)
REVERT: A  744 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7096 (ttp80)
REVERT: B  423 THR cc_start: 0.8843 (t) cc_final: 0.8612 (t)
REVERT: B  464 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6998 (tp30)
REVERT: B  533 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8307 (t)
REVERT: B  546 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7878 (mt-10)
REVERT: B  572 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5283 (mp0)
REVERT: B  626 SER cc_start: 0.7636 (t) cc_final: 0.7169 (m)
REVERT: B  648 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7349 (mm-30)
REVERT: B  719 LYS cc_start: 0.7365 (ttmt) cc_final: 0.6904 (tptt)
REVERT: B  751 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7947 (mm110)
REVERT: B  758 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.5986 (mp10)
REVERT: B  831 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8666 (p)
  outliers start: 42
  outliers final: 24
  residues processed: 202
  average time/residue: 2.2461
  time to fit residues: 509.8750
Evaluate side-chains
  194 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 2.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  695 THR
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  278 ASN
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  521 SER
Chi-restraints excluded: chain B residue  533 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  676 SER
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  697 LYS
Chi-restraints excluded: chain B residue  758 GLN
Chi-restraints excluded: chain B residue  777 SER
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  855 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 169 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 145 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0470
   chunk 146 optimal weight:    5.9990
   chunk 116 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 127 optimal weight:    1.9990
   overall best weight:    1.6084

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
B 278 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.091182 restraints weight = 50074.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.89
r_work: 0.2975 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.5455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13530  Z= 0.174
  Angle     :  0.573  15.349  18334  Z= 0.287
  Chirality :  0.057   1.680   2022
  Planarity :  0.004   0.044   2390
  Dihedral  :  4.073  40.282   1838
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 25.49 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.21), residues: 1714
  helix:  0.98 (0.21), residues: 688
  sheet: -0.64 (0.37), residues: 188
  loop : -0.50 (0.22), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 527 
 HIS   0.004   0.001   HIS A 829 
 PHE   0.011   0.001   PHE A 247 
 TYR   0.011   0.001   TYR A 113 
 ARG   0.005   0.000   ARG A 656 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04337 (  553)
  hydrogen bonds       : angle       4.49395 ( 1545)
  covalent geometry    : bond        0.00427 (13530)
  covalent geometry    : angle       0.57344 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 2.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7306 (tp30) cc_final: 0.6986 (tp30)
REVERT: A  528 VAL cc_start: 0.8445 (t) cc_final: 0.8236 (m)
REVERT: A  744 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7137 (ttp80)
REVERT: B  423 THR cc_start: 0.8827 (t) cc_final: 0.8599 (t)
REVERT: B  464 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7021 (tp30)
REVERT: B  533 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8290 (t)
REVERT: B  545 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7557 (mp0)
REVERT: B  546 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7913 (mt-10)
REVERT: B  626 SER cc_start: 0.7711 (t) cc_final: 0.7264 (m)
REVERT: B  648 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7312 (mm-30)
REVERT: B  719 LYS cc_start: 0.7350 (ttmt) cc_final: 0.6984 (tptt)
REVERT: B  751 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7960 (mm110)
REVERT: B  758 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.6065 (mp10)
REVERT: B  831 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8669 (p)
  outliers start: 32
  outliers final: 21
  residues processed: 192
  average time/residue: 2.3359
  time to fit residues: 500.5335
Evaluate side-chains
  192 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 166
  time to evaluate  : 2.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  533 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  676 SER
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  758 GLN
Chi-restraints excluded: chain B residue  777 SER
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  831 VAL
Chi-restraints excluded: chain B residue  855 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 149 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 145 optimal weight:    3.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 800 GLN
B 168 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.124683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.090151 restraints weight = 49938.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.86
r_work: 0.2955 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.5630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13530  Z= 0.207
  Angle     :  0.595  15.235  18334  Z= 0.300
  Chirality :  0.057   1.643   2022
  Planarity :  0.004   0.045   2390
  Dihedral  :  4.014  18.089   1836
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 25.56 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.21), residues: 1714
  helix:  0.91 (0.21), residues: 688
  sheet: -0.69 (0.37), residues: 188
  loop : -0.54 (0.22), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 629 
 HIS   0.005   0.001   HIS A 829 
 PHE   0.012   0.001   PHE A 247 
 TYR   0.011   0.001   TYR B 302 
 ARG   0.006   0.000   ARG A 656 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04519 (  553)
  hydrogen bonds       : angle       4.53793 ( 1545)
  covalent geometry    : bond        0.00510 (13530)
  covalent geometry    : angle       0.59461 (18334)

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

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

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3428 Ramachandran restraints generated.
    1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 1.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 GLU cc_start: 0.7299 (tp30) cc_final: 0.7007 (tp30)
REVERT: A  744 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7203 (ttp80)
REVERT: A  770 GLU cc_start: 0.8215 (mp0) cc_final: 0.7941 (mp0)
REVERT: B  423 THR cc_start: 0.8865 (t) cc_final: 0.8652 (t)
REVERT: B  464 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7038 (tp30)
REVERT: B  533 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8292 (t)
REVERT: B  545 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7636 (mp0)
REVERT: B  546 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7987 (mt-10)
REVERT: B  559 MET cc_start: 0.8099 (tmm) cc_final: 0.7777 (tpt)
REVERT: B  626 SER cc_start: 0.7759 (t) cc_final: 0.7350 (m)
REVERT: B  648 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7334 (mm-30)
REVERT: B  719 LYS cc_start: 0.7486 (ttmt) cc_final: 0.7092 (tptt)
REVERT: B  751 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7942 (mm110)
  outliers start: 31
  outliers final: 22
  residues processed: 191
  average time/residue: 2.3979
  time to fit residues: 508.6534
Evaluate side-chains
  190 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 1.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  403 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  572 GLU
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain B residue  509 CYS
Chi-restraints excluded: chain B residue  533 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  676 SER
Chi-restraints excluded: chain B residue  694 VAL
Chi-restraints excluded: chain B residue  777 SER
Chi-restraints excluded: chain B residue  802 CYS
Chi-restraints excluded: chain B residue  855 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 146 optimal weight:    5.9990
   chunk 168 optimal weight:    0.0370
   chunk 92 optimal weight:    0.4980
   chunk 95 optimal weight:    0.6980
   chunk 149 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 800 GLN
B 168 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.092656 restraints weight = 49439.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.86
r_work: 0.2991 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.5693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13530  Z= 0.113
  Angle     :  0.552  15.051  18334  Z= 0.276
  Chirality :  0.055   1.655   2022
  Planarity :  0.004   0.045   2390
  Dihedral  :  3.832  19.584   1836
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 26.25 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.21), residues: 1714
  helix:  1.14 (0.21), residues: 688
  sheet: -0.93 (0.36), residues: 182
  loop : -0.42 (0.22), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 527 
 HIS   0.004   0.001   HIS A 829 
 PHE   0.010   0.001   PHE A 577 
 TYR   0.012   0.001   TYR B 113 
 ARG   0.005   0.000   ARG A 656 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03946 (  553)
  hydrogen bonds       : angle       4.42683 ( 1545)
  covalent geometry    : bond        0.00273 (13530)
  covalent geometry    : angle       0.55183 (18334)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16530.03 seconds
wall clock time: 283 minutes 17.32 seconds (16997.32 seconds total)